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Apoptosis is a process of programmed cell death that occurs in multicellular organisms. There are two ways in which cells die: (1) They are killed by injurious agents or (2) they are induced to commit suicide.
Death by injury
Cells that are damaged by injury, such as by mechanical damage or exposure to toxic chemicals undergo a characteristic series of changes. They (and their organelles like mitochondria) swell (because the ability of the plasma membrane to control the passage of ions and water is disrupted). The cell contents leak out, leading to inflammation of surrounding tissues.
Death by Suicide
Cells that are induced to commit suicide:
• shrink
• develop bubble-like blebs on their surface
• have the chromatin (DNA and protein) in their nucleus degraded
• have their mitochondria break down with the release of cytochrome c
• break into small, membrane-wrapped, fragments
• release (at least in mammalian cells) ATP and UTP
• These nucleotides bind to receptors on wandering phagocytic cells like macrophages and dendritic cells and attract them to the dying cells (a "find-me" signal")
• The phospholipid phosphatidylserine, which is normally hidden in the inner layer of the plasma membrane, is exposed on the surface
• This "eat me" signal is bound by other receptors on the phagocytes which then engulf the cell fragments
• The phagocytic cells secrete cytokines that inhibit inflammation (e.g., IL-10 and TGF-β)
The pattern of events in death by suicide is so orderly that the process is often called programmed cell death or PCD. The cellular machinery of programmed cell death turns out to be as intrinsic to the cell as, say, mitosis. Programmed cell death is also called apoptosis. (There is no consensus yet on how to pronounce it; some say APE oh TOE sis; some say uh POP tuh sis.)
Why should a cell commit suicide?
There are two different reasons.
1. Programmed cell death is as needed for proper development as mitosis is.
Examples:
• The resorption of the tadpole tail at the time of its metamorphosis into a frog occurs by apoptosis.
• The formation of the fingers and toes of the fetus requires the removal, by apoptosis, of the tissue between them.
• The sloughing off of the inner lining of the uterus (the endometrium) at the start of menstruation occurs by apoptosis.
• The formation of the proper connections (synapses) between neurons in the brain requires that surplus cells be eliminated by apoptosis.
• The elimination of T cells that might otherwise mount an autoimmune attack on the body occurs by apoptosis.
• During the pupal stage of insects that undergo complete metamorphosis, most of the cells of the larva die by apoptosis thus providing the nutrients for the development of the structures of the adult.
2. Programmed cell death is needed to destroy cells that represent a threat to the integrity of the organism.
Examples:
Cells infected with viruses
One of the methods by which cytotoxic T lymphocytes (CTLs) kill virus-infected cells is by inducing apoptosis and some viruses mount countermeasures to thwart it.
Cells of the immune system
As cell-mediated immune responses wane, the effector cells must be removed to prevent them from attacking body constituents. CTLs induce apoptosis in each other and even in themselves. Defects in the apoptotic machinery is associated with autoimmune diseases such as systemic lupus erythematosus and rheumatoid arthritis.
Cells with DNA damage
Damage to its genome can cause a cell
• to disrupt proper embryonic development leading to birth defects
• to become cancerous.
Cells respond to DNA damage by increasing their production of p53. p53 is a potent inducer of apoptosis. Is it any wonder that mutations in the p53 gene, producing a defective protein, are so often found in cancer cells (that represent a lethal threat to the organism if permitted to live)?
Cancer cells
Radiation and chemicals used in cancer therapy induce apoptosis in some types of cancer cells.
What makes a cell decide to commit suicide?
The balance between the withdrawal of positive signals; that is, signals needed for continued survival, and the receipt of negative signals.
Withdrawal of positive signals
The continued survival of most cells requires that they receive continuous stimulation from other cells and, for many, continued adhesion to the surface on which they are growing. Some examples of positive signals: growth factors for neurons and Interleukin-2 (IL-2), an essential factor for the mitosis of lymphocytes
Receipt of negative signals
• increased levels of oxidants within the cell
• damage to DNA by these oxidants or other agents like ultraviolet light, X-rays and chemotherapeutic drugs
• accumulation of proteins that failed to fold properly into their proper tertiary structure
• molecules that bind to specific receptors on the cell surface and signal the cell to begin the apoptosis program. These death activators include:
• Tumor necrosis factor-alpha (TNF-α) that binds to the TNF receptor
• Lymphotoxin (also known as TNF-β) that also binds to the TNF receptor
• Fas ligand (FasL), a molecule that binds to a cell-surface receptor named Fas (also called CD95)
The Mechanisms of Apoptosis
There are 3 different mechanisms by which a cell commits suicide by apoptosis.
1. Generated by signals arising within the cell
2. Triggered by death activators binding to receptors at the cell surface:
• TNF-α
• Lymphotoxin
• Fas ligand (FasL)
3. Triggered by dangerous reactive oxygen species
Apoptosis triggered by internal signals
• In a healthy cell, the outer membranes of its mitochondria display the protein Bcl-2 on their surface. Bcl-2 inhibits apoptosis.
• Internal damage to the cell
• causes a related protein, Bax, to migrate to the surface of the mitochondrion where it inhibits the protective effect of Bcl-2 and inserts itself into the outer mitochondrial membrane punching holes in it and causing
• cytochrome c to leak out.
• The released cytochrome c binds to the protein Apaf-1 ("apoptotic protease activating factor-1").
• Using the energy provided by ATP, these complexes aggregate to form apoptosomes. The apoptosomes bind to and activate caspase-9. Caspase-9 is one of a family of over a dozen caspases. They are all proteases. They get their name because they cleave proteins — mostly each other — at aspartic acid (Asp) residues.
• Caspase-9 cleaves and, in so doing, activates other caspases (caspase-3 and -7).
• The activation of these "executioner" caspases creates an expanding cascade of proteolytic activity (rather like that in blood clotting and complement activation) which leads to
• digestion of structural proteins in the cytoplasm,
• degradation of chromosomal DNA
• phagocytosis of the cell
Apoptosis triggered by external signals
• Fas and the TNF receptor are integral membrane proteins with their receptor domains exposed at the surface of the cell
• Binding of the complementary death activator (FasL and TNF respectively) transmits a signal to the cytoplasm that leads to the activation of caspase 8
• Caspase 8 (like caspase 9) initiates a cascade of caspase activation leading to phagocytosis of the cell.
• Example: When cytotoxic T cells recognize (bind to) their target,
• They produce more FasL at their surface.
• This binds with the Fas on the surface of the target cell leading to its death by apoptosis.
The early steps in apoptosis are reversible — at least in C. elegans. In some cases, final destruction of the cell is guaranteed only with its engulfment by a phagocyte.
Apoptosis-Inducing Factor (AIF)
Neurons, and perhaps other cells, have another way to self-destruct that — unlike the two paths described above — does not use caspases. Apoptosis-inducing factor (AIF) is a protein that is normally located in the intermembrane space of mitochondria. When the cell receives a signal telling it that it is time to die, AIF is released from the mitochondria (like the release of cytochrome c in the first pathway). It migrates into the nucleus and binds to DNA, which triggers the destruction of the DNA and cell death.
Apoptosis and Cancer
Some viruses associated with cancers use tricks to prevent apoptosis of the cells they have transformed.
• Several human papilloma viruses (HPV) have been implicated in causing cervical cancer. One of them produces a protein (E6) that binds and inactivates the apoptosis promoter p53.
• Epstein-Barr Virus (EBV), the cause of mononucleosis and associated with some lymphomas
• produces a protein similar to Bcl-2
• produces another protein that causes the cell to increase its own production of Bcl-2. Both these actions make the cell more resistant to apoptosis (thus enabling a cancer cell to continue to proliferate).
Even cancer cells produced without the participation of viruses may have tricks to avoid apoptosis.
• Some B-cell leukemias and lymphomas express high levels of Bcl-2, thus blocking apoptotic signals they may receive. The high levels result from a translocation of the BCL-2 gene into an enhancer region for antibody production.
• Melanoma (the most dangerous type of skin cancer) cells avoid apoptosis by inhibiting the expression of the gene encoding Apaf-1.
• Some cancer cells, especially lung and colon cancer cells, secrete elevated levels of a soluble "decoy" molecule that binds to FasL, plugging it up so it cannot bind Fas. Thus, cytotoxic T cells (CTL) cannot kill the cancer cells by the mechanism shown above.
• Other cancer cells express high levels of FasL, and can kill any cytotoxic T cells (CTL) that try to kill them because CTL also express Fas (but are protected from their own FasL).
Apoptosis in the Immune System
The immune response to a foreign invader involves the proliferation of lymphocytes — T and/or B cells. When their job is done, they must be removed leaving only a small population of memory cells. This is done by apoptosis. Very rarely humans are encountered with genetic defects in apoptosis. The most common one is a mutation in the gene for Fas, but mutations in the gene for FasL or even one of the caspases are occasionally seen. In all cases, the genetic problem produces autoimmune lymphoproliferative syndrome or ALPS.
Features
• an accumulation of lymphocytes in the lymph nodes and spleen greatly enlarging them.
• the appearance of clones that are autoreactive; that is, attack "self" components producing such autoimmune disorders as
• hemolytic anemia
• thrombocytopenia
• the appearance of lymphoma — a cancerous clone of lymphocytes.
In most patients with ALPS, the mutation is present in the germline; that is, every cell in their body carries it. In a few cases, however, the mutation is somatic; that is, has occurred in a precursor cell in the bone marrow. These later patients are genetic mosaics — with some lymphocytes that undergo apoptosis normally and others that do not. The latter tend to out-compete the former and grow to become the major population in the lymph nodes and blood.
Apoptosis and Organ Transplants
For many years it has been known that certain parts of the body such as the anterior chamber of the eye and the testes are "immunologically privileged sites". Antigens within these sites fail to elicit an immune response. It turns out that cells in these sites differ from the other cells of the body in that they express high levels of FasL at all times. Thus antigen-reactive T cells, which express Fas, would be killed when they enter these sites. (This is the reverse of the mechanism described above.)
This finding raises the possibility of a new way of preventing graft rejection. If at least some of the cells on a transplanted kidney, liver, heart, etc. could be made to express high levels of FasL, that might protect the graft from attack by the T cells of the host's cell-mediated immune system. If so, then the present need for treatment with immunosuppressive drugs for the rest of the transplant recipient's life would be reduced or eliminated. So far, the results in animal experiments have been mixed. Allografts engineered to express FasL have shown increased survival for kidneys, but not for hearts or islets of Langerhans.
Apoptosis in Plants
Plants, too, can turn on a system of programmed cell death; for example, in an attempt to halt the spread of virus infection. The mechanism differs from that in animals although it, too, involves a protease that — like caspases — cleaves other proteins at Asp (and Asn) residues. Activation of this enzyme destroys the central vacuole, which is followed by disintegration of the rest of the cell. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/19%3A_Cellular_Mechanisms_of_Development/19.07%3A_Morphogenesis/19.7.01%3A_Apoptosis.txt |
What helps ensure the survival of a species?
Genetic variation. It is this variation that is the essence of evolution. Without genetic differences among individuals, "survival of the fittest" would not be likely. Either all survive, or all perish.
Genetic Variation
Sexual reproduction results in infinite possibilities of genetic variation. In other words, sexual reproduction results in offspring that are genetically unique. They differ from both parents and also from each other. This occurs for a number of reasons.
• When homologous chromosomes form pairs during prophase I of meiosis I, crossing-over can occur. Crossing-over is the exchange of genetic material between homologous chromosomes. It results in new combinations of genes on each chromosome.
• When cells divide during meiosis, homologous chromosomes are randomly distributed to daughter cells, and different chromosomes segregate independently of each other. This called is called independent assortment. It results in gametes that have unique combinations of chromosomes.
• In sexual reproduction, two gametes unite to produce an offspring. But which two of the millions of possible gametes will it be? This is likely to be a matter of chance. It is obviously another source of genetic variation in offspring. This is known as random fertilization.
All of these mechanisms working together result in an amazing amount of potential variation. Each human couple, for example, has the potential to produce more than 64 trillion genetically unique children. No wonder we are all different!
See Sources of Variation at http://learn.genetics.utah.edu/content/variation/sources/ for additional information.
Crossing-Over
Crossing-over occurs during prophase I, and it is the exchange of genetic material between non-sister chromatids of homologous chromosomes. Recall during prophase I, homologous chromosomes line up in pairs, gene-for-gene down their entire length, forming a configuration with four chromatids, known as a tetrad. At this point, the chromatids are very close to each other and some material from two chromatids switch chromosomes, that is, the material breaks off and reattaches at the same position on the homologous chromosome (Figure below). This exchange of genetic material can happen many times within the same pair of homologous chromosomes, creating unique combinations of genes. This process is also known as recombination.
Crossing-over. A maternal strand of DNA is shown in red. A paternal strand of DNA is shown in blue. Crossing over produces two chromosomes that have not previously existed. The process of recombination involves the breakage and rejoining of parental chromosomes (M, F). This results in the generation of novel chromosomes (C1, C2) that share DNA from both parents.
Independent Assortment and Random Fertilization
In humans, there are over 8 million configurations in which the chromosomes can line up during metaphase I of meiosis. It is the specific processes of meiosis, resulting in four unique haploid cells, that result in these many combinations. This independent assortment, in which the chromosome inherited from either the father or mother can sort into any gamete, produces the potential for tremendous genetic variation. Together with random fertilization, more possibilities for genetic variation exist between any two people than the number of individuals alive today. Sexual reproduction is the random fertilization of a gamete from the female using a gamete from the male. In humans, over 8 million (223) chromosome combinations exist in the production of gametes in both the male and female. A sperm cell, with over 8 million chromosome combinations, fertilizes an egg cell, which also has over 8 million chromosome combinations. That is over 64 trillion unique combinations, not counting the unique combinations produced by crossing-over. In other words, each human couple could produce a child with over 64 trillion unique chromosome combinations!
See How Cells Divide: Mitosis vs. Meiosis at http://www.pbs.org/wgbh/nova/miracle/divide.html for an animation comparing the two processes.
Summary
• Sexual reproduction has the potential to produce tremendous genetic variation in offspring.
• This variation is due to independent assortment and crossing-over during meiosis, and random union of gametes during fertilization.
Explore More
Use this resource to answer the questions that follow.
1. What is meant by genetic variation?
2. Would natural selection occur without genetic variation? Explain your response.
3. What causes genetic variation?
4. How would genetic variation result in a change in phenotype?
5. What are the sources of genetic variation? Explain your response.
Review
1. What is crossing-over and when does it occur?
2. Describe how crossing-over, independent assortment, and random fertilization lead to genetic variation.
3. How many combinations of chromosomes are possible from sexual reproduction in humans?
4. Create a diagram to show how crossing-over occurs and how it creates new gene combinations on each chromosome. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/20%3A_Genes_Within_Populations/20.01%3A_Genetic_Variation_and_Evolution.txt |
If two individuals mate that are heterozygous (e.g., Bb) for a trait, we find that
• 25% of their offspring are homozygous for the dominant allele (BB)
• 50% are heterozygous like their parents (Bb)
• 25% are homozygous for the recessive allele (bb) and thus, unlike their parents, express the recessive phenotype.
This is what Mendel found when he crossed monohybrids. It occurs because meiosis separates the two alleles of each heterozygous parent so that 50% of the gametes will carry one allele and 50% the other and when the gametes are brought together at random, each B (or b)-carrying egg will have a 1 in 2 probability of being fertilized by a sperm carrying B (or b). (Left table)
Results of random union of the two gametes produced by two individuals, each heterozygous for a given trait. As a result of meiosis, half the gametes produced by each parent with carry allele B; the other half allele b. Results of random union of the gametes produced by an entire population with a gene pool containing 80% B and 20% b.
0.5 B 0.5 b 0.8 B 0.2 b
0.5 B 0.25 BB 0.25 Bb 0.8 B 0.64 BB 0.16 Bb
0.5 b 0.25 Bb 0.25 bb 0.2 b 0.16 Bb 0.04 bb
However, the frequency of two alleles in an entire population of organisms is unlikely to be exactly the same. Let us take as a hypothetical case, a population of hamsters in which 80% of all the gametes in the population carry a dominant allele for black coat (B) and 20% carry the recessive allele for gray coat (b).
Random union of these gametes (right table) will produce a generation:
• 64% homozygous for BB (0.8 x 0.8 = 0.64)
• 32% Bb heterozygotes (0.8 x 0.2 x 2 = 0.32)
• 4% homozygous (bb) for gray coat (0.2 x 0.2 = 0.04)
So 96% of this generation will have black coats; only 4% gray coats.
Will gray coated hamsters eventually disappear? No. Let's see why not.
• All the gametes formed by BB hamsters will contain allele B as will one-half the gametes formed by heterozygous (Bb) hamsters.
• So, 80% (0.64 + .5*0.32) of the pool of gametes formed by this generation with contain B.
• All the gametes of the gray (bb) hamsters (4%) will contain b but one-half of the gametes of the heterozygous hamsters will as well.
• So 20% (0.04 + .5*0.32) of the gametes will contain b.
So we have duplicated the initial situation exactly. The proportion of allele b in the population has remained the same. The heterozygous hamsters ensure that each generation will contain 4% gray hamsters. Now let us look at an algebraic analysis of the same problem using the expansion of the binomial (p+q)2.
$(p+q)^2 = p^2 + 2pq + q^2$
The total number of genes in a population is its gene pool.
• Let $p$ represent the frequency of one gene in the pool and $q$ the frequency of its single allele.
• So, $p + q = 1$
• $p^2$ = the fraction of the population homozygous for $p$
• $q^2$ = the fraction homozygous for $q$
• $2pq$ = the fraction of heterozygotes
• In our example, p = 0.8, q = 0.2, and thus $(0.8 + 0.2)^2 = (0.8)^2 + 2(0.8)(0.2) + (0.2)^2 = 064 + 0.32 + 0.04$
The algebraic method enables us to work backward as well as forward. In fact, because we chose to make B fully dominant, the only way that the frequency of B and b in the gene pool could be known is by determining the frequency of the recessive phenotype (gray) and computing from it the value of q.
q2 = 0.04, so q = 0.2, the frequency of the b allele in the gene pool. Since p + q = 1, p = 0.8 and allele B makes up 80% of the gene pool. Because B is completely dominant over b, we cannot distinguish the Bb hamsters from the BB ones by their phenotype. But substituting in the middle term (2pq) of the expansion gives the percentage of heterozygous hamsters. 2pq = (2)(0.8)(0.2) = 0.32
So, recessive genes do not tend to be lost from a population no matter how small their representation.
Hardy-Weinberg law
So long as certain conditions are met (discussed below), gene frequencies and genotype ratios in a randomly-breeding population remain constant from generation to generation. This is known as the Hardy-Weinberg law.
The Hardy-Weinberg law is named in honor of the two men who first realized the significance of the binomial expansion to population genetics and hence to evolution. Evolution involves changes in the gene pool. A population in Hardy-Weinberg equilibrium shows no change. What the law tells us is that populations are able to maintain a reservoir of variability so that if future conditions require it, the gene pool can change. If recessive alleles were continually tending to disappear, the population would soon become homozygous. Under Hardy-Weinberg conditions, genes that have no present selective value will nonetheless be retained.
When the Hardy-Weinberg Law Fails
To see what forces lead to evolutionary change, we must examine the circumstances in which the Hardy-Weinberg law may fail to apply. There are five:
1. mutation
2. gene flow
3. genetic drift
4. nonrandom mating
5. natural selection
Mutation
The frequency of gene B and its allele b will not remain in Hardy-Weinberg equilibrium if the rate of mutation of B -> b (or vice versa) changes. By itself, this type of mutation probably plays only a minor role in evolution; the rates are simply too low. However, gene (and whole genome) duplication - a form of mutation - probably has played a major role in evolution. In any case, evolution absolutely depends on mutations because this is the only way that new alleles are created. After being shuffled in various combinations with the rest of the gene pool, these provide the raw material on which natural selection can act.
Gene Flow
Many species are made up of local populations whose members tend to breed within the group. Each local population can develop a gene pool distinct from that of other local populations. However, members of one population may breed with occasional immigrants from an adjacent population of the same species. This can introduce new genes or alter existing gene frequencies in the residents.
In many plants and some animals, gene flow can occur not only between subpopulations of the same species but also between different (but still related) species. This is called hybridization. If the hybrids later breed with one of the parental types, new genes are passed into the gene pool of that parent population. This process is called introgression. It is simply gene flow between species rather than within them.
Comparison of the genomes of contemporary humans with the genome recovered from Neanderthal remains shows that from 1–3% of our genes were acquired by introgression following mating between members of the two populations tens of thousands of years ago.
Whether within a species or between species, gene flow increases the variability of the gene pool.
Genetic Drift
As we have seen, interbreeding often is limited to the members of local populations. If the population is small, Hardy-Weinberg may be violated. Chance alone may eliminate certain members out of proportion to their numbers in the population. In such cases, the frequency of an allele may begin to drift toward higher or lower values. Ultimately, the allele may represent 100% of the gene pool or, just as likely, disappear from it.
Drift produces evolutionary change, but there is no guarantee that the new population will be more fit than the original one. Evolution by drift is aimless, not adaptive.
Nonrandom Mating
One of the cornerstones of the Hardy-Weinberg equilibrium is that mating in the population must be random. If individuals (usually females) are choosy in their selection of mates, the gene frequencies may become altered. Darwin called this sexual selection.
Nonrandom mating seems to be quite common. Breeding territories, courtship displays, "pecking orders" can all lead to it. In each case certain individuals do not get to make their proportionate contribution to the next generation.
Assortative mating
Humans seldom mate at random preferring phenotypes like themselves (e.g., size, age, ethnicity). This is called assortative mating. Marriage between close relatives is a special case of assortative mating. The closer the kinship, the more alleles shared and the greater the degree of inbreeding. Inbreeding can alter the gene pool. This is because it predisposes to homozygosity. Potentially harmful recessive alleles — invisible in the parents — become exposed to the forces of natural selection in the children.
It turns out that many species - plants as well as animals - have mechanisms be which they avoid inbreeding. Examples:
• Link to discussion of self-incompatibility in plants.
• Male mice use olfactory cues to discriminate against close relatives when selecting mates. The preference is learned in infancy - an example of imprinting. The distinguishing odors are controlled by the MHC alleles of the mice and are detected by the vomeronasal organ (VNO).
Natural Selection
If individuals having certain genes are better able to produce mature offspring than those without them, the frequency of those genes will increase. This is simply expressing Darwin's natural selection in terms of alterations in the gene pool. (Darwin knew nothing of genes.) Natural selection results from differential mortality and/or differential fecundity.
Mortality Selection
Certain genotypes are less successful than others in surviving through to the end of their reproductive period. The evolutionary impact of mortality selection can be felt anytime from the formation of a new zygote to the end (if there is one) of the organism's period of fertility. Mortality selection is simply another way of describing Darwin's criteria of fitness: survival.
Fecundity Selection
Certain phenotypes (thus genotypes) may make a disproportionate contribution to the gene pool of the next generation by producing a disproportionate number of young. Such fecundity selection is another way of describing another criterion of fitness described by Darwin: family size. In each of these examples of natural selection, certain phenotypes are better able than others to contribute their genes to the next generation. Thus, by Darwin's standards, they are more fit. The outcome is a gradual change in the gene frequencies in that population.
Calculating the Effect of Natural Selection on Gene Frequencies
The effect of natural selection on gene frequencies can be quantified. Let us assume a population containing
• 36% homozygous dominants (AA)
• 48% heterozygotes (Aa) and
• 16% homozygous recessives (aa)
The gene frequencies in this population are $p = 0.6$ and $q = 0.4$. The heterozygotes are just as successful at reproducing themselves as the homozygous dominants, but the homozygous recessives are only 80% as successful. That is, for every 100 AA (or Aa) individuals that reproduce successfully only 80 of the aa individuals succeed in doing so. The fitness ($w$) of the recessive phenotype is thus 80% or 0.8.
Their relative disadvantage can also be expressed as a selection coefficient, $s$, where
$s = 1 − w$
In this case,
$s = 1 − 0.8 = 0.2.$
The change in frequency of the dominant allele ($Δp$) after one generation is expressed by the equation
$Δp = \dfrac{s p_0 q_0^2}{1 - s q_0^2}$
where $p_0$ and $q_0$ are the initial frequencies of the dominant and recessive alleles respectively. Substituting, we get
\begin{align} Δp & = \dfrac{(0.2)(0.6)(0.4)^2}{1 − (0.2)(0.4)^2} \[5pt] &=\dfrac{0.019}{0.968} \[5pt] &=0.02 \end{align}
So, in one generation, the frequency of allele A rises from its initial value of 0.6 to 0.62 and that of allele a declines from 0.4 to 0.38 ($q = 1 − p$).
The new equilibrium produces a population of
• 38.4% homozygous dominants (an increase of 2.4%) (p2 = 0.384)
• 47.1% heterozygotes (a decline of 0.9%)(2pq = 0.471) and
• 14.4% homozygous recessives (a decline of 1.6%)(q2 = 0.144)
If the fitness of the homozygous recessives continues unchanged, the calculations can be reiterated for any number of generations. If you do so, you will find that although the frequency of the recessive genotype declines, the rate at which a is removed from the gene pool declines; that is, the process becomes less efficient at purging allele a. This is because when present in the heterozygote, a is protected from the effects of selection. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/20%3A_Genes_Within_Populations/20.02%3A_Changes_in_Allele_Frequency.txt |
Skills to Develop
• Describe the different types of variation in a population
• Explain why only heritable variation can be acted upon by natural selection
• Describe genetic drift and the bottleneck effect
• Explain how each evolutionary force can influence the allele frequencies of a population
Individuals of a population often display different phenotypes, or express different alleles of a particular gene, referred to as polymorphisms. Populations with two or more variations of particular characteristics are called polymorphic. The distribution of phenotypes among individuals, known as the population variation, is influenced by a number of factors, including the population’s genetic structure and the environment (Figure \(1\)). Understanding the sources of a phenotypic variation in a population is important for determining how a population will evolve in response to different evolutionary pressures.
Genetic Variance
Natural selection and some of the other evolutionary forces can only act on heritable traits, namely an organism’s genetic code. Because alleles are passed from parent to offspring, those that confer beneficial traits or behaviors may be selected for, while deleterious alleles may be selected against. Acquired traits, for the most part, are not heritable. For example, if an athlete works out in the gym every day, building up muscle strength, the athlete’s offspring will not necessarily grow up to be a body builder. If there is a genetic basis for the ability to run fast, on the other hand, this may be passed to a child.
Heritability is the fraction of phenotype variation that can be attributed to genetic differences, or genetic variance, among individuals in a population. The greater the hereditability of a population’s phenotypic variation, the more susceptible it is to the evolutionary forces that act on heritable variation.
The diversity of alleles and genotypes within a population is called genetic variance. When scientists are involved in the breeding of a species, such as with animals in zoos and nature preserves, they try to increase a population’s genetic variance to preserve as much of the phenotypic diversity as they can. This also helps reduce the risks associated with inbreeding, the mating of closely related individuals, which can have the undesirable effect of bringing together deleterious recessive mutations that can cause abnormalities and susceptibility to disease. For example, a disease that is caused by a rare, recessive allele might exist in a population, but it will only manifest itself when an individual carries two copies of the allele. Because the allele is rare in a normal, healthy population with unrestricted habitat, the chance that two carriers will mate is low, and even then, only 25 percent of their offspring will inherit the disease allele from both parents. While it is likely to happen at some point, it will not happen frequently enough for natural selection to be able to swiftly eliminate the allele from the population, and as a result, the allele will be maintained at low levels in the gene pool. However, if a family of carriers begins to interbreed with each other, this will dramatically increase the likelihood of two carriers mating and eventually producing diseased offspring, a phenomenon known as inbreeding depression.
Changes in allele frequencies that are identified in a population can shed light on how it is evolving. In addition to natural selection, there are other evolutionary forces that could be in play: genetic drift, gene flow, mutation, nonrandom mating, and environmental variances.
Genetic Drift
The theory of natural selection stems from the observation that some individuals in a population are more likely to survive longer and have more offspring than others; thus, they will pass on more of their genes to the next generation. A big, powerful male gorilla, for example, is much more likely than a smaller, weaker one to become the population’s silverback, the pack’s leader who mates far more than the other males of the group. The pack leader will father more offspring, who share half of his genes, and are likely to also grow bigger and stronger like their father. Over time, the genes for bigger size will increase in frequency in the population, and the population will, as a result, grow larger on average. That is, this would occur if this particular selection pressure, or driving selective force, were the only one acting on the population. In other examples, better camouflage or a stronger resistance to drought might pose a selection pressure.
Another way a population’s allele and genotype frequencies can change is genetic drift (Figure \(2\)), which is simply the effect of chance. By chance, some individuals will have more offspring than others—not due to an advantage conferred by some genetically-encoded trait, but just because one male happened to be in the right place at the right time (when the receptive female walked by) or because the other one happened to be in the wrong place at the wrong time (when a fox was hunting).
Exercise \(1\)
Do you think genetic drift would happen more quickly on an island or on the mainland?
Answer
Genetic drift is likely to occur more rapidly on an island where smaller populations are expected to occur.
Small populations are more susceptible to the forces of genetic drift. Large populations, on the other hand, are buffered against the effects of chance. If one individual of a population of 10 individuals happens to die at a young age before it leaves any offspring to the next generation, all of its genes—1/10 of the population’s gene pool—will be suddenly lost. In a population of 100, that’s only 1 percent of the overall gene pool; therefore, it is much less impactful on the population’s genetic structure.
Genetic drift can also be magnified by natural events, such as a natural disaster that kills—at random—a large portion of the population. Known as the bottleneck effect, it results in a large portion of the genome suddenly being wiped out (Figure \(3\)). In one fell swoop, the genetic structure of the survivors becomes the genetic structure of the entire population, which may be very different from the pre-disaster population.
Another scenario in which populations might experience a strong influence of genetic drift is if some portion of the population leaves to start a new population in a new location or if a population gets divided by a physical barrier of some kind. In this situation, those individuals are unlikely to be representative of the entire population, which results in the founder effect. The founder effect occurs when the genetic structure changes to match that of the new population’s founding fathers and mothers. The founder effect is believed to have been a key factor in the genetic history of the Afrikaner population of Dutch settlers in South Africa, as evidenced by mutations that are common in Afrikaners but rare in most other populations. This is likely due to the fact that a higher-than-normal proportion of the founding colonists carried these mutations. As a result, the population expresses unusually high incidences of Huntington’s disease (HD) and Fanconi anemia (FA), a genetic disorder known to cause blood marrow and congenital abnormalities—even cancer.1
Link to Learning
Watch this short video to learn more about the founder and bottleneck effects.
Scientific Method Connection: Testing the Bottleneck Effect
Question: How do natural disasters affect the genetic structure of a population?
Background: When much of a population is suddenly wiped out by an earthquake or hurricane, the individuals that survive the event are usually a random sampling of the original group. As a result, the genetic makeup of the population can change dramatically. This phenomenon is known as the bottleneck effect.
Hypothesis: Repeated natural disasters will yield different population genetic structures; therefore, each time this experiment is run, the results will vary.
Test the hypothesis: Count out the original population using different colored beads. For example, red, blue, and yellow beads might represent red, blue, and yellow individuals. After recording the number of each individual in the original population, place them all in a bottle with a narrow neck that will only allow a few beads out at a time. Then, pour 1/3 of the bottle’s contents into a bowl. This represents the surviving individuals after a natural disaster kills a majority of the population. Count the number of the different colored beads in the bowl, and record it. Then, place all of the beads back in the bottle and repeat the experiment four more times.
Analyze the data: Compare the five populations that resulted from the experiment. Do the populations all contain the same number of different colored beads, or do they vary? Remember, these populations all came from the same exact parent population.
Form a conclusion: Most likely, the five resulting populations will differ quite dramatically. This is because natural disasters are not selective—they kill and spare individuals at random. Now think about how this might affect a real population. What happens when a hurricane hits the Mississippi Gulf Coast? How do the seabirds that live on the beach fare?
Gene Flow
Another important evolutionary force is gene flow: the flow of alleles in and out of a population due to the migration of individuals or gametes (Figure \(4\)). While some populations are fairly stable, others experience more flux. Many plants, for example, send their pollen far and wide, by wind or by bird, to pollinate other populations of the same species some distance away. Even a population that may initially appear to be stable, such as a pride of lions, can experience its fair share of immigration and emigration as developing males leave their mothers to seek out a new pride with genetically unrelated females. This variable flow of individuals in and out of the group not only changes the gene structure of the population, but it can also introduce new genetic variation to populations in different geological locations and habitats.
Mutation
Mutations are changes to an organism’s DNA and are an important driver of diversity in populations. Species evolve because of the accumulation of mutations that occur over time. The appearance of new mutations is the most common way to introduce novel genotypic and phenotypic variance. Some mutations are unfavorable or harmful and are quickly eliminated from the population by natural selection. Others are beneficial and will spread through the population. Whether or not a mutation is beneficial or harmful is determined by whether it helps an organism survive to sexual maturity and reproduce. Some mutations do not do anything and can linger, unaffected by natural selection, in the genome. Some can have a dramatic effect on a gene and the resulting phenotype.
Nonrandom Mating
If individuals nonrandomly mate with their peers, the result can be a changing population. There are many reasons nonrandom mating occurs. One reason is simple mate choice; for example, female peahens may prefer peacocks with bigger, brighter tails. Traits that lead to more matings for an individual become selected for by natural selection. One common form of mate choice, called assortative mating, is an individual’s preference to mate with partners who are phenotypically similar to themselves.
Another cause of nonrandom mating is physical location. This is especially true in large populations spread over large geographic distances where not all individuals will have equal access to one another. Some might be miles apart through woods or over rough terrain, while others might live immediately nearby.
Environmental Variance
Genes are not the only players involved in determining population variation. Phenotypes are also influenced by other factors, such as the environment (Figure \(5\)). A beachgoer is likely to have darker skin than a city dweller, for example, due to regular exposure to the sun, an environmental factor. Some major characteristics, such as gender, are determined by the environment for some species. For example, some turtles and other reptiles have temperature-dependent sex determination (TSD). TSD means that individuals develop into males if their eggs are incubated within a certain temperature range, or females at a different temperature range.
Geographic separation between populations can lead to differences in the phenotypic variation between those populations. Such geographical variation is seen between most populations and can be significant. One type of geographic variation, called a cline, can be seen as populations of a given species vary gradually across an ecological gradient. Species of warm-blooded animals, for example, tend to have larger bodies in the cooler climates closer to the earth’s poles, allowing them to better conserve heat. This is considered a latitudinal cline. Alternatively, flowering plants tend to bloom at different times depending on where they are along the slope of a mountain, known as an altitudinal cline.
If there is gene flow between the populations, the individuals will likely show gradual differences in phenotype along the cline. Restricted gene flow, on the other hand, can lead to abrupt differences, even speciation.
Summary
Both genetic and environmental factors can cause phenotypic variation in a population. Different alleles can confer different phenotypes, and different environments can also cause individuals to look or act differently. Only those differences encoded in an individual’s genes, however, can be passed to its offspring and, thus, be a target of natural selection. Natural selection works by selecting for alleles that confer beneficial traits or behaviors, while selecting against those for deleterious qualities. Genetic drift stems from the chance occurrence that some individuals in the germ line have more offspring than others. When individuals leave or join the population, allele frequencies can change as a result of gene flow. Mutations to an individual’s DNA may introduce new variation into a population. Allele frequencies can also be altered when individuals do not randomly mate with others in the group.
Footnotes
1. 1 A. J. Tipping et al., “Molecular and Genealogical Evidence for a Founder Effect in Fanconi Anemia Families of the Afrikaner Population of South Africa,” PNAS 98, no. 10 (2001): 5734-5739, doi: 10.1073/pnas.091402398.
Glossary
assortative mating
when individuals tend to mate with those who are phenotypically similar to themselves
bottleneck effect
magnification of genetic drift as a result of natural events or catastrophes
cline
gradual geographic variation across an ecological gradient
gene flow
flow of alleles in and out of a population due to the migration of individuals or gametes
genetic drift
effect of chance on a population’s gene pool
genetic variance
diversity of alleles and genotypes in a population
geographical variation
differences in the phenotypic variation between populations that are separated geographically
heritability
fraction of population variation that can be attributed to its genetic variance
inbreeding
mating of closely related individuals
inbreeding depression
increase in abnormalities and disease in inbreeding populations
nonrandom mating
changes in a population’s gene pool due to mate choice or other forces that cause individuals to mate with certain phenotypes more than others
population variation
distribution of phenotypes in a population
selective pressure
environmental factor that causes one phenotype to be better than another | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/20%3A_Genes_Within_Populations/20.03%3A_Five_Agents_of_Evolutionary_Change.txt |
Natural selection drives adaptive evolution by selecting for and increasing the occurrence of beneficial traits in a population.
Learning Objectives
• Explain how natural selection leads to adaptive evolution
Key Points
• Natural selection increases or decreases biological traits within a population, thereby selecting for individuals with greater evolutionary fitness.
• An individual with a high evolutionary fitness will provide more beneficial contributions to the gene pool of the next generation.
• Relative fitness, which compares an organism’s fitness to the others in the population, allows researchers to establish how a population may evolve by determining which individuals are contributing additional offspring to the next generation.
• Stabilizing selection, directional selection, diversifying selection, frequency -dependent selection, and sexual selection all contribute to the way natural selection can affect variation within a population.
Key Terms
• natural selection: a process in which individual organisms or phenotypes that possess favorable traits are more likely to survive and reproduce
• fecundity: number, rate, or capacity of offspring production
• Darwinian fitness: the average contribution to the gene pool of the next generation that is made by an average individual of the specified genotype or phenotype
An Introduction to Adaptive Evolution
Natural selection only acts on the population’s heritable traits: selecting for beneficial alleles and, thus, increasing their frequency in the population, while selecting against deleterious alleles and, thereby, decreasing their frequency. This process is known as adaptive evolution. Natural selection does not act on individual alleles, however, but on entire organisms. An individual may carry a very beneficial genotype with a resulting phenotype that, for example, increases the ability to reproduce ( fecundity ), but if that same individual also carries an allele that results in a fatal childhood disease, that fecundity phenotype will not be passed on to the next generation because the individual will not live to reach reproductive age. Natural selection acts at the level of the individual; it selects for individuals with greater contributions to the gene pool of the next generation, known as an organism’s evolutionary fitness (or Darwinian fitness).
Fitness is often quantifiable and is measured by scientists in the field. However, it is not the absolute fitness of an individual that counts, but rather how it compares to the other organisms in the population. This concept, called relative fitness, allows researchers to determine which individuals are contributing additional offspring to the next generation and, thus, how the population might evolve.
There are several ways selection can affect population variation:
• stabilizing selection
• directional selection
• diversifying selection
• frequency-dependent selection
• sexual selection
As natural selection influences the allele frequencies in a population, individuals can either become more or less genetically similar and the phenotypes displayed can become more similar or more disparate. In the end, natural selection cannot produce perfect organisms from scratch, it can only generate populations that are better adapted to survive and successfully reproduce in their environments through the aforementioned selections.
Galápagos with David Attenborough: Two hundred years after Charles Darwin set foot on the shores of the Galápagos Islands, David Attenborough travels to this wild and mysterious archipelago. Amongst the flora and fauna of these enchanted volcanic islands, Darwin formulated his groundbreaking theories on evolution. Journey with Attenborough to explore how life on the islands has continued to evolve in biological isolation, and how the ever-changing volcanic landscape has given birth to species and sub-species that exist nowhere else in the world. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/20%3A_Genes_Within_Populations/20.04%3A_Quantifying_Natural_Selection/20.4.01%3A_Hardy-Weinberg.txt |
Sexual selection, the selection pressure on males and females to obtain matings, can result in traits designed to maximize sexual success.
Learning Objectives
• Discuss the effects of sexual dimorphism on the reproductive potential of an organism
Key Points
• Sexual selection often results in the development of secondary sexual characteristics, which help to maximize a species ‘ reproductive success, but do not provide any survival benefits.
• The handicap principle states that only the best males survive the risks from traits that may actually be detrimental to a species; therefore, they are more fit as mating partners.
• In the good genes hypothesis, females will choose males that show off impressive traits to ensure they pass on genetic superiority to their offspring.
• Sexual dimorphisms, obvious morphological differences between the sexes of a species, arise when there is more variance in the reproductive success of either males or females.
Key Terms
• sexual dimorphism: a physical difference between male and female individuals of the same species
• sexual selection: a type of natural selection, where members of the sexes acquire distinct forms because members choose mates with particular features or because competition for mates with certain traits succeed
• handicap principle: a theory that suggests that animals of greater biological fitness signal this status through a behavior or morphology that effectively lowers their chances of survival
Sexual Selection
The selection pressures on males and females to obtain matings is known as sexual selection. Sexual selection takes two major forms: intersexual selection (also known as ‘mate choice’ or ‘female choice’) in which males compete with each other to be chosen by females; and intrasexual selection (also known as ‘male–male competition’) in which members of the less limited sex (typically males) compete aggressively among themselves for access to the limiting sex. The limiting sex is the sex which has the higher parental investment, which therefore faces the most pressure to make a good mate decision.
Sexual Dimorphism
Males and females of certain species are often quite different from one another in ways beyond the reproductive organs. Males are often larger, for example, and display many elaborate colors and adornments, such as the peacock’s tail, while females tend to be smaller and duller in decoration. These differences are called sexual dimorphisms and arise from the variation in male reproductive success.
Females almost always mate, while mating is not guaranteed for males. The bigger, stronger, or more decorated males usually obtain the vast majority of the total matings, while other males receive none. This can occur because the males are better at fighting off other males, or because females will choose to mate with the bigger or more decorated males. In either case, this variation in reproductive success generates a strong selection pressure among males to obtain those matings, resulting in the evolution of bigger body size and elaborate ornaments in order to increase their chances of mating. Females, on the other hand, tend to get a handful of selected matings; therefore, they are more likely to select more desirable males.
Sexual dimorphism varies widely among species; some species are even sex-role reversed. In such cases, females tend to have a greater variation in their reproductive success than males and are, correspondingly, selected for the bigger body size and elaborate traits usually characteristic of males.
The Handicap Principle
Sexual selection can be so strong that it selects for traits that are actually detrimental to the individual’s survival, even though they maximize its reproductive success. For example, while the male peacock’s tail is beautiful and the male with the largest, most colorful tail will more probably win the female, it is not a practical appendage. In addition to being more visible to predators, it makes the males slower in their attempted escapes. There is some evidence that this risk, in fact, is why females like the big tails in the first place. Because large tails carry risk, only the best males survive that risk and therefore the bigger the tail, the more fit the male. This idea is known as the handicap principle.
The Good Genes Hypothesis
The good genes hypothesis states that males develop these impressive ornaments to show off their efficient metabolism or their ability to fight disease. Females then choose males with the most impressive traits because it signals their genetic superiority, which they will then pass on to their offspring. Though it might be argued that females should not be so selective because it will likely reduce their number of offspring, if better males father more fit offspring, it may be beneficial. Fewer, healthier offspring may increase the chances of survival more than many, weaker offspring.
BBC Planet Earth – Birds of Paradise mating dance: Extraordinary Courtship displays from these weird and wonderful creatures. From episode 1 “Pole to Pole”. This is an example of the extreme behaviors that arise from intense sexual selection pressure. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/20%3A_Genes_Within_Populations/20.05%3A_Reproductive_Strategies/20.5D%3A_Sexual_Selection.txt |
Natural selection drives adaptive evolution by selecting for and increasing the occurrence of beneficial traits in a population.
Learning Objectives
• Explain how natural selection leads to adaptive evolution
Key Points
• Natural selection increases or decreases biological traits within a population, thereby selecting for individuals with greater evolutionary fitness.
• An individual with a high evolutionary fitness will provide more beneficial contributions to the gene pool of the next generation.
• Relative fitness, which compares an organism’s fitness to the others in the population, allows researchers to establish how a population may evolve by determining which individuals are contributing additional offspring to the next generation.
• Stabilizing selection, directional selection, diversifying selection, frequency -dependent selection, and sexual selection all contribute to the way natural selection can affect variation within a population.
Key Terms
• natural selection: a process in which individual organisms or phenotypes that possess favorable traits are more likely to survive and reproduce
• fecundity: number, rate, or capacity of offspring production
• Darwinian fitness: the average contribution to the gene pool of the next generation that is made by an average individual of the specified genotype or phenotype
An Introduction to Adaptive Evolution
Natural selection only acts on the population’s heritable traits: selecting for beneficial alleles and, thus, increasing their frequency in the population, while selecting against deleterious alleles and, thereby, decreasing their frequency. This process is known as adaptive evolution. Natural selection does not act on individual alleles, however, but on entire organisms. An individual may carry a very beneficial genotype with a resulting phenotype that, for example, increases the ability to reproduce ( fecundity ), but if that same individual also carries an allele that results in a fatal childhood disease, that fecundity phenotype will not be passed on to the next generation because the individual will not live to reach reproductive age. Natural selection acts at the level of the individual; it selects for individuals with greater contributions to the gene pool of the next generation, known as an organism’s evolutionary fitness (or Darwinian fitness).
Fitness is often quantifiable and is measured by scientists in the field. However, it is not the absolute fitness of an individual that counts, but rather how it compares to the other organisms in the population. This concept, called relative fitness, allows researchers to determine which individuals are contributing additional offspring to the next generation and, thus, how the population might evolve.
There are several ways selection can affect population variation:
• stabilizing selection
• directional selection
• diversifying selection
• frequency-dependent selection
• sexual selection
As natural selection influences the allele frequencies in a population, individuals can either become more or less genetically similar and the phenotypes displayed can become more similar or more disparate. In the end, natural selection cannot produce perfect organisms from scratch, it can only generate populations that are better adapted to survive and successfully reproduce in their environments through the aforementioned selections.
Galápagos with David Attenborough: Two hundred years after Charles Darwin set foot on the shores of the Galápagos Islands, David Attenborough travels to this wild and mysterious archipelago. Amongst the flora and fauna of these enchanted volcanic islands, Darwin formulated his groundbreaking theories on evolution. Journey with Attenborough to explore how life on the islands has continued to evolve in biological isolation, and how the ever-changing volcanic landscape has given birth to species and sub-species that exist nowhere else in the world. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/20%3A_Genes_Within_Populations/20.06%3A_Natural_Selection%27s_Role_in_Maintaining_Variation/20.6.01%3A_Natural_Selection_and_Adaptive_Evolution.txt |
In frequency-dependent selection, phenotypes that are either common or rare are favored through natural selection.
Learning Objectives
• Describe frequency-dependent selection
Key Points
• Negative frequency -dependent selection selects for rare phenotypes in a population and increases a population’s genetic variance.
• Positive frequency-dependent selection selects for common phenotypes in a population and decreases genetic variance.
• In the example of male side-blotched lizards, populations of each color pattern increase or decrease at various stages depending on their frequency; this ensures that both common and rare phenotypes continue to be cyclically present.
• Infectious agents such as microbes can exhibit negative frequency-dependent selection; as a host population becomes immune to a common strain of the microbe, less common strains of the microbe are automatically favored.
• Variation in color pattern mimicry by the scarlet kingsnake is dependent on the prevalence of the eastern coral snake, the model for this mimicry, in a particular geographical region. The more prevalent the coral snake is in a region, the more common and variable the scarlet kingsnake’s color pattern will be, making this an example of positive frequency-dependent selection.
Key Terms
• frequency-dependent selection: the term given to an evolutionary process where the fitness of a phenotype is dependent on its frequency relative to other phenotypes in a given population
• polygynous: having more than one female as mate
Frequency-dependent Selection
Another type of selection, called frequency-dependent selection, favors phenotypes that are either common (positive frequency-dependent selection) or rare (negative frequency-dependent selection).
Negative Frequency-dependent Selection
An interesting example of this type of selection is seen in a unique group of lizards of the Pacific Northwest. Male common side-blotched lizards come in three throat-color patterns: orange, blue, and yellow. Each of these forms has a different reproductive strategy: orange males are the strongest and can fight other males for access to their females; blue males are medium-sized and form strong pair bonds with their mates; and yellow males are the smallest and look a bit like female, allowing them to sneak copulations. Like a game of rock-paper-scissors, orange beats blue, blue beats yellow, and yellow beats orange in the competition for females. The big, strong orange males can fight off the blue males to mate with the blue’s pair-bonded females; the blue males are successful at guarding their mates against yellow sneaker males; and the yellow males can sneak copulations from the potential mates of the large, polygynous orange males.
In this scenario, orange males will be favored by natural selection when the population is dominated by blue males, blue males will thrive when the population is mostly yellow males, and yellow males will be selected for when orange males are the most populous. As a result, populations of side-blotched lizards cycle in the distribution of these phenotypes. In one generation, orange might be predominant and then yellow males will begin to rise in frequency. Once yellow males make up a majority of the population, blue males will be selected for.Finally, when blue males become common, orange males will once again be favored.
An example of negative frequency-dependent selection can also be seen in the interaction between the human immune system and various infectious microbes such as pathogenic bacteria or viruses. As a particular human population is infected by a common strain of microbe, the majority of individuals in the population become immune to it. This then selects for rarer strains of the microbe which can still infect the population because of genome mutations; these strains have greater evolutionary fitness because they are less common.
Positive Frequency-dependent Selection
An example of positive frequency-dependent selection is the mimicry of the warning coloration of dangerous species of animals by other species that are harmless. The scarlet kingsnake, a harmless species, mimics the coloration of the eastern coral snake, a venomous species typically found in the same geographical region. Predators learn to avoid both species of snake due to the similar coloration, and as a result the scarlet kingsnake becomes more common, and its coloration phenotype becomes more variable due to relaxed selection. This phenotype is therefore more “fit” as the population of species that possess it (both dangerous and harmless) becomes more numerous. In geographic areas where the coral snake is less common, the pattern becomes less advantageous to the kingsnake, and much less variable in its expression, presumably because predators in these regions are not “educated” to avoid the pattern.
Negative frequency-dependent selection serves to increase the population’s genetic variance by selecting for rare phenotypes, whereas positive frequency-dependent selection usually decreases genetic variance by selecting for common phenotypes. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/20%3A_Genes_Within_Populations/20.06%3A_Natural_Selection%27s_Role_in_Maintaining_Variation/20.6.02%3A_Frequency-Dependent_Selection.txt |
Stabilizing, directional, and diversifying selection either decrease, shift, or increase the genetic variance of a population.
Learning Objectives
• Contrast stabilizing selection, directional selection, and diversifying selection.
Key Points
• Stabilizing selection results in a decrease of a population ‘s genetic variance when natural selection favors an average phenotype and selects against extreme variations.
• In directional selection, a population’s genetic variance shifts toward a new phenotype when exposed to environmental changes.
• Diversifying or disruptive selection increases genetic variance when natural selection selects for two or more extreme phenotypes that each have specific advantages.
• In diversifying or disruptive selection, average or intermediate phenotypes are often less fit than either extreme phenotype and are unlikely to feature prominently in a population.
Key Terms
• directional selection: a mode of natural selection in which a single phenotype is favored, causing the allele frequency to continuously shift in one direction
• disruptive selection: (or diversifying selection) a mode of natural selection in which extreme values for a trait are favored over intermediate values
• stabilizing selection: a type of natural selection in which genetic diversity decreases as the population stabilizes on a particular trait value
Stabilizing Selection
If natural selection favors an average phenotype by selecting against extreme variation, the population will undergo stabilizing selection. For example, in a population of mice that live in the woods, natural selection will tend to favor individuals that best blend in with the forest floor and are less likely to be spotted by predators. Assuming the ground is a fairly consistent shade of brown, those mice whose fur is most-closely matched to that color will most probably survive and reproduce, passing on their genes for their brown coat. Mice that carry alleles that make them slightly lighter or slightly darker will stand out against the ground and will more probably die from predation. As a result of this stabilizing selection, the population’s genetic variance will decrease.
Stabilizing selection: Stabilizing selection occurs when the population stabilizes on a particular trait value and genetic diversity decreases.
Directional Selection
When the environment changes, populations will often undergo directional selection, which selects for phenotypes at one end of the spectrum of existing variation.
A classic example of this type of selection is the evolution of the peppered moth in eighteenth- and nineteenth-century England. Prior to the Industrial Revolution, the moths were predominately light in color, which allowed them to blend in with the light-colored trees and lichens in their environment. As soot began spewing from factories, the trees darkened and the light-colored moths became easier for predatory birds to spot.
Directional selection: Directional selection occurs when a single phenotype is favored, causing the allele frequency to continuously shift in one direction.
Over time, the frequency of the melanic form of the moth increased because their darker coloration provided camouflage against the sooty tree; they had a higher survival rate in habitats affected by air pollution. Similarly, the hypothetical mouse population may evolve to take on a different coloration if their forest floor habitat changed. The result of this type of selection is a shift in the population’s genetic variance toward the new, fit phenotype.
Diversifying (or Disruptive) Selection
Sometimes natural selection can select for two or more distinct phenotypes that each have their advantages. In these cases, the intermediate phenotypes are often less fit than their extreme counterparts. Known as diversifying or disruptive selection, this is seen in many populations of animals that have multiple male mating strategies, such as lobsters. Large, dominant alpha males obtain mates by brute force, while small males can sneak in for furtive copulations with the females in an alpha male’s territory. In this case, both the alpha males and the “sneaking” males will be selected for, but medium-sized males, which cannot overtake the alpha males and are too big to sneak copulations, are selected against.
Diversifying (or disruptive) selection: Diversifying selection occurs when extreme values for a trait are favored over the intermediate values.This type of selection often drives speciation.
Diversifying selection can also occur when environmental changes favor individuals on either end of the phenotypic spectrum. Imagine a population of mice living at the beach where there is light-colored sand interspersed with patches of tall grass. In this scenario, light-colored mice that blend in with the sand would be favored, as well as dark-colored mice that can hide in the grass. Medium-colored mice, on the other hand, would not blend in with either the grass or the sand and, thus, would more probably be eaten by predators. The result of this type of selection is increased genetic variance as the population becomes more diverse. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/20%3A_Genes_Within_Populations/20.07%3A_Selection_Acting_on_Traits_Affected_by_Multiple_Genes/20.7B%3A_Stabilizing_Directional_and_Diversifying_Selection.txt |
Genetic variation is a measure of the variation that exists in the genetic makeup of individuals within population.
Learning Objectives
• Assess the ways in which genetic variance affects the evolution of populations
Key Points
• Genetic variation is an important force in evolution as it allows natural selection to increase or decrease frequency of alleles already in the population.
• Genetic variation can be caused by mutation (which can create entirely new alleles in a population), random mating, random fertilization, and recombination between homologous chromosomes during meiosis (which reshuffles alleles within an organism’s offspring).
• Genetic variation is advantageous to a population because it enables some individuals to adapt to the environment while maintaining the survival of the population.
Key Terms
• genetic diversity: the level of biodiversity, refers to the total number of genetic characteristics in the genetic makeup of a species
• crossing over: the exchange of genetic material between homologous chromosomes that results in recombinant chromosomes
• phenotypic variation: variation (due to underlying heritable genetic variation); a fundamental prerequisite for evolution by natural selection
• genetic variation: variation in alleles of genes that occurs both within and among populations
Genetic Variation
Genetic variation is a measure of the genetic differences that exist within a population. The genetic variation of an entire species is often called genetic diversity. Genetic variations are the differences in DNA segments or genes between individuals and each variation of a gene is called an allele.For example, a population with many different alleles at a single chromosome locus has a high amount of genetic variation. Genetic variation is essential for natural selection because natural selection can only increase or decrease frequency of alleles that already exist in the population.
Genetic variation is caused by:
• mutation
• random mating between organisms
• random fertilization
• crossing over (or recombination) between chromatids of homologous chromosomes during meiosis
The last three of these factors reshuffle alleles within a population, giving offspring combinations which differ from their parents and from others.
Evolution and Adaptation to the Environment
Variation allows some individuals within a population to adapt to the changing environment. Because natural selection acts directly only on phenotypes, more genetic variation within a population usually enables more phenotypic variation. Some new alleles increase an organism’s ability to survive and reproduce, which then ensures the survival of the allele in the population. Other new alleles may be immediately detrimental (such as a malformed oxygen-carrying protein) and organisms carrying these new mutations will die out. Neutral alleles are neither selected for nor against and usually remain in the population. Genetic variation is advantageous because it enables some individuals and, therefore, a population, to survive despite a changing environment.
Geographic Variation
Some species display geographic variation as well as variation within a population. Geographic variation, or the distinctions in the genetic makeup of different populations, often occurs when populations are geographically separated by environmental barriers or when they are under selection pressures from a different environment. One example of geographic variation are clines: graded changes in a character down a geographic axis.
Sources of Genetic Variation
Gene duplication, mutation, or other processes can produce new genes and alleles and increase genetic variation. New genetic variation can be created within generations in a population, so a population with rapid reproduction rates will probably have high genetic variation. However, existing genes can be arranged in new ways from chromosomal crossing over and recombination in sexual reproduction. Overall, the main sources of genetic variation are the formation of new alleles, the altering of gene number or position, rapid reproduction, and sexual reproduction. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/20%3A_Genes_Within_Populations/20.09%3A_Interactions_Among_Evolutionary_Forces/20.9A%3A_Genetic_Variation.txt |
Genetic drift is the change in allele frequencies of a population due to random chance events, such as natural disasters.
Learning Objectives
• Distinguish between selection and genetic drift
Key Points
• Genetic drift is the change in the frequency of an allele in a population due to random sampling and the random events that influence the survival and reproduction of those individuals.
• The bottleneck effect occurs when a natural disaster or similar event randomly kills a large portion (i.e. random sample) of the population, leaving survivors that have allele frequencies that were very different from the previous population.
• The founder effect occurs when a portion of the population (i.e. “founders”) separates from the old population to start a new population with different allele frequencies.
• Small populations are more susceptible genetic drift than large populations, whose larger numbers can buffer the population against chance events.
Key Terms
• genetic drift: an overall shift of allele distribution in an isolated population, due to random sampling
• founder effect: a decrease in genetic variation that occurs when an entire population descends from a small number of founders
• random sampling: a subset of individuals (a sample) chosen from a larger set (a population) by chance
Genetic Drift vs. Natural Selection
Genetic drift is the converse of natural selection. The theory of natural selection maintains that some individuals in a population have traits that enable to survive and produce more offspring, while other individuals have traits that are detrimental and may cause them to die before reproducing. Over successive generation, these selection pressures can change the gene pool and the traits within the population. For example, a big, powerful male gorilla will mate with more females than a small, weak male and therefore more of his genes will be passed on to the next generation. His offspring may continue to dominate the troop and pass on their genes as well. Over time, the selection pressure will cause the allele frequencies in the gorilla population to shift toward large, strong males.
Unlike natural selection, genetic drift describes the effect of chance on populations in the absence of positive or negative selection pressure. Through random sampling, or the survival or and reproduction of a random sample of individuals within a population, allele frequencies within a population may change. Rather than a male gorilla producing more offspring because he is stronger, he may be the only male available when a female is ready to mate. His genes are passed on to future generation because of chance, not because he was the biggest or the strongest. Genetic drift is the shift of alleles within a population due to chance events that cause random samples of the population to reproduce or not.
Small populations are more susceptible to the forces of genetic drift. Large populations, on the other hand, are buffered against the effects of chance. If one individual of a population of 10 individuals happens to die at a young age before leaving any offspring to the next generation, all of its genes (1/10 of the population’s gene pool) will be suddenly lost. In a population of 100, that individual represents only 1 percent of the overall gene pool; therefore, genetic drift has much less impact on the larger population’s genetic structure.
The Bottleneck Effect
Genetic drift can also be magnified by natural events, such as a natural disaster that kills a large portion of the population at random. The bottleneck effect occurs when only a few individuals survive and reduces variation in the gene pool of a population. The genetic structure of the survivors becomes the genetic structure of the entire population, which may be very different from the pre-disaster population.
The Founder Effect
Another scenario in which populations might experience a strong influence of genetic drift is if some portion of the population leaves to start a new population in a new location or if a population gets divided by a physical barrier of some kind. In this situation, it is improbable that those individuals are representative of the entire population, which results in the founder effect. The founder effect occurs when the genetic structure changes to match that of the new population’s founding fathers and mothers.
The founder effect is believed to have been a key factor in the genetic history of the Afrikaner population of Dutch settlers in South Africa, as evidenced by mutations that are common in Afrikaners, but rare in most other populations. This was probably due to the fact that a higher-than-normal proportion of the founding colonists carried these mutations. As a result, the population expresses unusually high incidences of Huntington’s disease (HD) and Fanconi anemia (FA), a genetic disorder known to cause blood marrow and congenital abnormalities, even cancer.
Drift and fixation
The Hardy–Weinberg principle states that within sufficiently large populations, the allele frequencies remain constant from one generation to the next unless the equilibrium is disturbed by migration, genetic mutation, or selection.
Because the random sampling can remove, but not replace, an allele, and because random declines or increases in allele frequency influence expected allele distributions for the next generation, genetic drift drives a population towards genetic uniformity over time. When an allele reaches a frequency of 1 (100%) it is said to be “fixed” in the population and when an allele reaches a frequency of 0 (0%) it is lost. Once an allele becomes fixed, genetic drift for that allele comes to a halt, and the allele frequency cannot change unless a new allele is introduced in the population via mutation or gene flow. Thus even while genetic drift is a random, directionless process, it acts to eliminate genetic variation over time. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/20%3A_Genes_Within_Populations/20.09%3A_Interactions_Among_Evolutionary_Forces/20.9B%3A_Genetic_Drift.txt |
A population’s genetic variation changes as individuals migrate into or out of a population and when mutations introduce new alleles.
Learning Objectives
• Explain how gene flow and mutations can influence the allele frequencies of a population
Key Points
• Plant populations experience gene flow by spreading their pollen long distances.
• Animals experience gene flow when individuals leave a family group or herd to join other populations.
• The flow of individuals in and out of a population introduces new alleles and increases genetic variation within that population.
• Mutations are changes to an organism’s DNA that create diversity within a population by introducing new alleles.
• Some mutations are harmful and are quickly eliminated from the population by natural selection; harmful mutations prevent organisms from reaching sexual maturity and reproducing.
• Other mutations are beneficial and can increase in a population if they help organisms reach sexual maturity and reproduce.
Key Terms
• gene flow: the transfer of alleles or genes from one population to another
• mutation: any heritable change of the base-pair sequence of genetic material
Gene Flow
An important evolutionary force is gene flow: the flow of alleles in and out of a population due to the migration of individuals or gametes. While some populations are fairly stable, others experience more movement and fluctuation. Many plants, for example, send their pollen by wind, insects, or birds to pollinate other populations of the same species some distance away. Even a population that may initially appear to be stable, such as a pride of lions, can receive new genetic variation as developing males leave their mothers to form new prides with genetically-unrelated females. This variable flow of individuals in and out of the group not only changes the gene structure of the population, but can also introduce new genetic variation to populations in different geological locations and habitats.
Maintained gene flow between two populations can also lead to a combination of the two gene pools, reducing the genetic variation between the two groups. Gene flow strongly acts against speciation, by recombining the gene pools of the groups, and thus, repairing the developing differences in genetic variation that would have led to full speciation and creation of daughter species.
For example, if a species of grass grows on both sides of a highway, pollen is likely to be transported from one side to the other and vice versa. If this pollen is able to fertilize the plant where it ends up and produce viable offspring, then the alleles in the pollen have effectively linked the population on one side of the highway with the other.
Mutation
Mutations are changes to an organism’s DNA and are an important driver of diversity in populations. Species evolve because of the accumulation of mutations that occur over time. The appearance of new mutations is the most common way to introduce novel genotypic and phenotypic variance. Some mutations are unfavorable or harmful and are quickly eliminated from the population by natural selection. Others are beneficial and will spread through the population. Whether or not a mutation is beneficial or harmful is determined by whether it helps an organism survive to sexual maturity and reproduce. Some mutations have no effect on an organism and can linger, unaffected by natural selection, in the genome while others can have a dramatic effect on a gene and the resulting phenotype. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/20%3A_Genes_Within_Populations/20.09%3A_Interactions_Among_Evolutionary_Forces/20.9C%3A_Gene_Flow_and_Mutation.txt |
Population structure can be altered by nonrandom mating (the preference of certain individuals for mates) as well as the environment.
Learning Objectives
• Explain how environmental variance and nonrandom mating can change gene frequencies in a population
Key Points
• Nonrandom mating can occur when individuals prefer mates with particular superior physical characteristics or by the preference of individuals to mate with individuals similar to themselves.
• Nonrandom mating can also occur when mates are chosen based on physical accessibility; that is, the availability of some mates over others.
• Phenotypes of individuals can also be influenced by the environment in which they live, such as temperature, terrain, or other factors.
• A cline occurs when populations of a given species vary gradually across an ecological gradient.
Key Terms
• cline: a gradation in a character or phenotype within a species or other group
• sexual selection: a mode of natural selection in which some individuals out-reproduce others of a population because they are better at securing mates
• assortative mating: between males and females of a species, the mutual attraction or selection, for reproductive purposes, of individuals with similar characteristics
Nonrandom Mating
If individuals nonrandomly mate with other individuals in the population, i.e. they choose their mate, choices can drive evolution within a population. There are many reasons nonrandom mating occurs. One reason is simple mate choice or sexual selection; for example, female peahens may prefer peacocks with bigger, brighter tails. Traits that lead to more matings for an individual lead to more offspring and through natural selection, eventually lead to a higher frequency of that trait in the population. One common form of mate choice, called positive assortative mating, is an individual’s preference to mate with partners that are phenotypically similar to themselves.
Another cause of nonrandom mating is physical location. This is especially true in large populations spread over large geographic distances where not all individuals will have equal access to one another. Some might be miles apart through woods or over rough terrain, while others might live immediately nearby.
Environmental Variance
Genes are not the only players involved in determining population variation. Phenotypes are also influenced by other factors, such as the environment. A beachgoer is likely to have darker skin than a city dweller, for example, due to regular exposure to the sun, an environmental factor. Some major characteristics, such as gender, are determined by the environment for some species. For example, some turtles and other reptiles have temperature-dependent sex determination (TSD). TSD means that individuals develop into males if their eggs are incubated within a certain temperature range, or females at a different temperature range.
Geographic separation between populations can lead to differences in the phenotypic variation between those populations. Such geographical variation is seen between most populations and can be significant. One type of geographic variation, called a cline, can be seen as populations of a given species vary gradually across an ecological gradient.
Geographic variation in moose: This graph shows geographical variation in moose; body mass increase positively with latitude. Bergmann’s Rule is an ecologic principle which states that as latitude increases the body mass of a particular species increases. The data are taken from a Swedish study investigating the size of moose as latitude increases as shows the positive relationship between the two, supporting Bergmann’s Rule.
Species of warm-blooded animals, for example, tend to have larger bodies in the cooler climates closer to the earth’s poles, allowing them to better conserve heat. This is considered a latitudinal cline. Alternatively, flowering plants tend to bloom at different times depending on where they are along the slope of a mountain, known as an altitudinal cline.
If there is gene flow between the populations, the individuals will likely show gradual differences in phenotype along the cline. Restricted gene flow, on the other hand, can lead to abrupt differences, even speciation.
Contributions and Attributions
• Structural Biochemistry/Organismic and Evolutionary Biology. Provided by: Wikibooks. Located at: en.wikibooks.org/wiki/Structu...ionary_Biology. License: CC BY-SA: Attribution-ShareAlike
• OpenStax College, Biology. October 22, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44584/latest...ol11448/latest. License: CC BY: Attribution
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• phenotypic variation. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/phenotypic%20variation. License: CC BY-SA: Attribution-ShareAlike
• Genetic Diversity. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/Genetic_diversity. License: CC BY-SA: Attribution-ShareAlike
• Coquina variation3. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/File:Co...variation3.jpg. License: CC BY-SA: Attribution-ShareAlike
• Cheetah genetic diversity. Provided by: Wikimedia. Located at: en.Wikipedia.org/wiki/File:Ch..._diversity.jpg. License: CC BY-SA: Attribution-ShareAlike
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• genetic drift. Provided by: Wiktionary. Located at: en.wiktionary.org/wiki/genetic_drift. License: CC BY-SA: Attribution-ShareAlike
• Coquina variation3. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/File:Co...variation3.jpg. License: CC BY-SA: Attribution-ShareAlike
• Cheetah genetic diversity. Provided by: Wikimedia. Located at: en.Wikipedia.org/wiki/File:Ch..._diversity.jpg. License: CC BY-SA: Attribution-ShareAlike
• Founder effect with drift. Provided by: Wikimedia. Located at: en.Wikipedia.org/wiki/File:Fo...with_drift.jpg. License: CC BY-SA: Attribution-ShareAlike
• OpenStax College, Population Genetics. October 16, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44584/latest...e_19_02_02.png. License: CC BY: Attribution
• Random genetic drift chart. Provided by: Wikimedia. Located at: en.Wikipedia.org/wiki/Genetic...rift_chart.png. License: CC BY-SA: Attribution-ShareAlike
• OpenStax College, Population Genetics. October 16, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44584/latest...e_19_02_03.jpg. License: CC BY: Attribution
• OpenStax College, Biology. October 16, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44584/latest...ol11448/latest. License: CC BY: Attribution
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• OpenStax College, Population Genetics. October 16, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44584/latest...e_19_02_02.png. License: CC BY: Attribution
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• American Robin Close-Up. Provided by: Wikimedia. Located at: en.Wikipedia.org/wiki/America...n_Close-Up.JPG. License: CC BY-SA: Attribution-ShareAlike | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/20%3A_Genes_Within_Populations/20.09%3A_Interactions_Among_Evolutionary_Forces/20.9D%3A_Nonrandom_Mating_and_Environmental_Variance.txt |
Natural selection cannot create novel, perfect species because it only selects on existing variations in a population.
Learning Objectives
• Explain the limitations encountered in natural selection
Key Points
• Natural selection is limited by a population ‘s existing genetic variation.
• Natural selection is limited through linkage disequilibrium, where alleles that are physically proximate on the chromosome are passed on together at greater frequencies.
• In a polymorphic population, two phenotypes may be maintained in the population despite the higher fitness of one morph if the intermediate phenotype is detrimental.
• Evolution is not purposefully adaptive; it is the result of various selection forces working together to influence genetic and phenotypical variances within a population.
Key Terms
• linkage disequilibrium: a non-random association of two or more alleles at two or more loci; normally caused by an interaction between genes
• genetic hitchhiking: changes in the frequency of an allele because of linkage with a positively or negatively selected allele at another locus
• polymorphism: the regular existence of two or more different genotypes within a given species or population
No Perfect Organism
Natural selection is a driving force in evolution and can generate populations that are adapted to survive and successfully reproduce in their environments. However, natural selection cannot produce the perfect organism. Natural selection can only select on existing variation in the population; it cannot create anything from scratch. Therefore, the process of evolution is limited by a population’s existing genetic variance, the physical proximity of alleles, non-beneficial intermediate morphs in a polymorphic population, and non-adaptive evolutionary forces.
Natural Selection Acts on Individuals, not Alleles
Natural selection is also limited because it acts on the phenotypes of individuals, not alleles. Some alleles may be more likely to be passed on with alleles that confer a beneficial phenotype because of their physical proximity on the chromosomes. Alleles that are carried together are in linkage disequilibrium. When a neutral allele is linked to beneficial allele, consequently meaning that it has a selective advantage, the allele frequency can increase in the population through genetic hitchhiking (also called genetic draft).
Any given individual may carry some beneficial alleles and some unfavorable alleles. Natural selection acts on the net effect of these alleles and corresponding fitness of the phenotype. As a result, good alleles can be lost if they are carried by individuals that also have several overwhelmingly bad alleles; similarly, bad alleles can be kept if they are carried by individuals that have enough good alleles to result in an overall fitness benefit.
Polymorphism
Furthermore, natural selection can be constrained by the relationships between different polymorphisms. One morph may confer a higher fitness than another, but may not increase in frequency because the intermediate morph is detrimental.
Polymorphism in the grove snail: Color and pattern morphs of the grove snail, Cepaea nemoralis.The polymorphism, when two or more different genotypes exist within a given species, in grove snails seems to have several causes, including predation by thrushes.
For example, consider a hypothetical population of mice that live in the desert. Some are light-colored and blend in with the sand, while others are dark and blend in with the patches of black rock. The dark-colored mice may be more fit than the light-colored mice, and according to the principles of natural selection the frequency of light-colored mice is expected to decrease over time. However, the intermediate phenotype of a medium-colored coat is very bad for the mice: these cannot blend in with either the sand or the rock and will more vulnerable to predators. As a result, the frequency of a dark-colored mice would not increase because the intermediate morphs are less fit than either light-colored or dark-colored mice. This a common example of disruptive selection.
Not all Evolution is Adaptive
Finally, it is important to understand that not all evolution is adaptive. While natural selection selects the fittest individuals and often results in a more fit population overall, other forces of evolution, including genetic drift and gene flow, often do the opposite by introducing deleterious alleles to the population’s gene pool. Evolution has no purpose. It is not changing a population into a preconceived ideal. It is simply the sum of various forces and their influence on the genetic and phenotypic variance of a population.
Contributions and Attributions
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• Lampropeltis elapsoides. Provided by: WikiPedia. Located at: en.Wikipedia.org/wiki/File:G-Bartolotti_SK.jpg. License: CC BY-SA: Attribution-ShareAlike
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• 21.1: The Beaks of Darwin's Finches- Evidence of Natural Selection
Evolution by natural selection arises from three conditions: individuals within a species vary, some of those variations are heritable, and organisms have more offspring than resources can support. The consequence is that individuals with relatively advantageous variations will be more likely to survive and have higher reproductive rates than those individuals with different traits. The advantageous traits will be passed on to offspring in greater proportion.
• 21.2: Speciation
A species is an actually or potentially interbreeding population that does not interbreed with other such populations when there is opportunity to do so.
• 21.3: Artificial Selection- Human-Initiated Change
• 21.4: Fossil Evidence of Evolution
• 21.5: Anatomical Evidence of Evolution
The evidence for evolution is found at all levels of organization in living things and in the extinct species we know about through fossils. Fossils provide evidence for the evolutionary change through now extinct forms that led to modern species. For example, there is a rich fossil record that shows the evolutionary transitions from horse ancestors to modern horses that document intermediate forms and a gradual adaptation t changing ecosystems.
• 21.6: Convergent Evolution and the Biogeographical Record
• 21.7: Darwin's Critics
Although the theory of evolution initially generated some controversy, by 20 years after the publication of On the Origin of Species it was almost universally accepted by biologists, particularly younger biologists. Nevertheless, the theory of evolution is a difficult concept and misconceptions about how it works abound. In addition, there are those that reject it as an explanation for the diversity of life.
21: The Evidence for Evolution
The theory of evolution by natural selection describes a mechanism for species change over time. That species change had been suggested and debated well before Darwin. The view that species were static and unchanging was grounded in the writings of Plato, yet there were also ancient Greeks that expressed evolutionary ideas.
In the eighteenth century, ideas about the evolution of animals were reintroduced by the naturalist Georges-Louis Leclerc, Comte de Buffon and even by Charles Darwin’s grandfather, Erasmus Darwin. During this time, it was also accepted that there were extinct species. At the same time, James Hutton, the Scottish naturalist, proposed that geological change occurred gradually by the accumulation of small changes from processes (over long periods of time) just like those happening today. This contrasted with the predominant view that the geology of the planet was a consequence of catastrophic events occurring during a relatively brief past. Hutton’s view was later popularized by the geologist Charles Lyell in the nineteenth century. Lyell became a friend to Darwin and his ideas were very influential on Darwin’s thinking. Lyell argued that the greater age of Earth gave more time for gradual change in species, and the process provided an analogy for gradual change in species.
In the early nineteenth century, Jean-Baptiste Lamarck published a book that detailed a mechanism for evolutionary change that is now referred to as inheritance of acquired characteristics. In Lamarck’s theory, modifications in an individual caused by its environment, or the use or disuse of a structure during its lifetime, could be inherited by its offspring and, thus, bring about change in a species. While this mechanism for evolutionary change as described by Lamarck was discredited, Lamarck’s ideas were an important influence on evolutionary thought. The inscription on the statue of Lamarck that stands at the gates of the Jardin des Plantes in Paris describes him as the “founder of the doctrine of evolution.”
Charles Darwin and Natural Selection
The actual mechanism for evolution was independently conceived of and described by two naturalists, Charles Darwin and Alfred Russell Wallace, in the mid-nineteenth century. Importantly, each spent time exploring the natural world on expeditions to the tropics. From 1831 to 1836, Darwin traveled around the world on H.M.S. Beagle, visiting South America, Australia, and the southern tip of Africa. Wallace traveled to Brazil to collect insects in the Amazon rainforest from 1848 to 1852 and to the Malay Archipelago from 1854 to 1862. Darwin’s journey, like Wallace’s later journeys in the Malay Archipelago, included stops at several island chains, the last being the Galápagos Islands (west of Ecuador). On these islands, Darwin observed species of organisms on different islands that were clearly similar, yet had distinct differences. For example, the ground finches inhabiting the Galápagos Islands comprised several species that each had a unique beak shape (Figure \(1\)). He observed both that these finches closely resembled another finch species on the mainland of South America and that the group of species in the Galápagos formed a graded series of beak sizes and shapes, with very small differences between the most similar. Darwin imagined that the island species might be all species modified from one original mainland species. In 1860, he wrote, “Seeing this gradation and diversity of structure in one small, intimately related group of birds, one might really fancy that from an original paucity of birds in this archipelago, one species had been taken and modified for different ends.”1
Wallace and Darwin both observed similar patterns in other organisms and independently conceived a mechanism to explain how and why such changes could take place. Darwin called this mechanism natural selection. Natural selection, Darwin argued, was an inevitable outcome of three principles that operated in nature. First, the characteristics of organisms are inherited, or passed from parent to offspring. Second, more offspring are produced than are able to survive; in other words, resources for survival and reproduction are limited. The capacity for reproduction in all organisms outstrips the availability of resources to support their numbers. Thus, there is a competition for those resources in each generation. Both Darwin and Wallace’s understanding of this principle came from reading an essay by the economist Thomas Malthus, who discussed this principle in relation to human populations. Third, offspring vary among each other in regard to their characteristics and those variations are inherited. Out of these three principles, Darwin and Wallace reasoned that offspring with inherited characteristics that allow them to best compete for limited resources will survive and have more offspring than those individuals with variations that are less able to compete. Because characteristics are inherited, these traits will be better represented in the next generation. This will lead to change in populations over generations in a process that Darwin called “descent with modification.”
Papers by Darwin and Wallace (Figure \(2\)) presenting the idea of natural selection were read together in 1858 before the Linnaean Society in London. The following year Darwin’s book, On the Origin of Species, was published, which outlined in considerable detail his arguments for evolution by natural selection.
Demonstrations of evolution by natural selection can be time consuming. One of the best demonstrations has been in the very birds that helped to inspire the theory, the Galápagos finches. Peter and Rosemary Grant and their colleagues have studied Galápagos finch populations every year since 1976 and have provided important demonstrations of the operation of natural selection. The Grants found changes from one generation to the next in the beak shapes of the medium ground finches on the Galápagos island of Daphne Major. The medium ground finch feeds on seeds. The birds have inherited variation in the bill shape with some individuals having wide, deep bills and others having thinner bills. Large-billed birds feed more efficiently on large, hard seeds, whereas smaller billed birds feed more efficiently on small, soft seeds. During 1977, a drought period altered vegetation on the island. After this period, the number of seeds declined dramatically: the decline in small, soft seeds was greater than the decline in large, hard seeds. The large-billed birds were able to survive better than the small-billed birds the following year. The year following the drought when the Grants measured beak sizes in the much-reduced population, they found that the average bill size was larger (Figure \(3\)). This was clear evidence for natural selection (differences in survival) of bill size caused by the availability of seeds. The Grants had studied the inheritance of bill sizes and knew that the surviving large-billed birds would tend to produce offspring with larger bills, so the selection would lead to evolution of bill size. Subsequent studies by the Grants have demonstrated selection on and evolution of bill size in this species in response to changing conditions on the island. The evolution has occurred both to larger bills, as in this case, and to smaller bills when large seeds became rare.
Variation and Adaptation
Natural selection can only take place if there is variation, or differences, among individuals in a population. Importantly, these differences must have some genetic basis; otherwise, selection will not lead to change in the next generation. This is critical because variation among individuals can be caused by non-genetic reasons, such as an individual being taller because of better nutrition rather than different genes.
Genetic diversity in a population comes from two main sources: mutation and sexual reproduction. Mutation, a change in DNA, is the ultimate source of new alleles or new genetic variation in any population. An individual that has a mutated gene might have a different trait than other individuals in the population. However, this is not always the case. A mutation can have one of three outcomes on the organisms’ appearance (or phenotype):
• A mutation may affect the phenotype of the organism in a way that gives it reduced fitness—lower likelihood of survival, resulting in fewer offspring.
• A mutation may produce a phenotype with a beneficial effect on fitness.
• Many mutations, called neutral mutations, will have no effect on fitness.
Mutations may also have a whole range of effect sizes on the fitness of the organism that expresses them in their phenotype, from a small effect to a great effect. Sexual reproduction and crossing over in meiosis also lead to genetic diversity: when two parents reproduce, unique combinations of alleles assemble to produce unique genotypes and, thus, phenotypes in each of the offspring.
A heritable trait that aids the survival and reproduction of an organism in its present environment is called an adaptation. An adaptation is a “match” of the organism to the environment. Adaptation to an environment comes about when a change in the range of genetic variation occurs over time that increases or maintains the match of the population with its environment. The variations in finch beaks shifted from generation to generation providing adaptation to food availability.
Whether or not a trait is favorable depends on the environment at the time. The same traits do not always have the same relative benefit or disadvantage because environmental conditions can change. For example, finches with large bills were benefited in one climate, while small bills were a disadvantage; in a different climate, the relationship reversed.
Patterns of Evolution
The evolution of species has resulted in enormous variation in form and function. When two species evolve in different directions from a common point, it is called divergent evolution. Such divergent evolution can be seen in the forms of the reproductive organs of flowering plants, which share the same basic anatomies; however, they can look very different as a result of selection in different physical environments, and adaptation to different kinds of pollinators (Figure \(4\)).
In other cases, similar phenotypes evolve independently in distantly related species. For example, flight has evolved in both bats and insects, and they both have structures we refer to as wings, which are adaptations to flight. The wings of bats and insects, however, evolved from very different original structures. When similar structures arise through evolution independently in different species it is called convergent evolution. The wings of bats and insects are called analogous structures; they are similar in function and appearance, but do not share an origin in a common ancestor. Instead they evolved independently in the two lineages. The wings of a hummingbird and an ostrich are homologous structures, meaning they share similarities (despite their differences resulting from evolutionary divergence). The wings of hummingbirds and ostriches did not evolve independently in the hummingbird lineage and the ostrich lineage—they descended from a common ancestor with wings.
The Modern Synthesis
The mechanisms of inheritance, genetics, were not understood at the time Darwin and Wallace were developing their idea of natural selection. This lack of understanding was a stumbling block to comprehending many aspects of evolution. In fact, blending inheritance was the predominant (and incorrect) genetic theory of the time, which made it difficult to understand how natural selection might operate. Darwin and Wallace were unaware of the genetics work by Austrian monk Gregor Mendel, which was published in 1866, not long after publication of On the Origin of Species. Mendel’s work was rediscovered in the early twentieth century at which time geneticists were rapidly coming to an understanding of the basics of inheritance. Initially, the newly discovered particulate nature of genes made it difficult for biologists to understand how gradual evolution could occur. But over the next few decades genetics and evolution were integrated in what became known as the modern synthesis—the coherent understanding of the relationship between natural selection and genetics that took shape by the 1940s and is generally accepted today. In sum, the modern synthesis describes how evolutionary pressures, such as natural selection, can affect a population’s genetic makeup, and, in turn, how this can result in the gradual evolution of populations and species. The theory also connects this gradual change of a population over time, called microevolution, with the processes that gave rise to new species and higher taxonomic groups with widely divergent characters, called macroevolution.
Population Genetics
Recall that a gene for a particular character may have several variants, or alleles, that code for different traits associated with that character. For example, in the ABO blood type system in humans, three alleles determine the particular blood-type protein on the surface of red blood cells. Each individual in a population of diploid organisms can only carry two alleles for a particular gene, but more than two may be present in the individuals that make up the population. Mendel followed alleles as they were inherited from parent to offspring. In the early twentieth century, biologists began to study what happens to all the alleles in a population in a field of study known as population genetics.
Until now, we have defined evolution as a change in the characteristics of a population of organisms, but behind that phenotypic change is genetic change. In population genetic terms, evolution is defined as a change in the frequency of an allele in a population. Using the ABO system as an example, the frequency of one of the alleles, IA, is the number of copies of that allele divided by all the copies of the ABO gene in the population. For example, a study in Jordan found a frequency of IA to be 26.1 percent.2 The IB, I0 alleles made up 13.4 percent and 60.5 percent of the alleles respectively, and all of the frequencies add up to 100 percent. A change in this frequency over time would constitute evolution in the population.
There are several ways the allele frequencies of a population can change. One of those ways is natural selection. If a given allele confers a phenotype that allows an individual to have more offspring that survive and reproduce, that allele, by virtue of being inherited by those offspring, will be in greater frequency in the next generation. Since allele frequencies always add up to 100 percent, an increase in the frequency of one allele always means a corresponding decrease in one or more of the other alleles. Highly beneficial alleles may, over a very few generations, become “fixed” in this way, meaning that every individual of the population will carry the allele. Similarly, detrimental alleles may be swiftly eliminated from the gene pool, the sum of all the alleles in a population. Part of the study of population genetics is tracking how selective forces change the allele frequencies in a population over time, which can give scientists clues regarding the selective forces that may be operating on a given population. The studies of changes in wing coloration in the peppered moth from mottled white to dark in response to soot-covered tree trunks and then back to mottled white when factories stopped producing so much soot is a classic example of studying evolution in natural populations (Figure \(5\)).
In the early twentieth century, English mathematician Godfrey Hardy and German physician Wilhelm Weinberg independently provided an explanation for a somewhat counterintuitive concept. Hardy’s original explanation was in response to a misunderstanding as to why a “dominant” allele, one that masks a recessive allele, should not increase in frequency in a population until it eliminated all the other alleles. The question resulted from a common confusion about what “dominant” means, but it forced Hardy, who was not even a biologist, to point out that if there are no factors that affect an allele frequency those frequencies will remain constant from one generation to the next. This principle is now known as the Hardy-Weinberg equilibrium. The theory states that a population’s allele and genotype frequencies are inherently stable—unless some kind of evolutionary force is acting on the population, the population would carry the same alleles in the same proportions generation after generation. Individuals would, as a whole, look essentially the same and this would be unrelated to whether the alleles were dominant or recessive. The four most important evolutionary forces, which will disrupt the equilibrium, are natural selection, mutation, genetic drift, and migration into or out of a population. A fifth factor, nonrandom mating, will also disrupt the Hardy-Weinberg equilibrium but only by shifting genotype frequencies, not allele frequencies. In nonrandom mating, individuals are more likely to mate with like individuals (or unlike individuals) rather than at random. Since nonrandom mating does not change allele frequencies, it does not cause evolution directly. Natural selection has been described. Mutation creates one allele out of another one and changes an allele’s frequency by a small, but continuous amount each generation. Each allele is generated by a low, constant mutation rate that will slowly increase the allele’s frequency in a population if no other forces act on the allele. If natural selection acts against the allele, it will be removed from the population at a low rate leading to a frequency that results from a balance between selection and mutation. This is one reason that genetic diseases remain in the human population at very low frequencies. If the allele is favored by selection, it will increase in frequency. Genetic drift causes random changes in allele frequencies when populations are small. Genetic drift can often be important in evolution, as discussed in the next section. Finally, if two populations of a species have different allele frequencies, migration of individuals between them will cause frequency changes in both populations. As it happens, there is no population in which one or more of these processes are not operating, so populations are always evolving, and the Hardy-Weinberg equilibrium will never be exactly observed. However, the Hardy-Weinberg principle gives scientists a baseline expectation for allele frequencies in a non-evolving population to which they can compare evolving populations and thereby infer what evolutionary forces might be at play. The population is evolving if the frequencies of alleles or genotypes deviate from the value expected from the Hardy-Weinberg principle.
Darwin identified a special case of natural selection that he called sexual selection. Sexual selection affects an individual’s ability to mate and thus produce offspring, and it leads to the evolution of dramatic traits that often appear maladaptive in terms of survival but persist because they give their owners greater reproductive success. Sexual selection occurs in two ways: through male–male competition for mates and through female selection of mates. Male–male competition takes the form of conflicts between males, which are often ritualized, but may also pose significant threats to a male’s survival. Sometimes the competition is for territory, with females more likely to mate with males with higher quality territories. Female choice occurs when females choose a male based on a particular trait, such as feather colors, the performance of a mating dance, or the building of an elaborate structure. In some cases male–male competition and female choice combine in the mating process. In each of these cases, the traits selected for, such as fighting ability or feather color and length, become enhanced in the males. In general, it is thought that sexual selection can proceed to a point at which natural selection against a character’s further enhancement prevents its further evolution because it negatively impacts the male’s ability to survive. For example, colorful feathers or an elaborate display make the male more obvious to predators.
Summary
Evolution by natural selection arises from three conditions: individuals within a species vary, some of those variations are heritable, and organisms have more offspring than resources can support. The consequence is that individuals with relatively advantageous variations will be more likely to survive and have higher reproductive rates than those individuals with different traits. The advantageous traits will be passed on to offspring in greater proportion. Thus, the trait will have higher representation in the next and subsequent generations leading to genetic change in the population.
The modern synthesis of evolutionary theory grew out of the reconciliation of Darwin’s, Wallace’s, and Mendel’s thoughts on evolution and heredity. Population genetics is a theoretical framework for describing evolutionary change in populations through the change in allele frequencies. Population genetics defines evolution as a change in allele frequency over generations. In the absence of evolutionary forces allele frequencies will not change in a population; this is known as Hardy-Weinberg equilibrium principle. However, in all populations, mutation, natural selection, genetic drift, and migration act to change allele frequencies.
Footnotes
1. 1 Charles Darwin, Journal of Researches into the Natural History and Geology of the Countries Visited during the Voyage of H.M.S. Beagle Round the World, under the Command of Capt. Fitz Roy, R.N, 2nd. ed. (London: John Murray, 1860), http://www.archive.org/details/journalofresea00darw.
2. 2 Sahar S. Hanania, Dhia S. Hassawi, and Nidal M. Irshaid, “Allele Frequency and Molecular Genotypes of ABO Blood Group System in a Jordanian Population,” Journal of Medical Sciences 7 (2007): 51-58, doi:10.3923/jms.2007.51.58
Glossary
adaptation
a heritable trait or behavior in an organism that aids in its survival in its present environment
analogous structure
a structure that is similar because of evolution in response to similar selection pressures resulting in convergent evolution, not similar because of descent from a common ancestor
convergent evolution
an evolution that results in similar forms on different species
divergent evolution
an evolution that results in different forms in two species with a common ancestor
gene pool
all of the alleles carried by all of the individuals in the population
genetic drift
the effect of chance on a population’s gene pool
homologous structure
a structure that is similar because of descent from a common ancestor
inheritance of acquired characteristics
a phrase that describes the mechanism of evolution proposed by Lamarck in which traits acquired by individuals through use or disuse could be passed on to their offspring thus leading to evolutionary change in the population
macroevolution
a broader scale of evolutionary changes seen over paleontological time
microevolution
the changes in a population’s genetic structure (i.e., allele frequency)
migration
the movement of individuals of a population to a new location; in population genetics it refers to the movement of individuals and their alleles from one population to another, potentially changing allele frequencies in both the old and the new population
modern synthesis
the overarching evolutionary paradigm that took shape by the 1940s and is generally accepted today
natural selection
the greater relative survival and reproduction of individuals in a population that have favorable heritable traits, leading to evolutionary change
population genetics
the study of how selective forces change the allele frequencies in a population over time
variation
the variety of alleles in a population | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/21%3A_The_Evidence_for_Evolution/21.01%3A_The_Beaks_of_Darwin%27s_Finches-_Evidence_of_Natural_Selection.txt |
One of the best definition os species is that of the evolutionary biologist Ernst Mayr: "A species is an actually or potentially interbreeding population that does not interbreed with other such populations when there is opportunity to do so." However, sometimes breeding may take place (as it can between a horse and a donkey) but if so, the offspring are not so fertile and/or well adapted as the parents (the mule produced is sterile).
Allopatric Speciation: the Role of Isolation in Speciation
The formation of two or more species often (some workers think always!) requires geographical isolation of subpopulations of the species. Only then can natural selection or perhaps genetic drift produce distinctive gene pools. It is no accident that the various races (or "subspecies") of animals almost never occupy the same territory. Their distribution is allopatric ("other country").
The seven distinct subspecies or races of the yellowthroat Geothlypis trichas (a warbler) in the continental U.S. would soon merge into a single homogeneous population if they occupied the same territory and bred with one another.
Darwin's Finches
As a young man of 26, Charles Darwin visited the Galapagos Islands off the coast of Ecuador. Among the animals he studied were what appeared to be 13 species* of finches found nowhere else on earth.
• Some have stout beaks for eating seeds of one size or another (#2, #3, #6).
• Others have beaks adapted for eating insects or nectar.
• One (#7) has a beak like a woodpecker's. It uses it to drill holes in wood, but lacking the long tongue of a true woodpecker, it uses a cactus spine held in its beak to dig the insect out.
• One (#12) looks more like a warbler than a finch, but its eggs, nest, and courtship behavior is like that of the other finches.
Darwin's finches. The finches numbered 1–7 are ground finches. They seek their food on the ground or in low shrubs. Those numbered 8–13 are tree finches. They live primarily on insects.
1. Large cactus finch (Geospiza conirostris)
2. Large ground finch (Geospiza magnirostris)
3. Medium ground finch (Geospiza fortis)
4. Cactus finch (Geospiza scandens)
5. Sharp-beaked ground finch (Geospiza difficilis)
6. Small ground finch (Geospiza fuliginosa)
7. Woodpecker finch (Cactospiza pallida)
8. Vegetarian tree finch (Platyspiza crassirostris)
9. Medium tree finch (Camarhynchus pauper)
10. Large tree finch (Camarhynchus psittacula)
11. Small tree finch (Camarhynchus parvulus)
12. Warbler finch (Certhidia olivacea)
13. Mangrove finch (Cactospiza heliobates)
(From BSCS, Biological Science: Molecules to Man, Houghton Mifflin Co., 1963)
* Genetic analysis provides evidence that:
• There are actually two species of warbler finch — Certhidia olivacea now called the green warbler finch and Certhidia fusca, the gray warbler finch.
• The various populations of Geospiza difficilis found on the different islands belong to one or another of three clades so genetically distinct that they deserve full species status.
Whether the number is 13 or 17, since Darwin's time, these birds have provided a case study of how a single species reaching the Galapagos from Central or South America could - over a few million years - give rise to the various species that live there today. Several factors have been identified that may contribute to speciation.
Ecological opportunity
When the ancestor of Darwin's finches reached the Galapagos, it found no predators (There were no mammals and few reptiles on the islands.) and few, if any, competitors. There were only a handful of other types of songbirds. In fact, if true warblers or woodpeckers had been present, their efficiency at exploiting their niches would surely have prevented the evolution of warblerlike and woodpeckerlike finches.
Geographical Isolation (allopatry)
The proximity of the various islands has permitted enough migration of Darwin's finches between them to enable distinct island populations to arise. But the distances between the islands is great enough to limit interbreeding between populations on different islands. This has made possible the formation of distinctive subspecies (= races) on the various islands.
The importance of geographical isolation is illuminated by a single, fourteenth, species of Darwin's finches that lives on Cocos Island, some 500 miles (800 km) to the northeast of the Galapagos. The first immigrants there must also have found relaxed selection pressures with few predators or competitors. How different the outcome, though. Where one immigrant species gave rise to at least 13 on the scattered Galapagos Islands, no such divergence has occurred on the single, isolated Cocos Island.
Evolutionary Change
In isolation, changes in the gene pool can occur through some combination of natural selection, genetic drift, and founder effect. These factors may produce distinct subpopulations on the different islands. So long as they remain separate (allopatric) we consider them races or subspecies. In fact, they might not be able to interbreed with other races but so long as we don't know, we assume that they could.
How much genetic change is needed to create a new species? Perhaps not as much as you might think. For example, changes at one or just a few gene loci might do the trick. For example, a single mutation altering flower color or petal shape could immediately prevent cross-pollination between the new and the parental types (a form of prezygotic isolating mechanism).
Reunion
The question of their status - subspecies or true species - is resolved if they ever do come to occupy the same territory again (become sympatric). If successful interbreeding occurs, the differences will gradually disappear, and a single population will be formed again. Speciation will not have occurred. If, on the other hand, two subspecies reunite but fail to resume breeding, speciation has occurred and they have become separate species.
An example: The medium tree finch Camarhynchus pauper is found only on Floreana Island. Its close relative, the large tree finch, Camarhynchus psittacula, is found on all the central islands including Floreana. Were it not for its presence on Floreana, both forms would be considered subspecies of the same species. Because they do coexist and maintain their separate identity on Floreana, we know that speciation has occurred.
Isolating Mechanisms
What might keep two subpopulations from interbreeding when reunited geographically? There are several mechanisms.
Prezygotic Isolating Mechanisms act before fertilization occurs. Sexual selection - a failure to elicit mating behavior. On Floreana, Camarhynchus psittacula has a longer beak than Camarhynchus pauper, and the research teams led by Peter and Rosemary Grant have demonstrated that beak size is an important criterion by which Darwin's finches choose their mates. Two subpopulations may occupy different habitats in the same area and thus fail to meet at breeding time. In plants, a shift in the time of flowering can prevent pollination between the two subpopulations. Structural differences in the sex organs may become an isolating mechanism. The sperm may fail to reach or fuse with the egg.
Postzygotic Isolating Mechanisms act even if fertilization does occur. Even if a zygote is formed, genetic differences may have become so great that the resulting hybrids are less viable or less fertile than the parental types. The sterile mule produced by mating a horse with a donkey is an example. Sterility in the males produced by hybridization is more common than in females. In fact, it is the most common postzygotic isolating mechanism. When Drosophila melanogaster attempts to mate with its relative Drosophila simulans, no viable males are even produced. Mutations in a single gene (encoding a component of the nuclear pore complex) are responsible.
Reinforcement
When two species that have separated in allopatry become reunited, their prezygotic and postzygotic isolating mechanisms may become more stringent than those between the same species existing apart from each other. This phenomenon is called reinforcement. It arises from natural selection working to favor individuals that avoid interspecific matings, which would produce less-fit hybrids, when the two species are first reunited.
Speciation by Hybridization
Hybridization between related angiosperms is sometimes followed by a doubling of the chromosome number. The resulting polyploids are now fully fertile with each other although unable to breed with either parental type - a new species has been created. This appears to have been a frequent mechanism of speciation in angiosperms. Even without forming a polyploid, interspecific hybridization can occasionally lead to a new species of angiosperm. Two species of sunflower, the "common sunflower", Helianthus annuus, and the "prairie sunflower", H. petiolaris, grow widely over the western half of the United States. They can interbreed, but only rarely are fertile offspring produced.
However, Rieseberg and colleagues have found evidence that successful hybridization between them has happened naturally in the past. They have shown that three other species of sunflower (each growing in a habitat too harsh for either parental type) are each the product of an ancient hybridization between Helianthus annuus and H. petiolaris. Although each of these species has the same diploid number of chromosomes as the parents (2n = 34), they each have a pattern of chromosome segments that have been derived, by genetic recombination, from both the parental genomes. They demonstrated this in several ways, notably by combining RFLP analysis with the polymerase chain reaction (PCR).
They even went on to produce (at a low frequency) annuus x petiolaris hybrids in the greenhouse that mimicked the phenotypes and genotypes of the natural hybrids. (These monumental studies were described in the 29 August 2003 issue of Science.)
Another example. In Pennsylvania, hybrids between a species of fruit fly (not Drosophila) that feeds on blueberries and another species (again, not Drosophila) that feeds on snowberries feed on honeysuckle where they neither encounter competition from their parental species nor have an opportunity to breed with them (no introgression). This study was published in the 28 July 2005 issue of Nature. So speciation can occur as a result of hybridization between two related species, if the hybrid
• receives a genome that enables it to breed with other such hybrids but not breed with either parental species,
• can escape to a habitat where it does not have to compete with either parent,
• is adapted to live under those new conditions.
Adaptive Radiation
The processes described in this page can occur over and over. In the case of Darwin's finches, they must have been repeated a number of times forming new species that gradually divided the available habitats between them. From the first arrival have come a variety of ground-feeding and tree-feeding finches as well as the warblerlike finch and the tool-using woodpeckerlike finch. The formation of a number of diverse species from a single ancestral one is called an adaptive radiation.
Speciateion in theHouse mice on the island of Madeira
A report in the 13 January 2000 issue of Nature describes a study of house mouse populations on the island of Madeira off the Northwest coast of Africa. These workers (Janice Britton-Davidian et al) examined the karyotypes of 143 house mice (Mus musculus domesticus) from various locations along the coast of this mountainous island.
Their findings:
• There are 6 distinct populations (shown by different colors)
• Each of these has a distinct karyotype, with a diploid number less than the "normal" (2n = 40).
• The reduction in chromosome number has occurred through Robertsonian fusions. Mouse chromosomes tend to be acrocentric; that is, the centromere connects one long and one very short arm. Acrocentric chromosomes are at risk of translocations that fuse the long arms of two different chromosomes with the loss of the short arms.
• The different populations are allopatric; isolated in different valleys leading down to the sea.
• The distinct and uniform karyotype found in each population probably arose from genetic drift rather than natural selection.
• The 6 different populations are technically described as races because there is no opportunity for them to attempt interbreeding.
• However, they surely meet the definition of true species. While hybrids would form easily (no prezygotic isolating mechanisms), these would probably be infertile as proper synapsis and segregation of such different chromosomes would be difficult when the hybrids attempted to form gametes by meiosis.
Sympatric Speciation
Sympatric speciation refers to the formation of two or more descendant species from a single ancestral species all occupying the same geographic location. Some evolutionary biologists don't believe that it ever occurs. They feel that interbreeding would soon eliminate any genetic differences that might appear. But there is some compelling (albeit indirect) evidence that sympatric speciation can occur.
Speciation in three-spined sticklebacks
The three-spined sticklebacks, freshwater fishes that have been studied by Dolph Schluter (who received his Ph.D. for his work on Darwin's finches with Peter Grant) and his current colleagues in British Columbia, provide an intriguing example that is best explained by sympatric speciation.
They have found:
• Two different species of three-spined sticklebacks in each of five different lakes.
• a large benthic species with a large mouth that feeds on large prey in the littoral zone
• a smaller limnetic species with a smaller mouth that feeds on the small plankton in open water.
• DNA analysis indicates that each lake was colonized independently, presumably by a marine ancestor, after the last ice age.
• DNA analysis also shows that the two species in each lake are more closely related to each other than they are to any of the species in the other lakes.
• Nevertheless, the two species in each lake are reproductively isolated; neither mates with the other.
• However, aquarium tests showed that
• The benthic species from one lake will spawn with the benthic species from the other lakes and likewise the limnetic species from the different lakes will spawn with each other.
• These benthic and limnetic species even display their mating preferences when presented with sticklebacks from Japanese lakes; that is, a Canadian benthic prefers a Japanese benthic over its close limnetic cousin from its own lake.
• Their conclusion: in each lake, what began as a single population faced such competition for limited resources that
• disruptive selection — competition favoring fishes at either extreme of body size and mouth size over those nearer the mean — coupled with
• assortative mating — each size preferred mates like it
favored a divergence into two subpopulations exploiting different food in different parts of the lake.
• The fact that this pattern of speciation occurred the same way on three separate occasions suggests strongly that ecological factors in a sympatric population can cause speciation.
Sympatric speciation driven by ecological factors may also account for the extraordinary diversity of crustaceans living in the depths of Siberia's Lake Baikal.
How many genes are needed to start down the path to sympatric speciation?
Perhaps not very many. The European corn borer, Ostrinia nubilalis, (which despite its common name is a major pest in the U.S. as well) exists as two distinct races designated Z and E. Both can be found in the same area; that is, they are sympatric. But in the field, they practice assortative mating - only breeding with mates of their own race.
The females of both races synthesize and release a pheromone that is a sex attractant for the males. Both races use the same substance but different isomers of it. Which isomer is produced is under the control of a single enzyme-encoding gene locus. The ability of the males to respond to one isomer or the other is controlled by 2 loci.
The Problem of Clines
There is another possible way for new species to arise in the absence of geographical barriers. If a population ranges over a large area and if the individuals in that population can disperse over only a small portion of this range, then gene flow across these great distances would be reduced. The occurrence of gradual phenotypic (and genotypic) differences in a population across a large geographical area is called a cline. Successful interbreeding occurs freely at every point along the cline, but individuals at the ends of the cline may not be able to interbreed. This can be tested in the laboratory.
And, on occasions, it is tested in nature. If a cline bends around so that the ends meet, and the populations reunited at the junction cannot interbreed, then the definition of separate species has been met. Such species are called ring species and this type of speciation is called parapatric speciation.
Two examples:
1. The Caribbean slipper spurge Euphorbia tithymaloides.
Genetic analysis shows that this wildflower originated in Central America where Mexico and Guatemala share a common boundary. From there it spread in two directions
• northeast through the Yucatan peninsula and then island-hopped through Jamaica, the Dominican Republic, Puerto Rico and into the Virgin Islands;
• south through Central America, on through Venezuela, and then north through Barbados and the other islands of the Lesser Antilles finally also reaching the Virgin Islands.
Reunited in the Virgin Islands, the two populations have diverged sufficiently that they retain their distinctive genotypic and phenotypic traits. Ongoing studies will determine to what degree they may be reproductively isolated.
2. The large-blotched salamander Ensatina eschscholtzii.
This animal is found in California where it occurs in a number of different subspecies or races. A single subspecies is found in Northern California, and it is thought to be the founder of all the others. Over time that original population spread southward in two directions:
• down the Sierra Nevada mountains east of the great central San Joaquin Valley and
• down the coast range of mountains west of the valley.
South of the valley, the eastern group has moved west and now meets the western group, closing the ring. Here the two populations fail to interbreed successfully, maintaining their distinct identities. But each subspecies interbreeds in an unbroken chain up the two paths their ancestors took.
Ring species present a difficult problem in assigning species designations. It is easy to say that the populations at the ends of the cline represent separate species, but where did one give rise to the other? At every point along the cline, interbreeding goes on successfully.
The same problem faces paleontologists examining the gradual phenotypic changes seen in an unbroken line of ever-younger fossils from what one presumes to be a single line of descent. If one could resurrect the ancestral species (A) and the descendant species (B) and they could not interbreed, then they meet the definition of separate species. But there was no moment in time when one could say that A became B. So the clines of today are a model in space of Darwin's descent with modification occurring over time.
Although clines present a problem for classifiers, they are a beautiful demonstration of Darwin's conviction that the accumulation of small inherited differences can lead to the formation of new species. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/21%3A_The_Evidence_for_Evolution/21.02%3A_Speciation.txt |
The development of a new crop variety is an example of agricultural biotechnology, a range of tools that include both traditional breeding techniques and more modern lab-based methods. Traditional methods date back thousands of years, whereas biotechnology uses the tools of genetic engineering developed over the last few decades.
Selective Breeding (Artificial Selection)
Nearly all the fruits and vegetables found in your local market would not occur naturally. In fact, they exist only because of human intervention that began thousands of years ago. Humans created the vast majority of crop species by using traditional breeding practices on naturally-occurring, wild plants. These practices rely upon selective breeding (artificial selection), human-facilitated reproduction of individuals with desirable traits. For example, high yield varieties were produced through selective breeding. Traditional breeding practices, although low-tech and simple to perform, have the practical outcome of modifying an organism’s genetic information, thus producing new traits.
Selective breeding is limited, however, by the life cycle of the plant and the genetic variants that are naturally present. For example, even the fastest flowering corn variety has a generation time of 60 days (the time required for a seed to germinate, produce a mature plant, get pollinated, and ultimately produce more seeds) in perfect conditions. Each generation provides an opportunity to selectively breed individual plants and generate seeds that are slightly closer to the desired outcome (for example, producing bigger, juicier kernels). Furthermore, if no individuals happen to possess gene variants that result in bigger, juicier kernels, it is not possible to artificially select this trait. Finally, traditional breeding shuffles all of the genes between the two individuals being bred, which can number into the tens of thousands (maize, for example, has 32,000 genes). When mixing such a large number of genes, the results can be unpredictable.
An interesting example is maize (corn). Biologists have discovered that maize was developed from a wild plant called teosinte. Through traditional breeding practices, humans living thousands of years ago in what is now Southern Mexico began selecting for desirable traits until they were able to transform the plant into what is now known as maize (figure \(\PageIndex{a}\)). In doing so, they permanently (and unknowingly) altered its genetic instructions.
This history of genetic modification is common to nearly all crop species. For example, cabbage, broccoli, Brussel sprouts, cauliflower, and kale were all developed from a single species of wild mustard plant (figure \(\PageIndex{b}\)). Wild nightshade was the source of tomatoes, eggplant, tobacco, and potatoes, the latter developed by humans 7,000 – 10,000 years ago in South America.
Genetic Engineering
Genetic engineering is the process of directly altering an organism's DNA to produce the desired crops more rapidly than selective breeding. Because genes can be obtained from other species or even synthesized in the lab, scientists are not limited by existing genetic variation within a crop species (or closely related species with which they can be crossed). This broadens the possible traits that can be added to crops. Modern genetic engineering is more precise than selective breeding in the sense that biologists can modify just a single gene. Also, genetic engineering can introduce a gene between two distantly-related species, such as inserting a bacterial gene into a plant (figure \(\PageIndex{c}\)).
Genetically modified organisms (GMOs) are those that have had their DNA altered through genetic engineering. Genetically modified crops are sometimes called genetically engineered (GE) crops. Transgenic organisms are a type of genetically modified organism that contains genes from a different species. Because they contain unique combinations of genes and are not restricted to the laboratory, transgenic plants and other GMOs are closely monitored by government agencies to ensure that they are fit for human consumption and do not endanger other plant and animal life. Because these foreign genes (transgenes) can spread to other species in the environment, particularly in the pollen and seeds of plants, extensive testing is required to ensure ecological stability.
How to Genetically Modify Plant Cells
DNA can be inserted into plant cells through various techniques. For example, a gene gun propels DNA bound to gold particles into plant cells. (DNA is negatively charge and clings to positively charged gold.) A more traditional approach employs the plant pathogen Agrobacterium tumefaciens (figure \(\PageIndex{d}\)). Ordinarily, this bacterium causes crown gall disease in plants by inserting a circular piece of DNA, called the Ti plasmid, into plant cells. This DNA incorporates into plant chromosomes, giving them genes to produce the gall (figure \(\PageIndex{e}\)), which provides a home for the bacterial pathogen.
Scientists alters the process by which Agrobacterium infects and genetically alter plant cells to produce genetically modified plants with agriculturally beneficial traits as follows (figure \(\PageIndex{f}\)):
1. T-DNA, which codes for the crown gall is removed from the Ti plasmid, and genes for desired traits are added.
2. The modified plasmid is then added back to Agrobacterium.
3. Agrobacterium infects undifferentiated plant cells (stem cells that can develop into any part of the plant; figure \(\PageIndex{g}\)).
4. The modified plant cells are given hormones to produce the entire plant.
Examples of Genetically Modified Crops
Many genetically modified crops have been approved in the U.S. and produce our foods. The first genetically modified organism approved by the U.S. Food and Drug Administration (FDA) in 1994 was Flavr Savr™ tomatoes, which have a longer shelf life (delayed rotting) because a gene responsible for breaking down cells in inhibited. Flavr Savr tomatoes are genetically modified (because their DNA has been altered) but not trasgenic (because they do not contain genes from another species). The Flavr Savr tomato did not successfully stay in the market because of problems maintaining and shipping the crop. Golden rice produces β-carotene, a precursor to vitamin A (figure \(\PageIndex{h}\); β-carotene is also in high concentrations in carrots, sweet potatoes, and cantaloupe, giving them their orange color.) Roundup Ready® corn, cotton, and soybeans are resistant to this common herbicide, making it easier to uniformly spray it in a field to kill the weeds without harming the crops (figure \(\PageIndex{i}\)).
Crops have also been engineered to produce insecticides. Bacillus thuringiensis (Bt) is a bacterium that produces protein crystals that are toxic to many insect species that feed on plants. Insects that have eaten Bt toxin stop feeding on the plants within a few hours. After the toxin is activated in the intestines of the insects, death occurs within a couple of days. The gene to produce Bt toxin has been added to many crops including corn (figure \(\PageIndex{j}\)), potatoes, and cotton, providing plants with defense against insects.
Genetically modified foods are widespread in the United States. For example, 94% of soy crops were genetically modified for herbicide resistance in 2020. Likewise, 8% of cotton and 10% of corn crops were modified for herbicide resistance in addition to the 83% of cotton and 79% of corn crops that were genetically modified in multiple ways.
Genetically modified animals have recently entered the market as well. AquaAdvantage® salmon are modified to grow more rapidly and were approved in November of 2015. However, as of March 2021, they have still not been sold due to legal challenges. In 2020, the FDA approved GalSafe™ pigs for medicine and food production. These pigs lack a molecule on the outside of their cells that cause allergies in some people.
Advantages of Genetically Modified Crops
Advances in biotechnology may provide consumers with foods that are nutritionally-enriched, longer-lasting, or that contain lower levels of certain naturally occurring toxins present in some food plants. For example, researchers are using biotechnology to try to reduce saturated fats in cooking oils and reduce allergens in foods. Whether these benefits will reach the people who need them most remains to be seen. While cultivating golden rice could address vitamin A deficiency in millions of people, it has not historically been accessible to these people because it is patented and expensive. Similarly, genetically modified seeds could increase the income of impoverished farmers if they were available at low or no cost, but this is not always the case.
Rainbow and SunUp papayas are a success story of how genetically modified crops can benefit small farmers and the economy in general. In the early 1990s, an emerging disease was destroying Hawaii’s production of papaya and threatening to decimate the \$11-million industry (figure \(\PageIndex{k}\)). Fortunately, a man named Dennis Gonsalves (figure \(\PageIndex{l}\)), who was raised on a sugar plantation and then became a plant physiologist at Cornell University, would develop papaya plants genetically engineered to resist the deadly virus. By the end of the decade, the Hawaiian papaya industry and the livelihoods of many farmers were saved thanks to the free distribution of Dr. Gonsalves's seeds.
The effect of genetically modified crops on the environment depends on the specific genetic modification and which agricultural practices it promotes. For example, Bt crops produce their own insecticides such that external application of these chemicals is unnecessary, reducing the negative impacts of industrial agriculture. Ongoing research is exploring whether crops can be engineered to fix nitrogen in the atmosphere (as some bacteria do) rather than relying on ammonium, nitrites, and nitrates in the soil. If these crops were successfully engineered, they could reduce synthetic fertilizer application and minimize nutrient runoff that leads to eutrophication.
Genetically modified crops may have the potential to conserve natural resources, enable animals to more effectively use nutrients present in feed, and help meet the increasing world food and land demands. In practice, however, countries that use genetically modified crops compared to those that do not only enjoy a slight (or nonexistent) increase in yield.
Disadvantages of Genetically Modified Crops
Social Concerns
Intellectual property rights are one of the important factors in the current debate on genetically modified crops. Genetically modified crops can be patented by agribusinesses, which can lead to them controlling and potentially exploiting agricultural markets. Some accuse companies, such as Monsanto, of allegedly controlling seed production and pricing, much to the detriment of farmers (figure \(\PageIndex{m}\)).
Environmental Concerns
Genetically modified crops present several environmental concerns. Monoculture farming already reduces biodiversity, and cultivating genetically modified crops, for which individual plants are quite similar genetically, exacerbates this. The use of Roundup Ready® crops naturally encourages widespread herbicide use, which could unintentionally kill nearby native plants. This practice would also increase herbicide residues on produce. While Bt crops are beneficial in the sense that they do not require external insecticide application, but Bt toxin is spread in their pollen. An early study found that Bt corn pollen may be harmful to monarch caterpillars (figure \(\PageIndex{n}\)), but only at concentrations that are seldom reached in nature. Follow-up studies found that most of Bt corn grown did not harm monarchs; however, the one strain of Bt corn did was consequently removed from the market.
Through interbreeding, or hybridization, genetically modified crops might share their transgenes with wild relatives. This could affect the genetics of those wild relatives and have unforeseen consequences on their populations and could even have implications for the larger ecosystem. For example, if a gene engineered to confer herbicide resistance were to pass from a genetically modified crop to a wild relative, it might transform the wild species into a super weed – a species that could not be controlled by herbicide. Its rampant growth could then displace other wild species and the wildlife that depends on it, thus inflecting ecological harm.
Not only could escaped genes alter weedy species, but they could also enter populations of native species. This could make some native species better competitors than they were previously, disrupting ecosystem dynamics. (They could potentially outcompete other native species with which they would otherwise coexist.)
While there is evidence of genetic transfer between genetically modified crops and wild relatives, there is not yet evidence of ecological harm from that transfer. Clearly, continued monitoring, especially for newly-developed crops, is warranted.
The escape of genetically modified animals has potential to disrupt ecosystems as well. For example, if AquaAdvantage salmon were to escape into natural ecosystem, as farmed fish often do, they could outcompete native salmon, including endangered species. Their genetic modification, which facilitates rapid growth, could result in a competitive advantage.
Health Concerns
In addition to environmental risks, some people are concerned about potential health risks of genetically modified crops because they feel that genetic modification alters the intrinsic properties, or essence, of an organism. As discussed above, however, it is known that both traditional breeding practices and modern genetic engineering produce permanent genetic changes. Furthermore, selective breeding actually has a larger and more unpredictable impact on a species’s genetics because of its comparably crude nature.
To address these concerns (and others), the US National Academies of Sciences, Engineering, and Medicine (NASEM) published a comprehensive, 500-page report in 2016 that summarized the current scientific knowledge regarding genetically modified crops. The report, titled Genetically Engineered Crops: Experiences and Prospects, reviewed more than 900 research articles, in addition to public comments and expert testimony. NASEM’s GE Crop Report found “no substantiated evidence of a difference in risks to human health between current commercially available genetically engineered (GE) crops and conventionally bred crops, nor did it find conclusive cause-and-effect evidence of environmental problems from the GE crops.” Additionally, the UN’s Food and Agriculture Organization has concluded that risks to human and animal health from the use of GMOs are negligible. The scientific consensus on genetically modified crops is quite clear: they are safe for human consumption.
The potential of genetically modified crops to be allergenic is one of the potential adverse health effects, and it should continue to be studied, especially because some scientific evidence indicates that animals fed genetically modified crops have been harmed. NASEM’s GE Crop Report concluded that when developing new crops, it is the product that should be studied for potential health and environmental risks, not the process that achieved that product. What this means is, because both traditional breeding practices and modern genetic engineering produce new traits through genetic modification, they both present potential risks. Thus, for the safety of the environment and human health, both should be adequately studied.
Are Genetically Modified Crops the Solution We Need?
Significant resources, both financial and intellectual, have been allocated to answering the question: are genetically modified crops safe for human consumption? After many hundreds of scientific studies, the answer is yes. But a significant question still remains: are they necessary? Certainly, such as in instances like Hawaii’s papaya, which were threatened with eradication due to an aggressive disease, genetic engineering was a quick and effective solution that would have been extremely difficult, if not impossible, to solve using traditional breeding practices.
However, in many cases, the early promises of genetically engineered crops – that they would improve nutritional quality of foods, confer disease resistance, and provide unparalleled advances in crop yields – have largely failed to come to fruition. NASEM’s GE Crop Report states that while genetically modified crops have resulted in the reduction of agricultural loss from pests, reduced pesticide use, and reduced rates of injury from insecticides for farm workers, they have not increased the rate at which crop yields are advancing when compared to non-GE crops. Additionally, while there are some notable exceptions like golden rice or virus-resistant papayas, very few genetically engineered crops have been produced to increase nutritional capacity or to prevent plant disease that can devastate a farmer’s income and reduce food security. The vast majority of genetically modified crops are developed for only two purposes: to introduce herbicide resistance or pest resistance. Genetically modified crops are concentrated in developed countries, and their availability in developing countries, where they are perhaps most needed, is limited (figure \(\PageIndex{o}\)).
Attributions
Modified by Melissa Ha from the following sources: | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/21%3A_The_Evidence_for_Evolution/21.03%3A_Artificial_Selection-_Human-Initiated_Change.txt |
Fossils tell us when organisms lived, as well as provide evidence for the progression and evolution of life on earth over millions of years.
Learning Objectives
• Synthesize the contributions of the fossil record to our understanding of evolution
Key Points
• Fossils are the preserved remains or traces of animals, plants, and other organisms from the past.
• Fossils are important evidence for evolution because they show that life on earth was once different from life found on earth today.
• Usually only a portion of an organism is preserved as a fossil, such as body fossils (bones and exoskeletons ), trace fossils (feces and footprints), and chemofossils (biochemical signals).
• Paleontologists can determine the age of fossils using methods like radiometric dating and categorize them to determine the evolutionary relationships between organisms.
Key Terms
• biomarker: A substance used as an indicator of a biological state, most commonly disease.
• trace fossil: A type of fossil reflecting the reworking of sediments and hard substrates by organisms including structures like burrows, trails, and impressions.
• fossil record: All discovered and undiscovered fossils and their placement in rock formations and sedimentary layers.
• strata: Layers of sedimentary rock.
• fossiliferous: Containing fossils.
What Fossils Tell Us
Fossils are the preserved remains or traces of animals, plants, and other organisms from the past. Fossils range in age from 10,000 to 3.48 billion years old. The observation that certain fossils were associated with certain rock strata led 19th century geologists to recognize a geological timescale. Like extant organisms, fossils vary in size from microscopic, like single-celled bacteria, to gigantic, like dinosaurs and trees.
Permineralization
Permineralization is a process of fossilization that occurs when an organism is buried. The empty spaces within an organism (spaces filled with liquid or gas during life) become filled with mineral-rich groundwater. Minerals precipitate from the groundwater, occupying the empty spaces. This process can occur in very small spaces, such as within the cell wall of a plant cell. Small-scale permineralization can produce very detailed fossils. For permineralization to occur, the organism must be covered by sediment soon after death, or soon after the initial decay process.
The degree to which the remains are decayed when covered determines the later details of the fossil. Fossils usually consist of the portion of the organisms that was partially mineralized during life, such as the bones and teeth of vertebrates or the chitinous or calcareous exoskeletons of invertebrates. However, other fossils contain traces of skin, feathers or even soft tissues.
Trace Fossils
Fossils may also consist of the marks left behind by the organism while it was alive, such as footprints or feces. These types of fossils are called trace fossils, or ichnofossils, as opposed to body fossils. Past life may also leave some markers that cannot be seen but can be detected in the form of biochemical signals; these are known as chemofossils or biomarkers.
The Fossil Record
The totality of fossils, both discovered and undiscovered, and their placement in fossiliferous (fossil-containing) rock formations and sedimentary layers (strata) is known as the fossil record. The fossil record was one of the early sources of data underlying the study of evolution and continues to be relevant to the history of life on Earth. The development of radiometric dating techniques in the early 20th century allowed geologists to determine the numerical or “absolute” age of various strata and their included fossils.
Evidence for Evolution
Fossils provide solid evidence that organisms from the past are not the same as those found today; fossils show a progression of evolution. Fossils, along with the comparative anatomy of present-day organisms, constitute the morphological, or anatomical, record. By comparing the anatomies of both modern and extinct species, paleontologists can infer the lineages of those species. This approach is most successful for organisms that had hard body parts, such as shells, bones or teeth. The resulting fossil record tells the story of the past and shows the evolution of form over millions of years. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/21%3A_The_Evidence_for_Evolution/21.04%3A_Fossil_Evidence_of_Evolution/21.4A%3A_The_Fossil_Record_as_Evidence_for_Evolution.txt |
Fossils can form under ideal conditions by preservation, permineralization, molding (casting), replacement, or compression.
Learning Objectives
• Predict the conditions suitable to fossil formation
Key Points
• Preservation of remains in amber or other substances is the rarest from of fossilization; this mechanism allows scientists to study the skin, hair, and organs of ancient creatures.
• Permineralization, where minerals like silica fill the empty spaces of shells, is the most common form of fossilization.
• Molds form when shells or bones dissolve, leaving behind an empty depression; a cast is then formed when the depression is filled by sediment.
• Replacement occurs when the original shell or bone dissolves away and is replaced by a different mineral; when this occurs with permineralization, it is called petrification.
• In compression, the most common form of fossilization of leaves and ferns, a dark imprint of the fossil remains.
• Decay, chemical weathering, erosion, and predators are factors that deter fossilization.
• Fossilization of soft body parts is rare, and hard parts are better preserved when buried.
Key Terms
• amber: a hard, generally yellow to brown translucent fossil resin
• permineralization: form of fossilization in which minerals are deposited in the pores of bone and similar hard animal parts
• petrification: process by which organic material is converted into stone through the replacement of the original material and the filling of the original pore spaces with minerals
Fossil Formation
The process of a once living organism becoming a fossil is called fossilization. Fossilization is a very rare process, and of all the organisms that have lived on Earth, only a tiny percentage of them ever become fossils. To see why, imagine an antelope that dies on the African plain. Most of its body is quickly eaten by scavengers, and the remaining flesh is soon eaten by insects and bacteria, leaving behind only scattered bones. As the years go by, the bones are scattered and fragmented into small pieces, eventually turning into dust and returning their nutrients to the soil. As a result, it would be rare for any of the antelope’s remains to actually be preserved as a fossil.
Fossilization can occur in many ways. Most fossils are preserved in one of five processes:
• preserved remains
• permineralization
• molds and casts
• replacement
• compression
Preserved Remains
The rarest form of fossilization is the preservation of original skeletal material and even soft tissue. For example, some insects have been preserved perfectly in amber, which is ancient tree sap. In addition, several mammoths and even a Neanderthal hunter have been discovered frozen in glaciers. These preserved remains allow scientists the rare opportunity to examine the skin, hair, and organs of ancient creatures. Scientists have collected DNA from these remains and compared the DNA sequences to those of modern creatures.
Permineralization
The most common method of fossilization is permineralization. After a bone, wood fragment, or shell is buried in sediment, it may be exposed to mineral-rich water that moves through the sediment. This water will deposit minerals, typically silica, into empty spaces, producing a fossil. Fossilized dinosaur bones, petrified wood, and many marine fossils were formed by permineralization.
Molds and Casts
In some cases, the original bone or shell dissolves away, leaving behind an empty space in the shape of the shell or bone. This depression is called a mold. Later, the space may be filled with other sediments to form a matching cast in the shape of the original organism. Many mollusks (bivalves, snails, and squid) are commonly found as molds and casts because their shells dissolve easily.
Replacement
In some cases, the original shell or bone dissolves away and is replaced by a different mineral. For example, shells that were originally calcite may be replaced by dolomite, quartz, or pyrite. If quartz fossils are surrounded by a calcite matrix, the calcite can be dissolved away by acid, leaving behind an exquisitely preserved quartz fossil. When permineralization and replacement occur together, the organism is said to have undergone petrification, the process of turning organic material into stone. However, replacement can occur without permineralization and vice versa.
Compression
Some fossils form when their remains are compressed by high pressure. This can leave behind a dark imprint of the fossil. Compression is most common for fossils of leaves and ferns but also can occur with other organisms.
Conditions for Fossilization
Following the death of an organism, several forces contribute to the dissolution of its remains. Decay, predators, or scavengers will typically rapidly remove the flesh. The hard parts, if they are separable at all, can be dispersed by predators, scavengers, or currents. The individual hard parts are subject to chemical weathering and erosion, as well as to splintering by predators or scavengers, which will crunch up bones for marrow and shells to extract the flesh inside. Also, an animal swallowed whole by a predator, such as a mouse swallowed by a snake, will have not just its flesh but some, and perhaps all, its bones destroyed by the gastric juices of the predator.
It would not be an exaggeration to say that the typical vertebrate fossil consists of a single bone, or tooth, or fish scale. The preservation of an intact skeleton with the bones in the relative positions they had in life requires a remarkable circumstances, such as burial in volcanic ash, burial in aeolian sand due to the sudden slumping of a sand dune, burial in a mudslide, burial by a turbidity current, and so forth. The mineralization of soft parts is even less common and is seen only in exceptionally rare chemical and biological conditions. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/21%3A_The_Evidence_for_Evolution/21.04%3A_Fossil_Evidence_of_Evolution/21.4B%3A_Fossil_Formation.txt |
Because not all animals have bodies which fossilize easily, the fossil record is considered incomplete.
Learning Objectives
• Explain the gap in the fossil record
Key Points
• The number of species known about through fossils is less than 1% of all species that have ever lived.
• Because hard body parts are more easily preserved than soft body parts, there are more fossils of animals with hard body parts, such as vertebrates, echinoderms, brachiopods, and some groups of arthropods.
• Very few fossils have been found in the period from 360 to 345 million years ago, known as Romer’s gap. Theories to explain this include the period’s geochemistry, errors in excavation, and limited vertebrate diversity.
Key Terms
• transitional fossil: Fossilized remains of a life form that exhibits traits common to both an ancestral group and its derived descendant group.
• Romer’s gap: A period in the tetrapod fossil record (360 to 345 million years ago) from which excavators have not yet found relevant fossils.
Incompleteness of the Fossil Record
Each fossil discovery represents a snapshot of the process of evolution. Because of the specialized and rare conditions required for a biological structure to fossilize, many important species or groups may never leave fossils at all. Even if they do leave fossils, humans may never find them—for example, if they are buried under hundreds of feet of ice in Antarctica. The number of species known about through the fossil record is less than 5% of the number of species alive today. Fossilized species may represent less than 1% of all the species that have ever lived.
Types of Fossils in the Fossil Record
The fossil record is very uneven and is mostly comprised of fossils of organisms with hard body parts, leaving most groups of soft-bodied organisms with little to no fossil record. Groups considered to have a good fossil record, including transitional fossils between these groups, are the vertebrates, the echinoderms, the brachiopods, and some groups of arthropods. Their hard bones and shells fossilize easily, unlike the bodies of organisms like cephalopods or jellyfish.
Romer’s Gap
Romer’s gap is an example of an apparent gap in the tetrapod fossil record used in the study of evolutionary biology. These gaps represent periods from which no relevant fossils have been found. Romer’s gap is named after paleontologist Alfred Romer, who first recognized it. Romer’s gap spanned from approximately 360 to 345 million years ago, corresponding to the first 15 million years of the Carboniferous Period.
There has been much debate over why there are so few fossils from this time period. Some scientists have suggested that the geochemistry of the time period caused bad conditions for fossil formation, so few organisms were fossilized. Another theory suggests that scientists have simply not yet discovered an excavation site for these fossils, due to inaccessibility or random chance.
21.4D: Carbon Dating and Estimating Fossil Age
The age of fossils can be determined using stratigraphy, biostratigraphy, and radiocarbon dating.
Learning Objectives
• Summarize the available methods for dating fossils
Key Points
• Determining the ages of fossils is an important step in mapping out how life evolved across geologic time.
• The study of stratigraphy enables scientists to determine the age of a fossil if they know the age of layers of rock that surround it.
• Biostratigraphy enables scientists to match rocks with particular fossils to other rocks with those fossils to determine age.
• Paleontology seeks to map out how life evolved across geologic time. A substantial hurdle is the difficulty of working out fossil ages.
• Scientists use carbon dating when determining the age of fossils that are less than 60,000 years old, and that are composed of organic materials such as wood or leather.
Key Terms
• half-life: The time required for half of the nuclei in a sample of a specific isotope to undergo radioactive decay.
• stratigraphy: The study of rock layers and the layering process.
• radiocarbon dating: A method of estimating the age of an artifact or biological vestige based on the relative amounts of various isotopes of carbon present in a sample.
Determining Fossil Ages
Paleontology seeks to map out how life evolved across geologic time. A substantial hurdle is the difficulty of working out fossil ages. There are several different methods for estimating the ages of fossils, including:
1. stratigraphy
2. biostratigraphy
3. carbon dating
Stratigraphy
Paleontologists rely on stratigraphy to date fossils. Stratigraphy is the science of understanding the strata, or layers, that form the sedimentary record. Strata are differentiated from each other by their different colors or compositions and are exposed in cliffs, quarries, and river banks. These rocks normally form relatively horizontal, parallel layers, with younger layers forming on top.
If a fossil is found between two layers of rock whose ages are known, the fossil’s age is thought to be between those two known ages. Because rock sequences are not continuous, but may be broken up by faults or periods of erosion, it is difficult to match up rock beds that are not directly adjacent.
Biostratigraphy
Fossils of species that survived for a relatively short time can be used to match isolated rocks: this technique is called biostratigraphy. For instance, the extinct chordate Eoplacognathus pseudoplanus is thought to have existed during a short range in the Middle Ordovician period. If rocks of unknown age have traces of E. pseudoplanus, they have a mid-Ordovician age. Such index fossils must be distinctive, globally distributed, and occupy a short time range to be useful. Misleading results can occur if the index fossils are incorrectly dated.
Relative Dating
Stratigraphy and biostratigraphy can in general provide only relative dating (A was before B), which is often sufficient for studying evolution. This is difficult for some time periods, however, because of the barriers involved in matching rocks of the same age across continents. Family-tree relationships can help to narrow down the date when lineages first appeared. For example, if fossils of B date to X million years ago and the calculated “family tree” says A was an ancestor of B, then A must have evolved earlier.
It is also possible to estimate how long ago two living branches of a family tree diverged by assuming that DNA mutations accumulate at a constant rate. However, these “molecular clocks” are sometimes inaccurate and provide only approximate timing. For example, they are not sufficiently precise and reliable for estimating when the groups that feature in the Cambrian explosion first evolved, and estimates produced by different approaches to this method may vary as well.
Carbon Dating
Together with stratigraphic principles, radiometric dating methods are used in geochronology to establish the geological time scale. Beds that preserve fossils typically lack the radioactive elements needed for radiometric dating (” radiocarbon dating ” or simply “carbon dating”). The principle of radiocarbon dating is simple: the rates at which various radioactive elements decay are known, and the ratio of the radioactive element to its decay products shows how long the radioactive element has existed in the rock. This rate is represented by the half-life, which is the time it takes for half of a sample to decay.
The half-life of carbon-14 is 5,730 years, so carbon dating is only relevant for dating fossils less than 60,000 years old. Radioactive elements are common only in rocks with a volcanic origin, so the only fossil-bearing rocks that can be dated radiometrically are volcanic ash layers. Carbon dating uses the decay of carbon-14 to estimate the age of organic materials, such as wood and leather. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/21%3A_The_Evidence_for_Evolution/21.04%3A_Fossil_Evidence_of_Evolution/21.4C%3A_Gaps_in_the_Fossil_Record.txt |
Learning Objectives
• Analyze the fossil record to understand the evolution of horses
Fossils provide evidence that organisms from the past are not the same as those found today, and demonstrate a progression of evolution. Scientists date and categorize fossils to determine when the organisms lived relative to each other. The resulting fossil record tells the story of the past and shows the evolution of forms over millions of years.
Case Study: Evolution of the Modern Horse
Highly detailed fossil records have been recovered for sequences in the evolution of modern horses. The fossil record of horses in North America is especially rich and contains transition fossils: fossils that show intermediate stages between earlier and later forms. The fossil record extends back to a dog-like ancestor some 55 million years ago, which gave rise to the first horse-like species 55 to 42 million years ago in the genus Eohippus.
The first equid fossil was found in the gypsum quarries in Montmartre, Paris in the 1820s. The tooth was sent to the Paris Conservatory, where Georges Cuvier identified it as a browsing equine related to the tapir. His sketch of the entire animal matched later skeletons found at the site. During the H.M.S. Beagle survey expedition, Charles Darwin had remarkable success with fossil hunting in Patagonia. In 1833 in Santa Fe, Argentina, he was “filled with astonishment” when he found a horse’s tooth in the same stratum as fossils of giant armadillos and wondered if it might have been washed down from a later layer, but concluded this was “not very probable.” In 1836, the anatomist Richard Owen confirmed the tooth was from an extinct species, which he subsequently named Equus curvidens.
The original sequence of species believed to have evolved into the horse was based on fossils discovered in North America in the 1870s by paleontologist Othniel Charles Marsh. The sequence, from Eohippus to the modern horse (Equus), was popularized by Thomas Huxley and became one of the most widely known examples of a clear evolutionary progression. The sequence of transitional fossils was assembled by the American Museum of Natural History into an exhibit that emphasized the gradual, “straight-line” evolution of the horse.
Since then, as the number of equid fossils has increased, the actual evolutionary progression from Eohippus to Equus has been discovered to be much more complex and multibranched than was initially supposed. Detailed fossil information on the rate and distribution of new equid species has also revealed that the progression between species was not as smooth and consistent as was once believed.
Although some transitions were indeed gradual progressions, a number of others were relatively abrupt in geologic time, taking place over only a few million years. Both anagenesis, a gradual change in an entire population ‘s gene frequency, and cladogenesis, a population “splitting” into two distinct evolutionary branches, occurred, and many species coexisted with “ancestor” species at various times.
Adaptation for Grazing
The series of fossils tracks the change in anatomy resulting from a gradual drying trend that changed the landscape from a forested habitat to a prairie habitat. Early horse ancestors were originally specialized for tropical forests, while modern horses are now adapted to life on drier land. Successive fossils show the evolution of teeth shapes and foot and leg anatomy to a grazing habit with adaptations for escaping predators.
The horse belongs to the order Perissodactyla (odd-toed ungulates), the members of which all share hoofed feet and an odd number of toes on each foot, as well as mobile upper lips and a similar tooth structure. This means that horses share a common ancestry with tapirs and rhinoceroses. Later species showed gains in size, such as those of Hipparion, which existed from about 23 to 2 million years ago. The fossil record shows several adaptive radiations in the horse lineage, which is now much reduced to only one genus, Equus, with several species. Paleozoologists have been able to piece together a more complete outline of the modern horse’s evolutionary lineage than that of any other animal.
Key Points
• A dog-like organism gave rise to the first horse ancestors 55-42 million years ago.
• The fossil record shows modern horses moved from tropical forests to prairie habitats, developed teeth, and grew in size.
• The first equid fossil was a tooth from the extinct species Equus curvidens found in Paris in the 1820s.
• Thomas Huxley popularized the evolutionary sequence of horses, which became one of the most common examples of clear evolutionary progression.
• Horse evolution was previously believed to be a linear progress, but after more fossils were discovered, it was determined the evolution of horses was more complex and multi-branched.
• Horses have evolved from gradual change ( anagenesis ) as well as abrupt progression and division ( cladogenesis ).
Key Terms
• cladogenesis: An evolutionary splitting event in which each branch and its smaller branches forms a clade.
• equid: A member of the horse family.
• anagenesis: Evolution of a new species through a large scale change in gene frequency so that the new species replaces the old, rather than branching to produce an additional species. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/21%3A_The_Evidence_for_Evolution/21.04%3A_Fossil_Evidence_of_Evolution/21.4E%3A_The_Fossil_Record_and_the_Evolution_of_the_Modern_Horse.txt |
Homologous structures are similar structures that evolved from a common ancestor.
Learning Objectives
• Describe the connection between evolution and the appearance of homologous structures
Key Points
• Homology is a relationship defined between structures or DNA derived from a common ancestor and illustrates descent from a common ancestor.
• Analogous structures are physically (but not genetically) similar structures that were not present the last common ancestor.
• Homology can also be partial; new structures can evolve through the combination or parts of developmental pathways.
• Analogy may also be referred to as homoplasy, which is further divided into parallelism, reversal, and convergence.
Key Terms
• homology: A correspondence of structures in two life forms with a common evolutionary origin, such as flippers and hands.
• analogy: The relationship between characteristics that are apparently similar but did not develop from the same structure
• homoplasy: A correspondence between the parts or organs of different species acquired as the result of parallel evolution or convergence.
Homologous Structures
Homology is the relationship between structures or DNA derived from the most recent common ancestor. A common example of homologous structures in evolutionary biology are the wings of bats and the arms of primates. Although these two structures do not look similar or have the same function, genetically, they come from the same structure of the last common ancestor. Homologous traits of organisms are therefore explained by descent from a common ancestor.
It’s important to note that defining two structures as homologous depends on what ancestor is being described as the common ancestor. If we go all the way back to the beginning of life, all structures are homologous!
In genetics, homology is measured by comparing protein or DNA sequences. Homologous gene sequences share a high similarity, supporting the hypothesis that they share a common ancestor.
Homology can also be partial: new structures can evolve through the combination of developmental pathways or parts of them. As a result, hybrid or mosaic structures can evolve that exhibit partial homologies. For example, certain compound leaves of flowering plants are partially homologous both to leaves and shoots because they combine some traits of leaves and some of shoots.
Paralogous Structures
Homologous sequences are considered paralogous if they were separated by a gene duplication event; if a gene in an organism is duplicated to occupy two different positions in the same genome, then the two copies are paralogous.
A set of sequences that are paralogous are called paralogs of each other. Paralogs typically have the same or similar function, but sometimes do not. It is considered that due to lack of the original selective pressure upon one copy of the duplicated gene, this copy is free to mutate and acquire new functions.
Paralogous genes often belong to the same species, but not always. For example, the hemoglobin gene of humans and the myoglobin gene of chimpanzees are considered paralogs. This is a common problem in bioinformatics; when genomes of different species have been sequenced and homologous genes have been found, one can not immediately conclude that these genes have the same or similar function, as they could be paralogs whose function has diverged.
Analogous Structures
The opposite of homologous structures are analogous structures, which are physically similar structures between two taxa that evolved separately (rather than being present in the last common ancestor). Bat wings and bird wings evolved independently and are considered analogous structures. Genetically, a bat wing and a bird wing have very little in common; the last common ancestor of bats and birds did not have wings like either bats or birds. Wings evolved independently in each lineage after diverging from ancestors with forelimbs that were not used as wings (terrestrial mammals and theropod dinosaurs, respectively).
It is important to distinguish between different hierarchical levels of homology in order to make informative biological comparisons. In the above example, the bird and bat wings are analogous as wings, but homologous as forelimbs because the organ served as a forearm (not a wing) in the last common ancestor of tetrapods.
Analogy is different than homology. Although analogous characteristics are superficially similar, they are not homologous because they are phylogenetically independent. The wings of a maple seed and the wings of an albatross are analogous but not homologous (they both allow the organism to travel on the wind, but they didn’t both develop from the same structure). Analogy is commonly also referred to as homoplasy. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/21%3A_The_Evidence_for_Evolution/21.04%3A_Fossil_Evidence_of_Evolution/21.4F%3A_Homologous_Structures.txt |
Convergent evolution occurs in different species that have evolved similar traits independently of each other.
Learning Objectives
• Predict the circumstances supporting convergent evolution of two species
Key Points
• Examples of convergent evolution include the relationship between bat and insect wings, shark and dolphin bodies, and vertebrate and cephalopod eyes.
• Analogous structures arise from convergent evolution, but homologous structures do not.
• Convergent evolution is the opposite of divergent evolution, in which related species evolve different traits.
• Convergent evolution is similar to parallel evolution, in which two similar but independent species evolve in the same direction and independently acquire similar characteristics.
Key Terms
• parallel evolution: the development of a similar trait in related, but distinct, species descending from the same ancestor, but from different clades
• convergent evolution: a trait of evolution in which species not of similar recent origin acquire similar properties due to natural selection
• divergent evolution: the process by which a species with similar traits become groups that are tremendously different from each other over many generations
• morphology: the form and structure of an organism
Convergent Evolution
Sometimes, similar phenotypes evolve independently in distantly related species. For example, flight has evolved in both bats and insects, and they both have wings, which are adaptations to flight. However, the wings of bats and insects have evolved from very different original structures. This phenomenon is called convergent evolution, where similar traits evolve independently in species that do not share a recent common ancestry.
Examples of Convergent Evolution
Convergent evolution describes the independent evolution of similar features in species of different lineages. The two species came to the same function, flying, but did so separately from each other. They have “converged” on this useful trait. Both sharks and dolphins have similar body forms, yet are only distantly related: sharks are fish and dolphins are mammals. Such similarities are a result of both populations being exposed to the same selective pressures. Within both groups, changes that aid swimming have been favored. Thus, over time, they developed similar appearances (morphology), even though they are not closely related.
One of the most well-known examples of convergent evolution is the camera eye of cephalopods (e.g., octopus), vertebrates (e.g., mammals), and cnidaria (e.g., box jellies). Their last common ancestor had at most a very simple photoreceptive spot, but a range of processes led to the progressive refinement of this structure to the advanced camera eye. There is, however, one subtle difference: the cephalopod eye is “wired” in the opposite direction, with blood and nerve vessels entering from the back of the retina, rather than the front as in vertebrates.
Convergent evolution is similar to, but distinguishable from, the phenomenon of parallel evolution. Parallel evolution occurs when two independent but similar species evolve in the same direction and thus independently acquire similar characteristics; for example, gliding frogs have evolved in parallel from multiple types of tree frog.
Analogous Structures
Traits arising through convergent evolution are analogous structures, in contrast to homologous structures, which have a common origin, but not necessarily similar function. The British anatomist Richard Owen was the first scientist to recognize the fundamental difference between analogies and homologies. Bat and pterosaur wings are an example of analogous structures, while the bat wing is homologous to human and other mammal forearms, sharing an ancestral state despite serving different functions.
Divergent Evolution
The opposite of convergent evolution is divergent evolution, whereby related species evolve different traits. On a molecular level, this can happen due to random mutation unrelated to adaptive changes. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/21%3A_The_Evidence_for_Evolution/21.04%3A_Fossil_Evidence_of_Evolution/21.4G%3A_Convergent_Evolution.txt |
Vestigial structures have no function but may still be inherited to maintain fitness.
Learning Objectives
• Discuss the connection between evolution and the existence of vestigial structures
Key Points
• Structures that have no apparent function and appear to be residual parts from a past ancestor are called vestigial structures.
• Examples of vestigial structures include the human appendix, the pelvic bone of a snake, and the wings of flightless birds.
• Vestigial structures can become detrimental, but in most cases these structures are harmless; however, these structures, like any other structure, require extra energy and are at risk for disease.
• Vestigial structures, especially non-harmful ones, take a long time to be phased out since eliminating them would require major alterations that could result in negative side effects.
Key Terms
• vestigial structure: Genetically determined structures or attributes that have lost most or all of their ancestral function in a given species.
• adaptation: A modification of something or its parts that makes it more fit for existence under the conditions of its current environment.
What Are Vestigial Structures?
Some organisms possess structures with no apparent function which appear to be residual parts from a past ancestor. For example, some snakes have pelvic bones despite having no legs because they descended from reptiles that did have legs. Another example of a structure with no function is the human vermiform appendix. These unused structures without function are called vestigial structures. Other examples of vestigial structures are wings (which may have other functions) on flightless birds like the ostrich, leaves on some cacti, traces of pelvic bones in whales, and the sightless eyes of cave animals.
There are also several reflexes and behaviors that are considered to be vestigial. The formation of goose bumps in humans under stress is a vestigial reflex its function in human ancestors was to raise the body’s hair, making the ancestor appear larger and scaring off predators. The arrector pili muscle, which is a band of smooth muscle that connects the hair follicle to connective tissue, contracts and creates the goose bumps on skin.
Vestigial Structures in Evolution
Vestigial structures are often homologous to structures that function normally in other species. Therefore, vestigial structures can be considered evidence for evolution, the process by which beneficial heritable traits arise in populations over an extended period of time. The existence of vestigial traits can be attributed to changes in the environment and behavior patterns of the organism in question. As the function of the trait is no longer beneficial for survival, the likelihood that future offspring will inherit the “normal” form of it decreases. In some cases the structure becomes detrimental to the organism.
If there are no selection pressures actively lowering the fitness of the individual, the trait will persist in future generations unless the trait is eliminated through genetic drift or other random events.
Although in many cases the vestigial structure is of no direct harm, all structures require extra energy in terms of development, maintenance, and weight and are also a risk in terms of disease (e.g., infection, cancer). This provides some selective pressure for the removal of parts that do not contribute to an organism’s fitness, but a structure that is not directly harmful will take longer to be ‘phased out’ than one that is. Some vestigial structures persist due to limitations in development, such that complete loss of the structure could not occur without major alterations of the organism’s developmental pattern, and such alterations would likely produce numerous negative side-effects.
The vestigial versions of a structure can be compared to the original version of the structure in other species in order to determine the homology of the structure. Homologous structures indicate common ancestry with those organisms that have a functional version of the structure. Vestigial traits can still be considered adaptations because an adaptation is often defined as a trait that has been favored by natural selection. Adaptations, therefore, need not be adaptive, as long as they were at some point. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/21%3A_The_Evidence_for_Evolution/21.04%3A_Fossil_Evidence_of_Evolution/21.4H%3A_Vestigial_Structures.txt |
The biological distribution of species is based on the movement of tectonic plates over a period of time.
Learning Objectives
• Relate biogeography and the distribution of species
Key Points
• Biogeography is the study of geological species distribution, which is influenced by both biotic and abiotic factors.
• Some species are endemic and are only found in a particular region, while others are generalists and are distributed worldwide.
• Species that evolved before the breakup of continents are distributed worldwide.
• Species that evolved after the breakup of continents are found in only certain regions of the planet.
Key Terms
• endemic: unique to a particular area or region; not found in other places
• generalist: species which can thrive in a wide variety of environmental conditions
• Pangaea: supercontinent that included all the landmasses of the earth before the Triassic period and that broke up into Laurasia and Gondwana
Distribution of Species
Biogeography is the study of the geographic distribution of living things and the abiotic factors that affect their distribution. Abiotic factors, such as temperature and rainfall, vary based on latitude and elevation, primarily. As these abiotic factors change, the composition of plant and animal communities also changes.
Patterns of Species Distribution
Ecologists who study biogeography examine patterns of species distribution. No species exists everywhere; for example, the Venus flytrap is endemic to a small area in North and South Carolina. An endemic species is one which is naturally found only in a specific geographic area that is usually restricted in size. Other species are generalists: species which live in a wide variety of geographic areas; the raccoon, for example, is native to most of North and Central America.
Since species distribution patterns are based on biotic and abiotic factors and their influences during the very long periods of time required for species evolution, early studies of biogeography were closely linked to the emergence of evolutionary thinking in the eighteenth century. Some of the most distinctive assemblages of plants and animals occur in regions that have been physically separated for millions of years by geographic barriers. Biologists estimate that Australia, for example, has between 600,000 and 700,000 species of plants and animals. Approximately 3/4 of living plant and mammal species are endemic species found solely in Australia.
The geographic distribution of organisms on the planet follows patterns that are best explained by evolution in conjunction with the movement of tectonic plates over geological time. Broad groups that evolved before the breakup of the supercontinent Pangaea (about 200 million years ago) are distributed worldwide. Groups that evolved since the breakup appear uniquely in regions of the planet, such as the unique flora and fauna of northern continents that formed from the supercontinent Laurasia and of the southern continents that formed from the supercontinent Gondwana. The presence of Proteaceae in Australia, southern Africa, and South America is best explained by the plant family’s presence there prior to the southern supercontinent Gondwana breaking up.
Contributions and Attributions
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• OpenStax College, Evidence of Evolution. December 6, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m45491/latest/. License: CC BY: Attribution
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• biomarker. Provided by: Wiktionary. Located at: en.wiktionary.org/wiki/biomarker. License: CC BY-SA: Attribution-ShareAlike
• 800px-Dinosaur_Ridge_tracks.JPG. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/Ichnol...dge_tracks.JPG. License: CC BY-SA: Attribution-ShareAlike
• 1024px-Sues_skeleton.jpg. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/Tyrann...s_skeleton.jpg. License: CC BY-SA: Attribution-ShareAlike
• Historical Geology/Fossils. Provided by: Wikibooks. Located at: en.wikibooks.org/wiki/Histori...eology/Fossils. License: CC BY-SA: Attribution-ShareAlike
• Historical Geology/Fossils. Provided by: Wikibooks. Located at: en.wikibooks.org/wiki/Histori...eology/Fossils. License: CC BY-SA: Attribution-ShareAlike
• High School Earth Science/Fossils. Provided by: Wikibooks. Located at: en.wikibooks.org/wiki/High_Sc...cience/Fossils. License: CC BY-SA: Attribution-ShareAlike
• amber. Provided by: Wiktionary. Located at: en.wiktionary.org/wiki/amber. License: CC BY-SA: Attribution-ShareAlike
• petrification. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/petrification. License: CC BY-SA: Attribution-ShareAlike
• permineralization. Provided by: Wiktionary. Located at: en.wiktionary.org/wiki/permineralization. License: CC BY-SA: Attribution-ShareAlike
• 800px-Dinosaur_Ridge_tracks.JPG. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/Ichnol...dge_tracks.JPG. License: CC BY-SA: Attribution-ShareAlike
• 1024px-Sues_skeleton.jpg. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/Tyrann...s_skeleton.jpg. License: CC BY-SA: Attribution-ShareAlike
• Historical Geology/Fossils. Provided by: Wikibooks. Located at: en.wikibooks.org/wiki/Histori...eology/Fossils. License: CC BY-SA: Attribution-ShareAlike
• Fossil. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/Fossil. License: CC BY: Attribution
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The evidence for evolution is compelling and extensive. Looking at every level of organization in living systems, biologists see the signature of past and present evolution. Darwin dedicated a large portion of his book, On the Origin of Species, identifying patterns in nature that were consistent with evolution and since Darwin our understanding has become clearer and broader.
Fossils
Fossils provide solid evidence that organisms from the past are not the same as those found today; fossils show a progression of evolution. Scientists determine the age of fossils and categorize them all over the world to determine when the organisms lived relative to each other. The resulting fossil record tells the story of the past, and shows the evolution of form over millions of years (Figure \(1\)). For example, highly detailed fossil records have been recovered for sequences of species in the evolution of whales and modern horses. The fossil record of horses in North America is especially rich and many contain transition fossils: those showing intermediate anatomy between earlier and later forms. The fossil record extends back to a dog-like ancestor some 55 million years ago that gave rise to the first horse-like species 55 to 42 million years ago in the genus Eohippus. The series of fossils tracks the change in anatomy resulting from a gradual drying trend that changed the landscape from a forested one to a prairie. Successive fossils show the evolution of teeth shapes and foot and leg anatomy to a grazing habit, with adaptations for escaping predators, for example in species of Mesohippus found from 40 to 30 million years ago. Later species showed gains in size, such as those of Hipparion, which existed from about 23 to 2 million years ago. The fossil record shows several adaptive radiations in the horse lineage, which is now much reduced to only one genus, Equus, with several species.
Anatomy and Embryology
Another type of evidence for evolution is the presence of structures in organisms that share the same basic form. For example, the bones in the appendages of a human, dog, bird, and whale all share the same overall construction (Figure \(2\)). That similarity results from their origin in the appendages of a common ancestor. Over time, evolution led to changes in the shapes and sizes of these bones in different species, but they have maintained the same overall layout, evidence of descent from a common ancestor. Scientists call these synonymous parts homologous structures. Some structures exist in organisms that have no apparent function at all, and appear to be residual parts from a past ancestor. For example, some snakes have pelvic bones despite having no legs because they descended from reptiles that did have legs. These unused structures without function are called vestigial structures. Other examples of vestigial structures are wings on flightless birds (which may have other functions), leaves on some cacti, traces of pelvic bones in whales, and the sightless eyes of cave animals.
Another evidence of evolution is the convergence of form in organisms that share similar environments. For example, species of unrelated animals, such as the arctic fox and ptarmigan (a bird), living in the arctic region have temporary white coverings during winter to blend with the snow and ice (Figure \(3\)). The similarity occurs not because of common ancestry, indeed one covering is of fur and the other of feathers, but because of similar selection pressures—the benefits of not being seen by predators.
Embryology, the study of the development of the anatomy of an organism to its adult form also provides evidence of relatedness between now widely divergent groups of organisms. Structures that are absent in some groups often appear in their embryonic forms and disappear by the time the adult or juvenile form is reached. For example, all vertebrate embryos, including humans, exhibit gill slits at some point in their early development. These disappear in the adults of terrestrial groups, but are maintained in adult forms of aquatic groups such as fish and some amphibians. Great ape embryos, including humans, have a tail structure during their development that is lost by the time of birth. The reason embryos of unrelated species are often similar is that mutational changes that affect the organism during embryonic development can cause amplified differences in the adult, even while the embryonic similarities are preserved.
Biogeography
The geographic distribution of organisms on the planet follows patterns that are best explained by evolution in conjunction with the movement of tectonic plates over geological time. Broad groups that evolved before the breakup of the supercontinent Pangaea (about 200 million years ago) are distributed worldwide. Groups that evolved since the breakup appear uniquely in regions of the planet, for example the unique flora and fauna of northern continents that formed from the supercontinent Laurasia and of the southern continents that formed from the supercontinent Gondwana. The presence of Proteaceae in Australia, southern Africa, and South America is best explained by the plant family’s presence there prior to the southern supercontinent Gondwana breaking up (Figure \(4\)).
The great diversification of the marsupials in Australia and the absence of other mammals reflects that island continent’s long isolation. Australia has an abundance of endemic species—species found nowhere else—which is typical of islands whose isolation by expanses of water prevents migration of species to other regions. Over time, these species diverge evolutionarily into new species that look very different from their ancestors that may exist on the mainland. The marsupials of Australia, the finches on the Galápagos, and many species on the Hawaiian Islands are all found nowhere else but on their island, yet display distant relationships to ancestral species on mainlands.
Molecular Biology
Like anatomical structures, the structures of the molecules of life reflect descent with modification. Evidence of a common ancestor for all of life is reflected in the universality of DNA as the genetic material and of the near universality of the genetic code and the machinery of DNA replication and expression. Fundamental divisions in life between the three domains are reflected in major structural differences in otherwise conservative structures such as the components of ribosomes and the structures of membranes. In general, the relatedness of groups of organisms is reflected in the similarity of their DNA sequences—exactly the pattern that would be expected from descent and diversification from a common ancestor.
DNA sequences have also shed light on some of the mechanisms of evolution. For example, it is clear that the evolution of new functions for proteins commonly occurs after gene duplication events. These duplications are a kind of mutation in which an entire gene is added as an extra copy (or many copies) in the genome. These duplications allow the free modification of one copy by mutation, selection, and drift, while the second copy continues to produce a functional protein. This allows the original function for the protein to be kept, while evolutionary forces tweak the copy until it functions in a new way.
Section Summary
The evidence for evolution is found at all levels of organization in living things and in the extinct species we know about through fossils. Fossils provide evidence for the evolutionary change through now extinct forms that led to modern species. For example, there is a rich fossil record that shows the evolutionary transitions from horse ancestors to modern horses that document intermediate forms and a gradual adaptation to changing ecosystems. The anatomy of species and the embryological development of that anatomy reveal common structures in divergent lineages that have been modified over time by evolution. The geographical distribution of living species reflects the origins of species in particular geographic locations and the history of continental movements. The structures of molecules, like anatomical structures, reflect the relationships of living species and match patterns of similarity expected from descent with modification.
Glossary
vestigial structure
a physical structure present in an organism but that has no apparent function and appears to be from a functional structure in a distant ancestor | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/21%3A_The_Evidence_for_Evolution/21.05%3A_Anatomical_Evidence_of_Evolution.txt |
Convergent evolution occurs in different species that have evolved similar traits independently of each other.
Learning Objectives
• Predict the circumstances supporting convergent evolution of two species
Key Points
• Examples of convergent evolution include the relationship between bat and insect wings, shark and dolphin bodies, and vertebrate and cephalopod eyes.
• Analogous structures arise from convergent evolution, but homologous structures do not.
• Convergent evolution is the opposite of divergent evolution, in which related species evolve different traits.
• Convergent evolution is similar to parallel evolution, in which two similar but independent species evolve in the same direction and independently acquire similar characteristics.
Key Terms
• parallel evolution: the development of a similar trait in related, but distinct, species descending from the same ancestor, but from different clades
• convergent evolution: a trait of evolution in which species not of similar recent origin acquire similar properties due to natural selection
• divergent evolution: the process by which a species with similar traits become groups that are tremendously different from each other over many generations
• morphology: the form and structure of an organism
Convergent Evolution
Sometimes, similar phenotypes evolve independently in distantly related species. For example, flight has evolved in both bats and insects, and they both have wings, which are adaptations to flight. However, the wings of bats and insects have evolved from very different original structures. This phenomenon is called convergent evolution, where similar traits evolve independently in species that do not share a recent common ancestry.
Examples of Convergent Evolution
Convergent evolution describes the independent evolution of similar features in species of different lineages. The two species came to the same function, flying, but did so separately from each other. They have “converged” on this useful trait. Both sharks and dolphins have similar body forms, yet are only distantly related: sharks are fish and dolphins are mammals. Such similarities are a result of both populations being exposed to the same selective pressures. Within both groups, changes that aid swimming have been favored. Thus, over time, they developed similar appearances (morphology), even though they are not closely related.
One of the most well-known examples of convergent evolution is the camera eye of cephalopods (e.g., octopus), vertebrates (e.g., mammals), and cnidaria (e.g., box jellies). Their last common ancestor had at most a very simple photoreceptive spot, but a range of processes led to the progressive refinement of this structure to the advanced camera eye. There is, however, one subtle difference: the cephalopod eye is “wired” in the opposite direction, with blood and nerve vessels entering from the back of the retina, rather than the front as in vertebrates.
Convergent evolution is similar to, but distinguishable from, the phenomenon of parallel evolution. Parallel evolution occurs when two independent but similar species evolve in the same direction and thus independently acquire similar characteristics; for example, gliding frogs have evolved in parallel from multiple types of tree frog.
Analogous Structures
Traits arising through convergent evolution are analogous structures, in contrast to homologous structures, which have a common origin, but not necessarily similar function. The British anatomist Richard Owen was the first scientist to recognize the fundamental difference between analogies and homologies. Bat and pterosaur wings are an example of analogous structures, while the bat wing is homologous to human and other mammal forearms, sharing an ancestral state despite serving different functions.
Divergent Evolution
The opposite of convergent evolution is divergent evolution, whereby related species evolve different traits. On a molecular level, this can happen due to random mutation unrelated to adaptive changes.
21.06: Convergent Evolution and the Biogeographical Record
The biological distribution of species is based on the movement of tectonic plates over a period of time.
Learning Objectives
• Relate biogeography and the distribution of species
Key Points
• Biogeography is the study of geological species distribution, which is influenced by both biotic and abiotic factors.
• Some species are endemic and are only found in a particular region, while others are generalists and are distributed worldwide.
• Species that evolved before the breakup of continents are distributed worldwide.
• Species that evolved after the breakup of continents are found in only certain regions of the planet.
Key Terms
• endemic: unique to a particular area or region; not found in other places
• generalist: species which can thrive in a wide variety of environmental conditions
• Pangaea: supercontinent that included all the landmasses of the earth before the Triassic period and that broke up into Laurasia and Gondwana
Distribution of Species
Biogeography is the study of the geographic distribution of living things and the abiotic factors that affect their distribution. Abiotic factors, such as temperature and rainfall, vary based on latitude and elevation, primarily. As these abiotic factors change, the composition of plant and animal communities also changes.
Patterns of Species Distribution
Ecologists who study biogeography examine patterns of species distribution. No species exists everywhere; for example, the Venus flytrap is endemic to a small area in North and South Carolina. An endemic species is one which is naturally found only in a specific geographic area that is usually restricted in size. Other species are generalists: species which live in a wide variety of geographic areas; the raccoon, for example, is native to most of North and Central America.
Since species distribution patterns are based on biotic and abiotic factors and their influences during the very long periods of time required for species evolution, early studies of biogeography were closely linked to the emergence of evolutionary thinking in the eighteenth century. Some of the most distinctive assemblages of plants and animals occur in regions that have been physically separated for millions of years by geographic barriers. Biologists estimate that Australia, for example, has between 600,000 and 700,000 species of plants and animals. Approximately 3/4 of living plant and mammal species are endemic species found solely in Australia.
The geographic distribution of organisms on the planet follows patterns that are best explained by evolution in conjunction with the movement of tectonic plates over geological time. Broad groups that evolved before the breakup of the supercontinent Pangaea (about 200 million years ago) are distributed worldwide. Groups that evolved since the breakup appear uniquely in regions of the planet, such as the unique flora and fauna of northern continents that formed from the supercontinent Laurasia and of the southern continents that formed from the supercontinent Gondwana. The presence of Proteaceae in Australia, southern Africa, and South America is best explained by the plant family’s presence there prior to the southern supercontinent Gondwana breaking up.
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• OpenStax College, Biogeography. December 7, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44857/latest/. License: CC BY: Attribution | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/21%3A_The_Evidence_for_Evolution/21.06%3A_Convergent_Evolution_and_the_Biogeographical_Record/21.6I%3A_Biogeographical_Record.txt |
Although the theory of evolution initially generated some controversy, by 20 years after the publication of On the Origin of Species it was almost universally accepted by biologists, particularly younger biologists. Nevertheless, the theory of evolution is a difficult concept and misconceptions about how it works abound. In addition, there are those that reject it as an explanation for the diversity of life.
CONCEPT IN ACTION
This website addresses some of the main misconceptions associated with the theory of evolution.
Evolution Is Just a Theory
Critics of the theory of evolution dismiss its importance by purposefully confounding the everyday usage of the word “theory” with the way scientists use the word. In science, a “theory” is understood to be a concept that has been extensively tested and supported over time. We have a theory of the atom, a theory of gravity, and the theory of relativity, each of which describes what scientists understand to be facts about the world. In the same way, the theory of evolution describes facts about the living world. As such, a theory in science has survived significant efforts to discredit it by scientists, who are naturally skeptical. While theories can sometimes be overturned or revised, this does not lessen their weight but simply reflects the constantly evolving state of scientific knowledge. In contrast, a “theory” in common vernacular means a guess or suggested explanation for something. This meaning is more akin to the concept of a “hypothesis” used by scientists, which is a tentative explanation for something that is proposed to either be supported or disproved. When critics of evolution say evolution is “just a theory,” they are implying that there is little evidence supporting it and that it is still in the process of being rigorously tested. This is a mischaracterization. If this were the case, geneticist Theodosius Dobzhansky would not have said that “nothing in biology makes sense, except in the light of evolution.”1
Individuals Evolve
An individual is born with the genes it has—these do not change as the individual ages. Therefore, an individual cannot evolve or adapt through natural selection. Evolution is the change in genetic composition of a population over time, specifically over generations, resulting from differential reproduction of individuals with certain alleles. Individuals do change over their lifetime, but this is called development; it involves changes programmed by the set of genes the individual acquired at birth in coordination with the individual’s environment. When thinking about the evolution of a characteristic, it is probably best to think about the change of the average value of the characteristic in the population over time. For example, when natural selection leads to bill-size change in medium ground finches in the Galápagos, this does not mean that individual bills on the finches are changing. If one measures the average bill size among all individuals in the population at one time, and then measures the average bill size in the population several years later after there has been a strong selective pressure, this average value may be different as a result of evolution. Although some individuals may survive from the first time to the second, those individuals will still have the same bill size. However, there may be enough new individuals with different bill sizes to change the average bill size.
Evolution Explains the Origin of Life
It is a common misunderstanding that evolution includes an explanation of life’s origins. Conversely, some of the theory’s critics complain that it cannot explain the origin of life. The theory does not try to explain the origin of life. The theory of evolution explains how populations change over time and how life diversifies—the origin of species. It does not shed light on the beginnings of life including the origins of the first cells, which is how life is defined. The mechanisms of the origin of life on Earth are a particularly difficult problem because it occurred a very long time ago, over a very long time, and presumably just occurred once. Importantly, biologists believe that the presence of life on Earth precludes the possibility that the events that led to life on Earth can be repeated because the intermediate stages would immediately become food for existing living things. The early stages of life included the formation of organic molecules such as carbohydrates, amino acids, or nucleotides. If these were formed from inorganic precursors today, they would simply be broken down by living things. The early stages of life also probably included more complex aggregations of molecules into enclosed structures with an internal environment, a boundary layer of some form, and the external environment. Such structures, if they were formed now, would be quickly consumed or broken down by living organisms.
However, once a mechanism of inheritance was in place in the form of a molecule like DNA or RNA, either within a cell or within a pre-cell, these entities would be subject to the principle of natural selection. More effective reproducers would increase in frequency at the expense of inefficient reproducers. So while evolution does not explain the origin of life, it may have something to say about some of the processes operating once pre-living entities acquired certain properties.
Organisms Evolve on Purpose
Statements such as “organisms evolve in response to a change in an environment,” are quite common. There are two easy misunderstandings possible with such a statement. First of all, the statement must not be understood to mean that individual organisms evolve, as was discussed above. The statement is shorthand for “a population evolves in response to a changing environment.” However, a second misunderstanding may arise by interpreting the statement to mean that the evolution is somehow intentional. A changed environment results in some individuals in the population, those with particular phenotypes, benefiting and, therefore, producing proportionately more offspring than other phenotypes. This results in change in the population if the characters are genetically determined.
It is also important to understand that the variation that natural selection works on is already in a population and does not arise in response to an environmental change. For example, applying antibiotics to a population of bacteria will, over time, select for a population of bacteria that are resistant to antibiotics. The resistance, which is caused by a gene, did not arise by mutation because of the application of the antibiotic. The gene for resistance was already present in the gene pool of the bacteria, likely at a low frequency. The antibiotic, which kills the bacterial cells without the resistance gene, strongly selects for individuals that are resistant, since these would be the only ones that survived and divided. Experiments have demonstrated that mutations for antibiotic resistance do not arise as a result of antibiotic application.
In a larger sense, evolution is also not goal directed. Species do not become “better” over time; they simply track their changing environment with adaptations that maximize their reproduction in a particular environment at a particular time. Evolution has no goal of making faster, bigger, more complex, or even smarter species. This kind of language is common in popular literature. Certain organisms, ourselves included, are described as the “pinnacle” of evolution, or “perfected” by evolution. What characteristics evolve in a species are a function of the variation present and the environment, both of which are constantly changing in a non-directional way. What trait is fit in one environment at one time may well be fatal at some point in the future. This holds equally well for a species of insect as it does the human species.
Evolution Is Controversial among Scientists
The theory of evolution was controversial when it was first proposed in 1859, yet within 20 years virtually every working biologist had accepted evolution as the explanation for the diversity of life. The rate of acceptance was extraordinarily rapid, partly because Darwin had amassed an impressive body of evidence. The early controversies involved both scientific arguments against the theory and the arguments of religious leaders. It was the arguments of the biologists that were resolved after a short time, while the arguments of religious leaders have persisted to this day.
The theory of evolution replaced the predominant theory at the time that species had all been specially created within relatively recent history. Despite the prevalence of this theory, it was becoming increasingly clear to naturalists during the nineteenth century that it could no longer explain many observations of geology and the living world. The persuasiveness of the theory of evolution to these naturalists lay in its ability to explain these phenomena, and it continues to hold extraordinary explanatory power to this day. Its continued rejection by some religious leaders results from its replacement of special creation, a tenet of their religious belief. These leaders cannot accept the replacement of special creation by a mechanistic process that excludes the actions of a deity as an explanation for the diversity of life including the origins of the human species. It should be noted, however, that most of the major denominations in the United States have statements supporting the acceptance of evidence for evolution as compatible with their theologies.
The nature of the arguments against evolution by religious leaders has evolved over time. One current argument is that the theory is still controversial among biologists. This claim is simply not true. The number of working scientists who reject the theory of evolution, or question its validity and say so, is small. A Pew Research poll in 2009 found that 97 percent of the 2500 scientists polled believe species evolve.2 The support for the theory is reflected in signed statements from many scientific societies such as the American Association for the Advancement of Science, which includes working scientists as members. Many of the scientists that reject or question the theory of evolution are non-biologists, such as engineers, physicians, and chemists. There are no experimental results or research programs that contradict the theory. There are no papers published in peer-reviewed scientific journals that appear to refute the theory. The latter observation might be considered a consequence of suppression of dissent, but it must be remembered that scientists are skeptics and that there is a long history of published reports that challenged scientific orthodoxy in unpopular ways. Examples include the endosymbiotic theory of eukaryotic origins, the theory of group selection, the microbial cause of stomach ulcers, the asteroid-impact theory of the Cretaceous extinction, and the theory of plate tectonics. Research with evidence and ideas with scientific merit are considered by the scientific community. Research that does not meet these standards is rejected.
Other Theories Should Be Taught
A common argument from some religious leaders is that alternative theories to evolution should be taught in public schools. Critics of evolution use this strategy to create uncertainty about the validity of the theory without offering actual evidence. In fact, there are no viable alternative scientific theories to evolution. The last such theory, proposed by Lamarck in the nineteenth century, was replaced by the theory of natural selection. A single exception was a research program in the Soviet Union based on Lamarck’s theory during the early twentieth century that set that country’s agricultural research back decades. Special creation is not a viable alternative scientific theory because it is not a scientific theory, since it relies on an untestable explanation. Intelligent design, despite the claims of its proponents, is also not a scientific explanation. This is because intelligent design posits the existence of an unknown designer of living organisms and their systems. Whether the designer is unknown or supernatural, it is a cause that cannot be measured; therefore, it is not a scientific explanation. There are two reasons not to teach nonscientific theories. First, these explanations for the diversity of life lack scientific usefulness because they do not, and cannot, give rise to research programs that promote our understanding of the natural world. Experiments cannot test non-material explanations for natural phenomena. For this reason, teaching these explanations as science in public schools is not in the public interest. Second, in the United States, it is illegal to teach them as science because the U.S. Supreme Court and lower courts have ruled that the teaching of religious belief, such as special creation or intelligent design, violates the establishment clause of the First Amendment of the U.S. Constitution, which prohibits government sponsorship of a particular religion.
The theory of evolution and science in general is, by definition, silent on the existence or non-existence of the spiritual world. Science is only able to study and know the material world. Individual biologists have sometimes been vocal atheists, but it is equally true that there are many deeply religious biologists. Nothing in biology precludes the existence of a god, indeed biology as a science has nothing to say about it. The individual biologist is free to reconcile her or his personal and scientific knowledge as they see fit. The Voices for Evolution project (http://ncse.com/voices), developed through the National Center for Science Education, works to gather the diversity of perspectives on evolution to advocate it being taught in public schools.
Section Summary
The theory of evolution is a difficult concept and misconceptions abound. The factual nature of evolution is often challenged by wrongly associating the scientific meaning of a theory with the vernacular meaning. Evolution is sometimes mistakenly interpreted to mean that individuals evolve, when in fact only populations can evolve as their gene frequencies change over time. Evolution is often assumed to explain the origin of life, which it does not speak to. It is often spoken in goal-directed terms by which organisms change through intention, and selection operates on mutations present in a population that have not arisen in response to a particular environmental stress. Evolution is often characterized as being controversial among scientists; however, it is accepted by the vast majority of working scientists. Critics of evolution often argue that alternative theories to evolution should be taught in public schools; however, there are no viable alternative scientific theories to evolution. The alternative religious beliefs should not be taught as science because it cannot be proven, and in the United States it is unconstitutional. Science is silent on the question of the existence of a god while scientists are able to reconcile religious belief and scientific knowledge.
Footnotes
1. 1 Theodosius Dobzhansky. “Biology, Molecular and Organismic.” American Zoologist 4, no. 4 (1964): 449.
2. 2 Pew Research Center for the People & the Press, Public Praises Science; Scientists Fault Public, Media (Washington, DC, 2009), 37.Contributors | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/21%3A_The_Evidence_for_Evolution/21.07%3A_Darwin%27s_Critics.txt |
Evolution, the unifying theory of biology, describes a mechanism for the change and diversification of species over time.
Learning Objectives
• Describe the historical influences on Darwin’s theory of evolution
Key Points
• Ancient Greeks expressed ideas about evolution, which were reintroduced in the eighteenth century by Georges-Louis Leclerc Comte de Buffon who observed different environments had different plant and animal populations.
• James Hutton proposed that geological changes occur gradually over time via the accumulation of small changes rather than through large catastrophic events.
• Charles Lyell popularized James Hutton’s theory; this theory of incremental change influenced Darwin’s theory of evolution.
• Jean-Baptiste Lamarck proposed the theory of the inheritance of acquired characterstics; this theory has now been discredited, but it served as an important influence on the theory of evolution.
Key Terms
• evolution: the change in the genetic composition of a population over successive generations
• inheritance of acquired characteristics: hypothesis that physiological changes acquired over the life of an organism may be transmitted to its offspring
Introduction: Evolution
All species of living organisms, including bacteria and chimpanzees, evolved at some point from a different species. Although it may seem that living things today stay the same, this is not the case: evolution is a gradual and ongoing process.
The theory of evolution is the unifying theory of biology, meaning it is the framework within which biologists ask questions about the living world. The Ukrainian-born American geneticist Theodosius Dobzhansky famously wrote that “nothing makes sense in biology except in the light of evolution.” The tenet that all species have evolved and diversified from a common ancestor is the foundation from which we approach all questions in biology. It provides a direction for predictions about living things, which has been validated through extensive scientific experimentation.
Evolution by natural selection describes a mechanism for the change of species over time. Well before Darwin began to explore the concept of evolution, the idea that species change over time had already been suggested and debated. The view that species are static and unchanging was grounded in the writings of Plato, yet there were also ancient Greeks who expressed ideas about evolution. During the eighteenth century, ideas about the evolution of animals were reintroduced by the naturalist Georges-Louis Leclerc Comte de Buffon who observed that various geographic regions have different plant and animal populations, even when the environments are similar. It was also accepted that there are extinct species.
During this time, a Scottish naturalist named James Hutton proposed that geological change occurs gradually by the accumulation of small changes over long periods of time. This theory contrasted with the predominant view of the time: that the geology of the planet is a consequence of catastrophic events that occurred during a relatively brief past. During the nineteenth century, Hutton’s views were popularized by the geologist Charles Lyell, who was a friend of Charles Darwin. Lyell’s ideas, in turn, influenced Darwin’s concept of evolution. The greater age of the earth proposed by Lyell supported the gradual evolution that Darwin proposed, and the slow process of geological change provided an analogy for the gradual change in species.
In the early nineteenth century, Jean-Baptiste Lamarck published a book that detailed a different mechanism for evolutionary change. This mechanism is now referred to as an inheritance of acquired characteristics. This idea states that modifications in an individual are caused by its environment, or the use or disuse of a structure during its lifetime, and that these changes can be inherited by its offspring, bringing about change in a species. While this mechanism for evolutionary change was discredited, Lamarck’s ideas were an important influence on the concept of evolution. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/22%3A_The_Origin_of_Species/22.01%3A_The_Nature_of_Species_and_the_Biological_Species_Concept/22.1.01%3A_Understanding_Evolution/22.1.1A%3A_What_is_Evolutio.txt |
Charles Darwin and Alfred Wallace independently developed the theories of evolution and its main operating principle: natural selection.
Learning Objectives
• Explain how natural selection can lead to evolution
Key Points
• Wallace traveled to Brazil to collect and observe insects from the Amazon rainforest.
• Darwin observed that finches in the Galápagos Islands had different beaks than finches in South America; these adaptations equiped the birds to acquire specific food sources.
• Wallace and Darwin observed similar patterns in the variation of organisms and independently developed the same explanation for how such variations could occur over time, a mechanism Darwin called natural selection.
• According to natural selection, also known as “survival of the fittest,” individuals with traits that enable them to survive are more reproductively successful; this leads to those traits becoming predominant within a population.
• Natural selection is an inevitable outcome of three principles: most characteristics are inherited, more offspring are produced than are able to survive, and offspring with more favorable characteristics will survive and have more offspring than those individuals with less favorable traits.
Key Terms
• natural selection: a process in which individual organisms or phenotypes that possess favorable traits are more likely to survive and reproduce
• descent with modification: change in populations over generations
Charles Darwin and Natural Selection
In the mid-nineteenth century, the mechanism for evolution was independently conceived of and described by two naturalists: Charles Darwin and Alfred Russel Wallace. Importantly, each naturalist spent time exploring the natural world on expeditions to the tropics. From 1831 to 1836, Darwin traveled around the world to places like South America, Australia, and the southern tip of Africa. Wallace traveled to Brazil to collect insects in the Amazon rainforest from 1848 to 1852 and to the Malay Archipelago from 1854 to 1862. Darwin’s journey, as with Wallace’s later journeys to the Malay Archipelago, included stops at several island chains, the last being the Galápagos Islands west of Ecuador. On these islands, Darwin observed that species of organisms on different islands were clearly similar, yet had distinct differences. For example, the ground finches inhabiting the Galápagos Islands comprised several species with a unique beak shape. The species on the islands had a graded series of beak sizes and shapes with very small differences between the most similar. He observed that these finches closely resembled another finch species on the mainland of South America. Darwin imagined that the island species might be modified from one of the original mainland species. Upon further study, he realized that the varied beaks of each finch helped the birds acquire a specific type of food. For example, seed-eating finches had stronger, thicker beaks for breaking seeds, while insect-eating finches had spear-like beaks for stabbing their prey.
Natural Selection
Wallace and Darwin observed similar patterns in other organisms and independently developed the same explanation for how and why such changes could take place. Darwin called this mechanism natural selection. Natural selection, also known as “survival of the fittest,” is the more prolific reproduction of individuals with favorable traits that survive environmental change because of those traits. This leads to evolutionary change, the trait becoming predominant within a population. For example, Darwin observed that a population of giant tortoises found in the Galapagos Archipelago have longer necks than those that lived on other islands with dry lowlands. These tortoises were “selected” because they could reach more leaves and access more food than those with short necks. In times of drought, when fewer leaves would be available, those that could reach more leaves had a better chance to eat and survive than those that could not reach the food source. Consequently, long-necked tortoises would more probably be reproductively successful and pass the long-necked trait to their offspring. Over time, only long-necked tortoises would be present in the population.
Natural selection, Darwin argued, was an inevitable outcome of three principles that operated in nature. First, most characteristics of organisms are inherited, or passed from parent to offspring, although how traits were inherited was unknown. Second, more offspring are produced than are able to survive. The capacity for reproduction in all organisms outstrips the availability of resources to support their numbers. Thus, there is competition for those resources in each generation. Both Darwin and Wallace were influenced by an essay written by economist Thomas Malthus who discussed this principle in relation to human populations. Third, Darwin and Wallace reasoned that offspring with the inherited characteristics that allow them to best compete for limited resources will survive and have more offspring than those individuals with variations that are less able to compete. Because characteristics are inherited, these traits will be better represented in the next generation. This will lead to change in populations over successive generations in a process that Darwin called descent with modification. Ultimately, natural selection leads to greater adaptation of the population to its local environment; it is the only mechanism known for adaptive evolution.
Papers by Darwin and Wallace presenting the idea of natural selection were read together in 1858 before the Linnean Society in London. The following year, Darwin’s book, On the Origin of Species, was published. His book outlined his arguments for evolution by natural selection. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/22%3A_The_Origin_of_Species/22.01%3A_The_Nature_of_Species_and_the_Biological_Species_Concept/22.1.01%3A_Understanding_Evolution/22.1.1B%3A_Charles_Darwin_a.txt |
The differences in shape and size of beaks in Darwin’s finches illustrate ongoing evolutionary change.
Learning Objectives
• Describe how finches provide visible evidence of evolution
Key Points
• Darwin observed the Galapagos finches had a graded series of beak sizes and shapes and predicted these species were modified from one original mainland species.
• Darwin called differences among species natural selection, which is caused by the inheritance of traits, competition between individuals, and the variation of traits.
• Offspring with inherited characteristics that allow them to best compete will survive and have more offspring than those individuals with variations that are less able to compete.
• Large-billed finches feed more efficiently on large, hard seeds, whereas smaller billed finches feed more efficiently on small, soft seeds.
• When small, soft seeds become rare, large-billed finches will survive better, and there will be more larger-billed birds in the following generation; when large, hard seeds become rare, the opposite will occur.
Key Terms
• natural selection: a process in which individual organisms or phenotypes that possess favorable traits are more likely to survive and reproduce
• evolution: the change in the genetic composition of a population over successive generations
Visible Evidence of Ongoing Evolution: Darwin’s Finches
From 1831 to 1836, Darwin traveled around the world, observing animals on different continents and islands. On the Galapagos Islands, Darwin observed several species of finches with unique beak shapes. He observed these finches closely resembled another finch species on the mainland of South America and that the group of species in the Galápagos formed a graded series of beak sizes and shapes, with very small differences between the most similar. Darwin imagined that the island species might be all species modified from one original mainland species. In 1860, he wrote, “seeing this gradation and diversity of structure in one small, intimately related group of birds, one might really fancy that from an original paucity of birds in this archipelago, one species had been taken and modified for different ends.”
Natural Selection
Darwin called this mechanism of change natural selection. Natural selection, Darwin argued, was an inevitable outcome of three principles that operated in nature. First, the characteristics of organisms are inherited, or passed from parent to offspring. Second, more offspring are produced than are able to survive; in other words, resources for survival and reproduction are limited. The capacity for reproduction in all organisms exceeds the availability of resources to support their numbers. Thus, there is a competition for those resources in each generation. Third, offspring vary among each other in regard to their characteristics and those variations are inherited. Out of these three principles, Darwin reasoned that offspring with inherited characteristics that allow them to best compete for limited resources will survive and have more offspring than those individuals with variations that are less able to compete. Because characteristics are inherited, these traits will be better represented in the next generation. This will lead to change in populations over generations in a process that Darwin called “descent with modification,” or evolution.
Studies of Natural Selection After Darwin
Demonstrations of evolution by natural selection can be time consuming. Peter and Rosemary Grant and their colleagues have studied Galápagos finch populations every year since 1976 and have provided important demonstrations of the operation of natural selection. The Grants found changes from one generation to the next in the beak shapes of the medium ground finches on the Galápagos island of Daphne Major.
The medium ground finch feeds on seeds. The birds have inherited variation in the bill shape with some individuals having wide, deep bills and others having thinner bills. Large-billed birds feed more efficiently on large, hard seeds, whereas smaller billed birds feed more efficiently on small, soft seeds. During 1977, a drought period altered vegetation on the island. After this period, the number of seeds declined dramatically; the decline in small, soft seeds was greater than the decline in large, hard seeds. The large-billed birds were able to survive better than the small-billed birds the following year.
The year following the drought when the Grants measured beak sizes in the much-reduced population, they found that the average bill size was larger. This was clear evidence for natural selection of bill size caused by the availability of seeds. The Grants had studied the inheritance of bill sizes and knew that the surviving large-billed birds would tend to produce offspring with larger bills, so the selection would lead to evolution of bill size. Subsequent studies by the Grants have demonstrated selection on and evolution of bill size in this species in response to other changing conditions on the island. The evolution has occurred both to larger bills, as in this case, and to smaller bills when large seeds became rare. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/22%3A_The_Origin_of_Species/22.01%3A_The_Nature_of_Species_and_the_Biological_Species_Concept/22.1.01%3A_Understanding_Evolution/22.1.1C%3A_The_Galapagos_Fi.txt |
Natural selection can only occur in the presence of genetic variation; environmental conditions determine which traits are selected.
Learning Objectives
• Explain why only heritable variation can be acted upon by natural selection
Key Points
• Genetic variation within a population is a result of mutations and sexual reproduction.
• A mutation may be neutral, reduce an organism’s fitness, or increase an organism’s fitness.
• An adaptation is a heritable trait that increases the survival and rate of reproduction of an organism in its present environment.
• Divergent evolution describes the process in which two species evolve in diverse directions from a common point.
• Convergent evolution is the process in which similar traits evolve independently in species that do not share a recent common ancestry.
Key Terms
• adaptation: modification of something or its parts that makes it more fit for existence under the conditions of its current environment
• divergent evolution: the process by which a species with similar traits become groups that are tremendously different from each other over many generations
• convergent evolution: a trait of evolution in which species not of similar recent origin acquire similar properties due to natural selection
Variation
Natural selection can only take place if there is variation, or differences, among individuals in a population. Importantly, these differences must have some genetic basis; otherwise, the selection will not lead to change in the next generation. This is critical because variation among individuals can be caused by non-genetic reasons, such as an individual being taller due to better nutrition rather than different genes.
Genetic diversity within a population comes from two main mechanisms: mutation and sexual reproduction. Mutation, a change in the DNA sequence, is the ultimate source of new alleles, or new genetic variation in any population. The genetic changes caused by mutation can have one of three outcomes:
• Many mutations will have no effect on the fitness of the phenotype; these are called neutral mutations.
• A mutation may affect the phenotype of the organism in a way that gives it reduced fitness (a lower likelihood of survival or fewer offspring).
• A mutation may produce a phenotype with a beneficial effect on fitness. Different mutations will have a range of effects on the fitness of an organism that expresses them in their phenotype, from a small effect to a great effect.
Sexual reproduction also leads to genetic diversity: when two parents reproduce, unique combinations of alleles assemble to produce the unique genotypes and thus phenotypes in each of the offspring. However, sexual reproduction can not lead to new genes, but rather provides a new combination of genes in a given individual.
Adaptations
A heritable trait that aids the survival and reproduction of an organism in its present environment is called an adaptation. Scientists describe groups of organisms becoming adapted to their environment when a change in the range of genetic variation occurs over time that increases or maintains the “fitness” of the population to its environment. The webbed feet of platypuses are an adaptation for swimming. The snow leopards’ thick fur is an adaptation for living in the cold. The cheetahs’ fast speed is an adaptation for catching prey.
Whether or not a trait is favorable depends on the environmental conditions at the time. The same traits are not always selected because environmental conditions can change. For example, consider a species of plant that grew in a moist climate and did not need to conserve water. Large leaves were selected because they allowed the plant to obtain more energy from the sun. Large leaves require more water to maintain than small leaves, and the moist environment provided favorable conditions to support large leaves. After thousands of years, the climate changed and the area no longer had excess water. The direction of natural selection shifted so that plants with small leaves were selected because those populations were able to conserve water to survive the new environmental conditions.
The evolution of species has resulted in enormous variation in form and function. Sometimes, evolution gives rise to groups of organisms that become tremendously different from each other. When two species evolve in diverse directions from a common point, it is called divergent evolution. Such divergent evolution can be seen in the forms of the reproductive organs of flowering plants which share the same basic anatomies; however, they can look very different as a result of selection in different physical environments and adaptation to different kinds of pollinators.
In other cases, similar phenotypes evolve independently in distantly-related species. For example, flight has evolved in both bats and insects; they both have structures we refer to as wings, which are adaptations to flight. However, the wings of bats and insects have evolved from very different original structures. This phenomenon is called convergent evolution, where similar traits evolve independently in species that do not share a recent common ancestry. The two species came to the same function, flying, but did so separately from each other.
These physical changes occur over enormous spans of time and help explain how evolution occurs. Natural selection acts on individual organisms, which in turn can shape an entire species. Although natural selection may work in a single generation on an individual, it can take thousands or even millions of years for the genotype of an entire species to evolve. It is over these large time spans that life on earth has changed and continues to change. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/22%3A_The_Origin_of_Species/22.01%3A_The_Nature_of_Species_and_the_Biological_Species_Concept/22.1.01%3A_Understanding_Evolution/22.1.1D%3A_Processes_and_Pa.txt |
Evidence for evolution has been obtained through fossil records, embryology, geography, and molecular biology.
Learning Objectives
• Explain the development of the theory of evolution
Key Points
• Fossils serve to highlight the differences and similarities between current and extinct species, showing the evolution of form over time.
• Similar anatomy across different species highlights their common origin and can be seen in homologous and vestigial structures.
• Embryology provides evidence for evolution since the embryonic forms of divergent groups are extremely similar.
• The natural distribution of species across different continents supports evolution; species that evolved before the breakup of the supercontinent are distributed worldwide, whereas species that evolved more recently are more localized.
• Molecular biology indicates that the molecular basis for life evolved very early and has been maintained with little variation across all life on the planet.
Key Terms
• homologous structure: the traits of organisms that result from sharing a common ancestor; such traits often have similar embryological origins and development
• biogeography: the study of the geographical distribution of living things
• vestigial structure: genetically determined structures or attributes that have apparently lost most or all of their ancestral function in a given species
Evidence of Evolution
The evidence for evolution is compelling and extensive. Looking at every level of organization in living systems, biologists see the signature of past and present evolution. Darwin dedicated a large portion of his book, On the Origin of Species, to identifying patterns in nature that were consistent with evolution. Since Darwin, our understanding has become clearer and broader.
Fossils, Anatomy, and Embryology
Fossils provide solid evidence that organisms from the past are not the same as those found today; they show a progression of evolution. Scientists calculate the age of fossils and categorize them to determine when the organisms lived relative to each other. The resulting fossil record tells the story of the past and shows the evolution of form over millions of years. For example, scientists have recovered highly-detailed records showing the evolution of humans and horses. The whale flipper shares a similar morphology to appendages of birds and mammals, indicating that these species share a common ancestor. Over time, evolution led to changes in the shapes and sizes of these bones in different species, but they have maintained the same overall layout. Scientists call these synonymous parts homologous structures.
Some structures exist in organisms that have no apparent function at all, appearing to be residual parts from a common ancestor. These unused structures (such as wings on flightless birds, leaves on some cacti, and hind leg bones in whales) are vestigial.
Embryology, the study of the development of the anatomy of an organism to its adult form, provides evidence for evolution as embryo formation in widely-divergent groups of organisms tends to be conserved. Structures that are absent in the adults of some groups often appear in their embryonic forms, disappearing by the time the adult or juvenile form is reached. For example, all vertebrate embryos, including humans, exhibit gill slits and tails at some point in their early development. These disappear in the adults of terrestrial groups, but are maintained in adults of aquatic groups, such as fish and some amphibians. Great ape embryos, including humans, have a tail structure during their development that is lost by birth.
Another form of evidence of evolution is the convergence of form in organisms that share similar environments. For example, species of unrelated animals, such as the arctic fox and ptarmigan living in the arctic region, have been selected for seasonal white phenotypes during winter to blend with the snow and ice. These similarities occur not because of common ancestry, but because of similar selection pressures: the benefits of not being seen by predators.
Biogeography
The geographic distribution of organisms on the planet follows patterns that are best explained by evolution in conjunction with the movement of tectonic plates over geological time. Broad groups that evolved before the breakup of the supercontinent Pangaea (about 200 million years ago) are distributed worldwide. Groups that evolved since the breakup appear uniquely in regions of the planet, such as the unique flora and fauna of northern continents that formed from the supercontinent Laurasia compared to that of the southern continents that formed from the supercontinent Gondwana.
The great diversification of marsupials in Australia and the absence of other mammals reflect Australia’s long isolation. Australia has an abundance of endemic species (those found nowhere else) which is typical of islands whose isolation by expanses of water prevents species from migrating. Over time, these species diverge evolutionarily into new species that look very different from their ancestors that may exist on the mainland. The marsupials of Australia, the finches on the Galápagos, and many species on the Hawaiian Islands are all unique to their one point of origin, yet they display distant relationships to ancestral species on mainlands.
Molecular Biology
Like anatomical structures, the structures of the molecules of life reflect descent with modification. Evidence of a common ancestor for all of life is reflected in the universality of DNA as the genetic material, in the near universality of the genetic code, and in the machinery of DNA replication and expression. In general, the relatedness of groups of organisms is reflected in the similarity of their DNA sequences. This is exactly the pattern that would be expected from descent and diversification from a common ancestor.
DNA sequences have also shed light on some of the mechanisms of evolution. For example, it is clear that the evolution of new functions for proteins commonly occurs after gene duplications that allow the free modification of one copy by mutation, selection, or drift (changes in a population ‘s gene pool resulting from chance), while the second copy continues to produce a functional protein. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/22%3A_The_Origin_of_Species/22.01%3A_The_Nature_of_Species_and_the_Biological_Species_Concept/22.1.01%3A_Understanding_Evolution/22.1.1E%3A_Evidence_of_Evol.txt |
There are many misconceptions about evolution, including the meaning of the word theory, the way populations change, and the origin of life.
Learning Objectives
• Discuss misconceptions about the theory of evolution
Key Points
• Attacks on the theory of evolution sometimes take issue with the word “theory”, which in the vernacular means a guess or suggested explanation. In scientific language, “theory” indicates a body of thoroughly-tested and verified explanations for a set of observations of the natural world.
• Evolution does not take place on an individual level; evolution is the average change of a characteristic within an entire population.
• Evolution does not explain the origin of life; the theory of evolution instead explains how populations change over time and how traits are selected in order to increase the fitness of a population.
• Favorable traits do not arise as a result of the environment as these traits are already present; individuals with favorable traits are more likely to survive and, thus, will have greater fitness than individuals with less desirable traits.
• Evolution and natural selection are not synonymous. Natural selection is just one mechanism by which evolution occurs.
Key Terms
• theory: a well-substantiated explanation of some aspect of the natural world based on knowledge that has been repeatedly confirmed through observation and experimentation
Misconceptions of Evolution
Although the theory of evolution generated controversy when it was first proposed, it was almost universally accepted by biologists within 20 years of the publication of On the Origin of Species. Nevertheless, the theory of evolution is a difficult concept and misconceptions about it abound.
Evolution is Just a Theory
Critics of the theory of evolution dismiss its importance by purposefully confounding the everyday usage of the word “theory” with the way scientists use the word. In science, a “theory” is understood to be a body of thoroughly-tested and verified explanations for a set of observations of the natural world. Scientists have a theory of the atom, a theory of gravity, and the theory of relativity, each of which describes understood facts about the world. In the same way, the theory of evolution describes facts about the living world. A theory in science has also survived significant efforts to discredit it by scientists. In contrast, a “theory” in common vernacular is a word meaning a guess or suggested explanation; this meaning is more akin to the scientific concept of “hypothesis. ” When critics of evolution say evolution is “just a theory,” they are implying that there is little evidence supporting it and that it is still in the process of being rigorously tested. This is a mis-characterization.
Individuals Evolve
Evolution is the change in genetic composition of a population over time, specifically over generations, resulting from differential reproduction of individuals with certain alleles. Individuals do change over their lifetime, obviously, but this is called development and involves changes programmed by the set of genes the individual acquired at birth in coordination with the individual’s environment. When thinking about the evolution of a characteristic, it is probably best to think about the change of the average value of the characteristic in the population over time. For example, when natural selection leads to bill-size change in medium-ground finches in the Galápagos, this does not mean that individual bills on the finches are changing. If one measures the average bill size among all individuals in the population at one time and then measures the average bill size in that population several years later, this average value of the population will be different as a result of evolution.
Evolution Explains the Origin of Life
It is a common misunderstanding that evolution includes an explanation of life’s origins. The theory of evolution explains how populations change over time. It does not shed light on the beginnings of life, including the origins of the first cells, which is how life is defined. The mechanisms of the origin of life on earth are a particularly difficult problem because it occurred a very long time ago and, presumably, it occurred just once. However, while evolution does not explain the origin of life, it may have something to say about some of the processes operating once pre-living entities acquired certain properties. Once a mechanism of inheritance was in place in the form of a molecule like DNA, either within a cell or pre-cell, these entities would be subject to the principle of natural selection. More effective reproducers would increase in frequency at the expense of inefficient reproducers.
Organisms Evolve on Purpose
Statements such as “organisms evolve in response to a change in an environment” may lead to the misunderstanding that evolution is somehow intentional. A changed environment results in some individuals in the population, those with particular phenotypes, benefiting and, therefore, producing proportionately more offspring than other phenotypes. This results in change in the population if the characteristics are genetically determined.
It is important to understand that the variation that natural selection works on is already present in a population and does not arise in response to an environmental change. For example, applying antibiotics to a population of bacteria will, over time, select a population of bacteria that are resistant to antibiotics. The resistance, which is caused by a gene, did not arise by mutation because of the application of the antibiotic. The gene for resistance was already present in the gene pool of the bacteria, probably at a low frequency. The antibiotic, which kills the bacterial cells without the resistance gene, strongly selects individuals that are resistant, since these would be the only ones that survived and divided. Experiments have demonstrated that mutations for antibiotic resistance do not arise as a result of antibiotics.
In a larger sense, evolution is not goal directed. Species do not become “better” over time; they track their changing environment with adaptations that maximize their reproduction. The characteristics that evolve in a species are a function of preexisting variation and the environment, both of which are constantly changing non-directionally. A trait that is fit in one environment at one time may also be fatal at some point in the future.
Evolution = Natural Selection
The terms “evolution” and “natural selection” are often conflated, as the two concepts are closely related. They are not, however, synonymous. Natural selection refers to the process by which organisms better suited for their environment are more likely to survive and produce offspring, thereby proliferating those favorable genetics in a population. Evolution is defined more broadly as any change in the genetic makeup of a population over time. As expounded by Darwin, natural selection is a major driving force of evolution, but it is not the only one.
Genetic drift, for example, is another mechanism by which evolution may occurs. Genetic drift occurs when allelic frequency is altered due to random sampling. It is evolution by chance, and the smaller the population, the more significant the effects on genetic distribution due to sampling error. For example, a population bottleneck, which occurs when an event such as a natural disaster dramatically reduces the size of a population, can result in the elimination or significant reduction of a trait within a population, regardless of how beneficial that trait may be to survival or reproduction. Thus evolution can occur without natural selection. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/22%3A_The_Origin_of_Species/22.01%3A_The_Nature_of_Species_and_the_Biological_Species_Concept/22.1.01%3A_Understanding_Evolution/22.1.1F%3A_Misconceptions_o.txt |
A species is defined as a group of individuals that, in nature, are able to mate and produce viable, fertile offspring.
Learning Objectives
• Explain the biological species concept
Key Points
• Members of the same species are similar both in their external appearance and their internal physiology; the closer the relationship between two organisms, the more similar they will be in these features.
• Some species can look very dissimilar, such as two very different breeds of dogs, but can still mate and produce viable offspring, which signifies that they belong to the same species.
• Some species may look very similar externally, but can be dissimilar enough in their genetic makeup that they cannot produce viable offspring and are, therefore, different species.
• Mutations can occur in any cell of the body, but if a change does not occur in a sperm or egg cell, it cannot be passed on to the organism’s offspring.
Key Terms
• species: a group of organsms that, in nature, are capable of mating and producing viable, fertile offspring
• hybrid: offspring resulting from cross-breeding different entities, e.g. two different species or two purebred parent strains
• gene pool: the complete set of unique alleles that would be found by inspecting the genetic material of every living member of a species or population
Species and the Ability to Reproduce
A species is a group of individual organisms that interbreed and produce fertile, viable offspring. According to this definition, one species is distinguished from another when, in nature, it is not possible for matings between individuals from each species to produce fertile offspring.
Members of the same species share both external and internal characteristics which develop from their DNA. The closer relationship two organisms share, the more DNA they have in common, just like people and their families. People’s DNA is likely to be more like their father or mother’s DNA than their cousin’s or grandparent’s DNA. Organisms of the same species have the highest level of DNA alignment and, therefore, share characteristics and behaviors that lead to successful reproduction.
Species’ appearance can be misleading in suggesting an ability or inability to mate. For example, even though domestic dogs (Canis lupus familiaris) display phenotypic differences, such as size, build, and coat, most dogs can interbreed and produce viable puppies that can mature and sexually reproduce.
In other cases, individuals may appear similar although they are not members of the same species. For example, even though bald eagles (Haliaeetus leucocephalus) and African fish eagles (Haliaeetus vocifer) are both birds and eagles, each belongs to a separate species group. If humans were to artificially intervene and fertilize the egg of a bald eagle with the sperm of an African fish eagle and a chick did hatch, that offspring, called a hybrid (a cross between two species), would probably be infertile: unable to successfully reproduce after it reached maturity. Different species may have different genes that are active in development; therefore, it may not be possible to develop a viable offspring with two different sets of directions. Thus, even though hybridization may take place, the two species still remain separate.
Populations of species share a gene pool: a collection of all the variants of genes in the species. Again, the basis to any changes in a group or population of organisms must be genetic for this is the only way to share and pass on traits. When variations occur within a species, they can only be passed to the next generation along two main pathways: asexual reproduction or sexual reproduction. The change will be passed on asexually simply if the reproducing cell possesses the changed trait. For the changed trait to be passed on by sexual reproduction, a gamete, such as a sperm or egg cell, must possess the changed trait. In other words, sexually-reproducing organisms can experience several genetic changes in their body cells, but if these changes do not occur in a sperm or egg cell, the changed trait will never reach the next generation. Only heritable traits can evolve. Therefore, reproduction plays a paramount role for genetic change to take root in a population or species. In short, organisms must be able to reproduce with each other to pass new traits to offspring. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/22%3A_The_Origin_of_Species/22.01%3A_The_Nature_of_Species_and_the_Biological_Species_Concept/22.1.02%3A_Formation_of_New_Species/22.1.2A%3A_The_Biological_.txt |
Reproductive isolation, through mechanical, behavioral, and physiological barriers, is an important component of speciation.
Learning Objectives
• Explain how reproductive isolation can result in speciation
Key Points
• Reproductive isolation can be either prezygotic (barriers that prevent fertilization ) or postzygotic (barriers that occur after zygote formation such as organisms that die as embryos or those that are born sterile).
• Some species may be prevented from mating with each other by the incompatibility of their anatomical mating structures, or a resulting offspring may be prevented by the incompatibility of their gametes.
• Postzygotic barriers include the creation of hybrid individuals that do not survive past the embryonic stages ( hybrid inviability ) or the creation of a hybrid that is sterile and unable to produce offspring ( hybrid sterility ).
• Temporal isolation can result in species that are physically similar and may even live in the same habitat, but if their breeding schedules do not overlap then interbreeding will never occur.
• Behavioral isolation, in which the behaviors involved in mating are so unique as to prevent mating, is a prezygotic barrier that can cause two otherwise-compatible species to be uninterested in mating with each other.
• Behavioral isolation, in which the behaviors involved in mating are so unique as to prevent mating, is a prezygotic barrier that can cause two otherwise compatible species to be uninterested in mating with each other.
Key Terms
• reproductive isolation: a collection of mechanisms, behaviors, and physiological processes that prevent two different species that mate from producing offspring, or which ensure that any offspring produced is not fertile
• temporal isolation: factors that prevent potentially fertile individuals from meeting that reproductively isolate the members of distinct species
• behavioral isolation: the presence or absence of a specific behavior that prevents reproduction between two species from taking place
• prezygotic barrier: a mechanism that blocks reproduction from taking place by preventing fertilization
• postzygotic barrier: a mechanism that blocks reproduction after fertilization and zygote formation
• hybrid inviability: a situation in which a mating between two individuals creates a hybrid that does not survive past the embryonic stages
• hybrid sterility: a situation in which a mating between two individuals creates a hybrid that is sterile
Reproductive Isolation
Given enough time, the genetic and phenotypic divergence between populations will affect characters that influence reproduction: if individuals of the two populations were to be brought together, mating would be improbable, but if mating did occur, offspring would be non-viable or infertile. Many types of diverging characters may affect reproductive isolation, the ability to interbreed, of the two populations. Reproductive isolation is a collection of mechanisms, behaviors, and physiological processes that prevent the members of two different species that cross or mate from producing offspring, or which ensure that any offspring that may be produced is not fertile.
Scientists classify reproductive isolation in two groups: prezygotic barriers and postzygotic barriers. Recall that a zygote is a fertilized egg: the first cell of the development of an organism that reproduces sexually. Therefore, a prezygotic barrier is a mechanism that blocks reproduction from taking place; this includes barriers that prevent fertilization when organisms attempt reproduction. A postzygotic barrier occurs after zygote formation; this includes organisms that don’t survive the embryonic stage and those that are born sterile.
Some types of prezygotic barriers prevent reproduction entirely. Many organisms only reproduce at certain times of the year, often just annually. Differences in breeding schedules, called temporal isolation, can act as a form of reproductive isolation. For example, two species of frogs inhabit the same area, but one reproduces from January to March, whereas the other reproduces from March to May.
In some cases, populations of a species move to a new habitat and take up residence in a place that no longer overlaps with other populations of the same species; this is called habitat isolation. Reproduction with the parent species ceases and a new group exists that is now reproductively and genetically independent. For example, a cricket population that was divided after a flood could no longer interact with each other. Over time, the forces of natural selection, mutation, and genetic drift will likely result in the divergence of the two groups.
Behavioral isolation occurs when the presence or absence of a specific behavior prevents reproduction from taking place. For example, male fireflies use specific light patterns to attract females. Various species display their lights differently; if a male of one species tried to attract the female of another, she would not recognize the light pattern and would not mate with the male.
Other prezygotic barriers work when differences in their gamete cells prevent fertilization from taking place; this is called a gametic barrier. Similarly, in some cases, closely-related organisms try to mate, but their reproductive structures simply do not fit together. For example, damselfly males of different species have differently-shaped reproductive organs. If one species tries to mate with the female of another, their body parts simply do not fit together..
In plants, certain structures aimed to attract one type of pollinator simultaneously prevent a different pollinator from accessing the pollen. The tunnel through which an animal must access nectar can vary in length and diameter, which prevents the plant from being cross-pollinated with a different species.
When fertilization takes place and a zygote forms, postzygotic barriers can prevent reproduction. Hybrid individuals in many cases cannot form normally in the womb and simply do not survive past the embryonic stages; this is called hybrid inviability. In another postzygotic situation, reproduction leads to the birth and growth of a hybrid that is sterile and unable to reproduce offspring of their own; this is called hybrid sterility. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/22%3A_The_Origin_of_Species/22.01%3A_The_Nature_of_Species_and_the_Biological_Species_Concept/22.1.02%3A_Formation_of_New_Species/22.1.2B%3A_Reproductive_Is.txt |
Speciation is an event in which a single species may branch to form two or more new species.
Learning Objectives
• Define speciation and discuss the ways in which it may occur
Key Points
• For the majority of species, the definition of a species is a group of animals that can potentially interbreed, although some different species are capable of producing hybrid offspring.
• Darwin was the first to envision speciation as the branching of two or more new species from one ancestral species; indicated by a diagram he made that bears a striking resemblance to modern-day phylogenetic diagrams.
• For a new species to be formed from an old species, certain events or changes must occur such that the new population is no longer capable of interbreeding with the old one.
• Speciation can occur either through allopatric speciation, when a population is geographically separated from one another, or through sympatric speciation, in which the two new species are not geographically separated.
• Speciation, the formation of two species from one original species, occurs as one species changes over time and branches to form more than one new species.
Key Terms
• sympatric: living in the same territory without interbreeding
• allopatric: not living in the same territory; geographically isolated and thus unable to crossbreed
• speciation: the process by which new distinct species evolve
Speciation
The biological definition of species, which works for sexually-reproducing organisms, is a group of actually or potentially interbreeding individuals. There are exceptions to this rule. Many species are similar enough that hybrid offspring are possible and may often occur in nature, but for the majority of species this rule generally holds. In fact, the presence in nature of hybrids between similar species suggests that they may have descended from a single interbreeding species: the speciation process may not yet be completed.
Given the extraordinary diversity of life on the planet, there must be mechanisms for speciation: the formation of two species from one original species. Darwin envisioned this process as a branching event and diagrammed the process in the only illustration found in On the Origin of Species, which bears some resemblance to the more modern phylogenetic diagram of elephant evolution. The diagram shows that as one species changes over time, it branches repeatedly to form more than one new species as long as the population survives or until the organism becomes extinct.
For speciation to occur, two new populations must be formed from one original population; they must evolve in such a way that it becomes impossible for individuals from the two new populations to interbreed. Biologists have proposed mechanisms by which this could occur that fall into two broad categories: allopatric speciation and sympatric speciation. Allopatric speciation (allo- = “other”; -patric = “homeland”) involves geographic separation of populations from a parent species and subsequent evolution. Sympatric speciation (sym- = “same”; -patric = “homeland”) involves speciation occurring within a parent species remaining in one location.
Biologists think of speciation events as the splitting of one ancestral species into two descendant species. There is no reason why there might not be more than two species formed at one time except that it is less likely; multiple events can be conceptualized as single splits occurring close in time. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/22%3A_The_Origin_of_Species/22.01%3A_The_Nature_of_Species_and_the_Biological_Species_Concept/22.1.02%3A_Formation_of_New_Species/22.1.2C%3A_Speciation.txt |
Allopatric speciation occurs when a single species becomes geographically separated; each group evolves new and distinctive traits.
Learning Objectives
• Give examples of allopatric speciation
Key Points
• When a population is geographically continuous, the allele frequencies among its members are similar; however, when a population becomes separated, the allele frequencies between the two groups can begin to vary.
• If the separation between groups continues for a long period of time, the differences between their alleles can become more and more pronounced due to differences in climate, predation, food sources, and other factors, eventually leading to the formation of a new species.
• Geographic separation between populations can occur in many ways; the severity of the separation depends on the travel capabilities of the species.
• Allopatric speciation events can occur either by dispersal, when a few members of a species move to a new geographical area, or by vicariance, when a natural situation, such as the formation of a river or valley, physically divide organisms.
• When a population disperses throughout an area, into new, different and often isolated habitats, multiple speciation events can occur in which the single original species gives rise to many new species; this phenomenon is called adaptive radiation.
Key Terms
• vicariance: the separation of a group of organisms by a geographic barrier, resulting in differentiation of the original group into new varieties or species
• adaptive radiation: the diversification of species into separate forms that each adapt to occupy a specific environmental niche
• dispersal: the movement of a few members of a species to a new geographical area, resulting in differentiation of the original group into new varieties or species
Allopatric Speciation
A geographically-continuous population has a gene pool that is relatively homogeneous. Gene flow, the movement of alleles across the range of the species, is relatively free because individuals can move and then mate with individuals in their new location. Thus, the frequency of an allele at one end of a distribution will be similar to the frequency of the allele at the other end. When populations become geographically discontinuous, that free-flow of alleles is prevented. When that separation continues for a period of time, the two populations are able to evolve along different trajectories. This is known as allopatric speciation. Thus, their allele frequencies at numerous genetic loci gradually become more and more different as new alleles independently arise by mutation in each population. Typically, environmental conditions, such as climate, resources, predators, and competitors for the two populations will differ causing natural selection to favor divergent adaptations in each group.
Isolation of populations leading to allopatric speciation can occur in a variety of ways: a river forming a new branch, erosion forming a new valley, a group of organisms traveling to a new location without the ability to return, or seeds floating over the ocean to an island. The nature of the geographic separation necessary to isolate populations depends entirely on the biology of the organism and its potential for dispersal. If two flying insect populations took up residence in separate nearby valleys, chances are individuals from each population would fly back and forth, continuing gene flow. However, if two rodent populations became divided by the formation of a new lake, continued gene flow would be improbable; therefore, speciation would be probably occur.
Biologists group allopatric processes into two categories: dispersal and vicariance. Dispersal occurs when a few members of a species move to a new geographical area, while vicariance occurs when a natural situation arises to physically divide organisms.
Scientists have documented numerous cases of allopatric speciation. For example, along the west coast of the United States, two separate sub-species of spotted owls exist. The northern spotted owl has genetic and phenotypic differences from its close relative, the Mexican spotted owl, which lives in the south.
Additionally, scientists have found that the further the distance between two groups that once were the same species, the more probable it is that speciation will occur. This seems logical because as the distance increases, the various environmental factors would generally have less in common than locations in close proximity. Consider the two owls: in the north, the climate is cooler than in the south causing the types of organisms in each ecosystem differ, as do their behaviors and habits. Also, the hunting habits and prey choices of the southern owls vary from the northern owls. These variances can lead to evolved differences in the owls, resulting in speciation.
Adaptive Radiation
In some cases, a population of one species disperses throughout an area with each finding a distinct niche or isolated habitat. Over time, the varied demands of their new lifestyles lead to multiple speciation events originating from a single species. This is called adaptive radiation because many adaptations evolve from a single point of origin, causing the species to radiate into several new ones. Island archipelagos like the Hawaiian Islands provide an ideal context for adaptive radiation events because water surrounds each island which leads to geographical isolation for many organisms. The Hawaiian honeycreeper illustrates one example of adaptive radiation. From a single species, called the founder species, numerous species have evolved.
In Hawaiian honeycreepers, the response to natural selection based on specific food sources in each new habitat led to the evolution of a different beak suited to the specific food source. The seed-eating birds have a thicker, stronger beak which is suited to break hard nuts. The nectar-eating birds have long beaks to dip into flowers to reach the nectar. The insect-eating birds have beaks like swords, appropriate for stabbing and impaling insects. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/22%3A_The_Origin_of_Species/22.01%3A_The_Nature_of_Species_and_the_Biological_Species_Concept/22.1.02%3A_Formation_of_New_Species/22.1.2D%3A_Allopatric_Spec.txt |
Sympatric speciation occurs when two individual populations diverge from an ancestral species without being separated geographically.
Learning Objectives
• Give examples of sympatric speciation
Key Points
• Sympatric speciation can occur when one individual develops an abnormal number of chromosomes, either extra chromosomes ( polyploidy ) or fewer, such that viable interbreeding can no longer occur.
• When the extra sets of chromosomes in a polyploid originate with the individual because their own gametes do not undergo cytokinesis after meiosis, the result is autopolyploidy.
• When individuals of two different species reproduce to form a viable offspring, such that the extra chromosomes come from two different species, the result is an allopolyploid.
• Once a species develops an abnormal number of chromosomes, it can then only interbreed with members of the population that have the same abnormal number, which can lead to the development of a new species.
Key Terms
• sympatric speciation: the process through which new species evolve from a single ancestral species while inhabiting the same geographic region
• autopolyploid: having more than two sets of chromosomes, derived from the same species, as a result of redoubling
• allopolyploid: having multiple complete sets of chromosomes derived from different species
Sympatric Speciation
Can divergence occur if no physical barriers are in place to separate individuals who continue to live and reproduce in the same habitat? The answer is yes. The process of speciation within the same space is called sympatric speciation. The prefix “sym” means same, so “sympatric” means “same homeland” in contrast to “allopatric” meaning “other homeland.” A number of mechanisms for sympatric speciation have been proposed and studied.
One form of sympatric speciation can begin with a serious chromosomal error during cell division. In a normal cell division event, chromosomes replicate, pair up, and then separate so that each new cell has the same number of chromosomes. However, sometimes the pairs separate and the end cell product has too many or too few individual chromosomes in a condition called aneuploidy.
Polyploidy is a condition in which a cell or organism has an extra set, or sets, of chromosomes. Scientists have identified two main types of polyploidy that can lead to reproductive isolation, or the inability to interbreed with normal individuals, of an individual in the polyploidy state. In some cases, a polyploid individual will have two or more complete sets of chromosomes from its own species in a condition called autopolyploidy. The prefix “auto-” means “self,” so the term means multiple chromosomes from one’s own species. Polyploidy results from an error in meiosis in which all of the chromosomes move into one cell instead of separating.
For example, if a plant species with 2n = 6 produces autopolyploid gametes that are also diploid (2n = 6, when they should be n = 3), the gametes now have twice as many chromosomes as they should have. These new gametes will be incompatible with the normal gametes produced by this plant species. However, they could either self-pollinate or reproduce with other autopolyploid plants with gametes having the same diploid number. In this way, sympatric speciation can occur quickly by forming offspring with 4n: a tetraploid. These individuals would immediately be able to reproduce only with those of this new kind and not those of the ancestral species.
The other form of polyploidy occurs when individuals of two different species reproduce to form a viable offspring called an allopolyploid. The prefix “allo-” means “other” (recall from allopatric). Therefore, an allopolyploid occurs when gametes from two different species combine. Notice how it takes two generations, or two reproductive acts, before the viable fertile hybrid results.
The cultivated forms of wheat, cotton, and tobacco plants are all allopolyploids. Although polyploidy occurs occasionally in animals, it takes place most commonly in plants. (Animals with any of the types of chromosomal aberrations described here are unlikely to survive and produce normal offspring. ) Scientists have discovered more than half of all plant species studied relate back to a species evolved through polyploidy. With such a high rate of polyploidy in plants, some scientists hypothesize that this mechanism takes place more as an adaptation than as an error. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/22%3A_The_Origin_of_Species/22.01%3A_The_Nature_of_Species_and_the_Biological_Species_Concept/22.1.02%3A_Formation_of_New_Species/22.1.2E%3A_Sympatric_Speci.txt |
Over time, two species may further diverge or reconnect, depending on the fitness strength and the reproductive barriers of the hybrids.
Learning Objectives
• Discuss how the fitness of a hybrid will lead to changes in the hybrid zone over time
Key Points
• After speciation, or sufficient evolutionary change for one species to become two distinct species, the two species may continue to co-habitate and interact.
• The area in which two closely-related species interact and reproduce is known as the hybrid zone; their offspring are known as hybrids.
• Depending on the fitness of the hybrid offspring relative to the parents, the two species may either stay as two distinct species (reinforcement), or become one species again ( reconnection ).
Key Terms
• hybrid zone: an area where the ranges of two interbreeding species meet and interbreed
• hybrid speciation: the formation of a new species as the direct result of mating between members of two existing species
• reconnection: a convergence of two species over time
Reconnection After Speciation
Speciation occurs over a span of evolutionary time. When a new species arises, there is a transition period during which the closely-related species continue to interact.
After speciation, two species may recombine or even continue interacting indefinitely. Individual organisms will mate with any nearby individual with which they are capable of breeding. An area where two closely-related species continue to interact and reproduce, forming hybrids, is called a hybrid zone. Over time, the hybrid zone may change depending on the fitness strength and the reproductive barriers of the hybrids.
Hybrids can have less fitness, more fitness, or about the same fitness level as the purebred parents. Usually, hybrids tend to be less fit; therefore, reproduction to produce hybrids will diminish over time, which nudges the two species to diverge further in a process called reinforcement. This term is used because the low success of the hybrids reinforces the original speciation. If the hybrids are less fit than the parents, reinforcement of speciation occurs, and the species will continue to diverge until they can no longer mate and produce viable offspring.
If the hybrids are as fit or more fit than the parents, or the reproductive barriers weaken, the two species may fuse back into one species (reconnection). For a hybrid form to persist, it will generally have to be able to exploit the available resources better than either parent species, with which, in most cases, it will have to compete.
Over time, via a process called hybrid speciation, the hybrids themselves can become a separate species. Reproductive isolation between hybrids and their parents was once thought to be particularly difficult to achieve; thus, hybrid species were thought to be extremely rare. With DNA analysis becoming more accessible in the 1990s, hybrid speciation has been shown to be a fairly common phenomenon, particularly in plants.
Scientists have also observed that sometimes two species will remain separate, but continue to interact to produce some hybrid individuals; this is classified as stability because no real net change is taking place. For a hybrid zone to be stable, the offspring produced by the hybrids have to be less fit than members of the parent species.
22.1.3B: Var
Two patterns are currently observed in the rates of speciation: gradual speciation and punctuated equilibrium.
Learning Objectives
• Explain how the interaction of an organism’s population size in association with environmental changes can lead to different rates of speciation
Key Points
• In the gradual speciation model, species diverge slowly over time in small steps while in the punctuated equilibrium model, a new species diverges rapidly from the parent species.
• The two key influencing factors on the change in speciation rate are the environmental conditions and the population size.
• Gradual speciation is most likely to occur in large populations that live in a stable environment, while the punctuation equilibrium model is more likely to occur in a small population with rapid environmental change.
Key Terms
• punctuated equilibrium: a theory of evolution holding that evolutionary change tends to be characterized by long periods of stability, with infrequent episodes of very fast development
• gradualism: in evolutionary biology, belief that evolution proceeds at a steady pace, without the sudden development of new species or biological features from one generation to the next
Varying Rates of Speciation
Scientists around the world study speciation, documenting observations both of living organisms and those found in the fossil record. As their ideas take shape and as research reveals new details about how life evolves, they develop models to help explain rates of speciation. In terms of how quickly speciation occurs, two patterns are currently observed: the gradual speciation model and the punctuated equilibrium model.
In the gradual speciation model, species diverge gradually over time in small steps. In the punctuated equilibrium model, a new species changes quickly from the parent species and then remains largely unchanged for long periods of time afterward. This early change model is called punctuated equilibrium, because it begins with a punctuated or periodic change and then remains in balance afterward. While punctuated equilibrium suggests a faster tempo, it does not necessarily exclude gradualism.
The primary influencing factor on changes in speciation rate is environmental conditions. Under some conditions, selection occurs quickly or radically. Consider a species of snails that had been living with the same basic form for many thousands of years. Layers of their fossils would appear similar for a long time. When a change in the environment takes place, such as a drop in the water level, a small number of organisms are separated from the rest in a brief period of time, essentially forming one large and one tiny population. The tiny population faces new environmental conditions. Because its gene pool quickly became so small, any variation that surfaces and that aids in surviving the new conditions becomes the predominant form. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/22%3A_The_Origin_of_Species/22.01%3A_The_Nature_of_Species_and_the_Biological_Species_Concept/22.1.03%3A_Hybrid_Zones_and_Rates_of_Speciation/22.1.3A%3A_Hyb.txt |
Genomic similarities between distant species can be established via analysis of genomes using advanced technology.
Learning Objectives
• Discuss the evolutionary implications of observed genome similarities between distant species
Key Points
• Genomic similarities between distant species can be explained by the theory that all organisms share a common ancestor.
• Genomic similarities between distant species can be analysed using genomic analysis tools to create phylogenetic trees that explain these relationships.
• Genetic distance is used to explain the genetic divergence between species or between populations within a species and can indicate how closely related they are and whether they have a recent common ancestor or recent interbreeding has taken place.
• Horizontal gene transfer (HGT) occurs when two unrelated species exchange genes, usually two prokaryotes, although HGT occurs in some eurokaryotes as well.
Key Terms
• conjugation: the temporary fusion of organisms, especially as part of sexual reproduction
• phylogeny: the evolutionary history of an organism
• horizontal gene transfer: the transfer of genetic material from one organism to another one that is not its offspring; especially common among bacteria
• transformation: the alteration of a bacterial cell caused by the transfer of DNA from another, especially if pathogenic
• transduction: horizontal gene transfer mechanism in prokaryotes where genes are transferred using a virus
Genomic Similarities Between Distant Species
Genetic distance refers to the genetic divergence between species or between populations within a species. Smaller genetic distances indicate that the populations have more similar genes, which indicates they are closely related; they have a recent common ancestor, or recent interbreeding has taken place. Genetic distance is useful in reconstructing the history of populations. For example, evidence from genetic distance suggests that humans arrived in America about 30,000 years ago. By examining the difference between allele frequencies between the populations, genetic distance can estimate how long ago the two populations were together.
Phylogenetic Relationships
Phylogeny describes the relationships of an organism, such as the relationship with its ancestors and the species it is most closely related. Phylogenetic relationships provide information on shared ancestry but not necessarily on how organisms are similar or different. The use of advanced genomic analysis has allowed us to establish phylogenetic trees, which map the relationship between species at a genetic and molecular level. The ability to use these technologies has established previously unknown relationships and has contributed to a more complex evolutionary history. These technologies have established genomic similarities between distant species by establishing genetic distances. In addition, the mechanisms by which genomic similarities between distant species occur can include horizontal gene transfer.
Horizontal Gene Transfer
Horizontal gene transfer (HGT), also known as lateral gene transfer, is the transfer of genes between unrelated species. Genes have been shown to be passed between species which are only distantly related using standard phylogeny, thus adding a layer of complexity to the understanding of phylogenetic relationships. The various ways that HGT occurs in prokaryotes is important to understanding phylogenies. Although at present, HGT is not viewed as important to eukaryotic evolution, HGT does occur in this domain as well. Finally, as an example of the ultimate gene transfer, theories of genome fusion between symbiotic or endosymbiotic organisms have been proposed to explain an event of great importance—the evolution of the first eukaryotic cell, without which humans could not have come into existence.
The mechanism of HGT has been shown to be quite common in the prokaryotic domains of Bacteria and Archaea, significantly changing the way their evolution is viewed. The majority of evolutionary models, such as in the endosymbiont theory, propose that eukaryotes descended from multiple prokaryotes, which makes HGT all the more important to understanding the phylogenetic relationships of all extant and extinct species. These gene transfers between species are the major mechanism whereby bacteria acquire resistance to antibiotics. Classically, this type of transfer has been thought to occur by three different mechanisms: transformation, transduction and conjugation.
Although it is easy to see how prokaryotes exchange genetic material by HGT, it was initially thought that this process was absent in eukaryotes, followed by the idea that the gene transfers between multicellular eukaryotes should be more difficult. In spite of this fact, HGT between distantly related organisms has been demonstrated in several eukaryotic species.
In animals, a particularly interesting example of HGT occurs within the aphid species. Aphids are insects that vary in color based on carotenoid content. Carotenoids are pigments made by a variety of plants, fungi, and microbes, and they serve a variety of functions in animals, who obtain these chemicals from their food. Humans require carotenoids to synthesize vitamin A, and we obtain them by eating orange fruits and vegetables: carrots, apricots, mangoes, and sweet potatoes. On the other hand, aphids have acquired the ability to make the carotenoids on their own. According to DNA analysis, this ability is due to the transfer of fungal genes into the insect by HGT, presumably as the insect consumed fungi for food. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/22%3A_The_Origin_of_Species/22.01%3A_The_Nature_of_Species_and_the_Biological_Species_Concept/22.1.04%3A_Evolution_of_Genomes/22.1.4A%3A_Genomic_Similiariti.txt |
Processes such as mutations, duplications, exon shuffling, transposable elements and pseudogenes have contributed to genomic evolution.
Learning Objectives
• Explain the importance of genomic changes in an evolutionary context
Key Points
• Gene and whole genome duplications have contributed accumulations that have contributed to genome evolution.
• Mutations are constantly occurring in an organism’s genome and can cause either a negative effect, positive effect or no effect at all; however, it will still result in changes to the genome.
• Transposable elements are regions of DNA that can be inserted into the genetic code and will causes changes within the genome.
• Pseudogenes are dysfunctional genes derived from previously functional gene relatives and will become a pseudogene by deletion or insertion of one or multiple nucleotides.
• Exon shuffling occurs when two or more exons from different genes are combined together or when exons are duplicated, and will result in new genes.
• Species can also exhibit genome reduction when subsets of their genes are not needed anymore.
Key Terms
• intron: a portion of a split gene that is included in pre-RNA transcripts but is removed during RNA processing and rapidly degraded
• exon: a region of a transcribed gene present in the final functional RNA molecule
• pseudogene: a segment of DNA that is part of the genome of an organism, and which is similar to a gene but does not code for a gene product
Accumulating Changes Over Time
The evolution of the genome is characterized by the accumulation of changes. The analaysis of genomes and their changes in sequence or size over time involves various fields. There are various mechanisms that have contributed to genome evolution and these include gene and genome duplications, polyploidy, mutation rates, transposable elements, pseudogenes, exon shuffling and genomic reduction and gene loss. The concepts of gene and whole-genome duplication are discussed as their own independent concepts, thus, the focus will be on other mechanisms.
Mutation Rates
Mutation rates differ between species and even between different regions of the genome of a single species. Spontaneous mutations often occur which can cause various changes in the genome. Mutations can result in the addition or deletion of one or more nucleotide bases. A change in the code can result in a frameshift mutation which causes the entire code to be read in the wrong order and thus often results in a protein becoming non-functional. A mutation in a promoter region, enhancer region or a region coding for transcription factors can also result in either a loss of function or and upregulation or downregulation in transcription of that gene. Mutations are constantly occurring in an organism’s genome and can cause either a negative effect, positive effect or no effect at all.
Transposable Elements
Transposable elements are regions of DNA that can be inserted into the genetic code through one of two mechanisms. These mechanisms work similarly to “cut-and-paste” and “copy-and-paste” functionalities in word processing programs. The “cut-and-paste” mechanism works by excising DNA from one place in the genome and inserting itself into another location in the code. The “copy-and-paste” mechanism works by making a genetic copy or copies of a specific region of DNA and inserting these copies elsewhere in the code. The most common transposable element in the human genome is the Alu sequence, which is present in the genome over one million times.
Pseudogenes
Often a result of spontaneous mutation, pseudogenes are dysfunctional genes derived from previously functional gene relatives. There are many mechanisms by which a functional gene can become a pseudogene including the deletion or insertion of one or multiple nucleotides. This can result in a shift of reading frame, causing the gene to longer code for the expected protein, a premature stop codon or a mutation in the promoter region. Often cited examples of pseudogenes within the human genome include the once functional olfactory gene families. Over time, many olfactory genes in the human genome became pseudogenes and were no longer able to produce functional proteins, explaining the poor sense of smell humans possess in comparison to their mammalian relatives.
Exon Shuffling
Exon shuffling is a mechanism by which new genes are created. This can occur when two or more exons from different genes are combined together or when exons are duplicated. Exon shuffling results in new genes by altering the current intron-exon structure. This can occur by any of the following processes: transposon mediated shuffling, sexual recombination or illegitimate recombination. Exon shuffling may introduce new genes into the genome that can be either selected against and deleted or selectively favored and conserved.
Genome Reduction and Gene Loss
Many species exhibit genome reduction when subsets of their genes are not needed anymore. This typically happens when organisms adapt to a parasitic life style, e.g. when their nutrients are supplied by a host. As a consequence, they lose the genes need to produce these nutrients. In many cases, there are both free living and parasitic species that can be compared and their lost genes identified. Good examples are the genomes of Mycobacterium tuberculosis and Mycobacterium leprae, the latter of which has a dramatically reduced genome. Another beautiful example are endosymbiont species. For instance, Polynucleobacter necessarius was first described as a cytoplasmic endosymbiont of the ciliate Euplotes aediculatus. The latter species dies soon after being cured of the endosymbiont. In the few cases in which P. necessarius is not present, a different and rarer bacterium apparently supplies the same function. No attempt to grow symbiotic P. necessarius outside their hosts has yet been successful, strongly suggesting that the relationship is obligate for both partners. Yet, closely related free-living relatives of P. necessarius have been identified. The endosymbionts have a significantly reduced genome when compared to their free-living relatives (1.56 Mbp vs. 2.16 Mbp). | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/22%3A_The_Origin_of_Species/22.01%3A_The_Nature_of_Species_and_the_Biological_Species_Concept/22.1.04%3A_Evolution_of_Genomes/22.1.4B%3A_Genome_Evolution.txt |
Whole-genome duplication is characterized by an organisms entire genetic information being copied once or multiple times.
Learning Objectives
• State the evolutionary implications of whole-genome duplication
Key Points
• Whole- genome duplication can provide an evolutionary advantage by providing the organism with multiple copies of a gene that is considered favorable.
• Whole-genome duplication can result in divergence and formation of new species over time.
• Whole-genome duplication can result in mutation and cause disease if the genes are rendered non-functional.
Key Terms
• polyploidy: having more than the usual two homologous sets of chromosomes
• palaeopolyploidization: the development of polyploid organisms in the geologic past
• sympatric speciation: the process through which new species evolve from a single ancestral species while inhabiting the same geographic region
Whole-Genome Duplication
Gene duplication is the process by which a region of DNA coding for a gene creates additional copies of the gene. Similar to gene duplication, whole-genome duplication is the process by which an organism’s entire genetic information is copied, once or multiple times, which is known as polyploidy. This may provide an evolutionary benefit to the organism by supplying it with multiple copies of a gene, thus, creating a greater possibility of functional and selectively favored genes.
Evolutionary importance
Paleopolyploidization events lead to massive cellular changes, including doubling of the genetic material, changes in gene expression and increased cell size. Gene loss during diploidization is not completely random, but heavily selected. Genes from large gene families are duplicated. On the other hand, individual genes are not duplicated. Overall, paleopolyploidy can have both short-term and long-term evolutionary effects on an organism’s fitness in the natural environment.
Genome diversity
Genome doubling provides organisms with redundant alleles that can evolve freely with little selection pressure. The duplicated genes can undergo neofunctionalization or subfunctionalization which could help the organism adapt to the new environment or survive different stress conditions.
Speciation
Sympatric speciation can begin with a chromosomal error during meiosis or the formation of a hybrid individual with too many chromosomes, such as polyploidy which can occur during whole-genome duplication. Scientists have identified types of polyploidy that can lead to reproductive isolation of an individual in the polyploid state. In some cases a polyploid individual will have two or more complete sets of chromosomes from its own species in a condition called autopolyploidy. The other form of polyploidy occurs when individuals of two different species reproduce to form a viable offspring called an allopolyploid. The prefix “allo” means “other” (recall from allopatric); therefore, an allopolyploid occurs when gametes from two different species combine.
It has been suggested that many polyploidization events created new species, via a gain of adaptive traits, or by sexual incompatibility with their diploid counterparts. An example would be the recent speciation of allopolyploid Spartina — S. anglica; the polyploid plant is so successful that it is listed as an invasive species in many regions.
Evidence of Whole-Genome Duplication
In 1997, Wolfe & Shields gave evidence for an ancient duplication of the Saccharomyces cerevisiae (Yeast) genome. It was initially noted that this yeast genome contained many individual gene duplications. Wolfe & Shields hypothesized that this was actually the result of an entire genome duplication in the yeast’s distant evolutionary history. They found 32 pairs of homologous chromosomal regions, accounting for over half of the yeast’s genome. They also noted that although homologs were present, they were often located on different chromosomes. Based on these observations, they determined that Saccharomyces cerevisiae underwent a whole-genome duplication soon after its evolutionary split from Kluyveromyces, a genus of ascomycetous yeasts. Over time, many of the duplicate genes were deleted and rendered non-functional. A number of chromosomal rearrangements broke the original duplicate chromosomes into the current manifestation of homologous chromosomal regions. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/22%3A_The_Origin_of_Species/22.01%3A_The_Nature_of_Species_and_the_Biological_Species_Concept/22.1.04%3A_Evolution_of_Genomes/22.1.4C%3A_Whole-Genome_Duplic.txt |
Learning Objectives
• Explain the mechanisms of gene duplication and divergence
Gene Duplication
Gene duplication is the process by which a region of DNA coding for a gene is copied. Gene duplication can occur as the result of an error in recombination or through a retrotransposition event. Duplicate genes are often immune to the selective pressure under which genes normally exist. This can result in a large number of mutations accumulating in the duplicate gene code. This may render the gene non-functional or in some cases confer some benefit to the organism. There are multiple mechanisms by which gene duplication can occur.
Ectopic Recombination
Duplications can arise from unequal crossing-over that occurs during meiosis between misaligned homologous chromosomes. The product of this recombination is a duplication at the site of the exchange and a reciprocal deletion. Ectopic recombination is typically mediated by sequence similarity at the duplicate breakpoints, which form direct repeats. Repetitive genetic elements, such as transposable elements, offer one source of repetitive DNA that can facilitate recombination, and they are often found at duplication breakpoints in plants and mammals.
Replication Slippage
Replication slippage is an error in DNA replication, which can produce duplications of short genetic sequences. During replication, DNA polymerase begins to copy the DNA, and at some point during the replication process, the polymerase dissociates from the DNA and replication stalls. When the polymerase reattaches to the DNA strand, it aligns the replicating strand to an incorrect position and incidentally copies the same section more than once. Replication slippage is also often facilitated by repetitive sequence but requires only a few bases of similarity.
Retrotransposition
During cellular invasion by a replicating retroelement or retrovirus, viral proteins copy their genome by reverse transcribing RNA to DNA. If viral proteins attach irregularly to cellular mRNA, they can reverse-transcribe copies of genes to create retrogenes. Retrogenes usually lack intronic sequence and often contain poly A sequences that are also integrated into the genome. Many retrogenes display changes in gene regulation in comparison to their parental gene sequences, which sometimes results in novel functions.
Aneuploidy
Aneuploidy occurs when nondisjunction at a single chromosome results in an abnormal number of chromosomes. Aneuploidy is often harmful and in mammals regularly leads to spontaneous abortions. Some aneuploid individuals are viable. For example, trisomy 21 in humans leads to Down syndrome, but it is not fatal. Aneuploidy often alters gene dosage in ways that are detrimental to the organism and therefore, will not likely spread through populations.
Gene duplication as an evolutionary event
Gene duplications are an essential source of genetic novelty that can lead to evolutionary innovation. Duplication creates genetic redundancy and if one copy of a gene experiences a mutation that affects its original function, the second copy can serve as a ‘spare part’ and continue to function correctly. Thus, duplicate genes accumulate mutations faster than a functional single-copy gene, over generations of organisms, and it is possible for one of the two copies to develop a new and different function. This is an examples of neofunctionalization.
Gene duplication is believed to play a major role in evolution; this stance has been held by members of the scientific community for over 100 years. It has been argued that gene duplication is the most important evolutionary force since the emergence of the universal common ancestor.
Another possible fate for duplicate genes is that both copies are equally free to accumulate degenerative mutations, so long as any defects are complemented by the other copy. This leads to a neutral “subfunctionalization” model, in which the functionality of the original gene is distributed among the two copies. Neither gene can be lost, as both now perform important non-redundant functions, but ultimately neither is able to achieve novel functionality. Subfunctionalization can occur through neutral processes in which mutations accumulate with no detrimental or beneficial effects. However, in some cases subfunctionalization can occur with clear adaptive benefits. If an ancestral gene is pleiotropic and performs two functions, often times neither one of these two functions can be changed without affecting the other function. In this way, partitioning the ancestral functions into two separate genes can allow for adaptive specialization of subfunctions, thereby providing an adaptive benefit.
Divergence
Genetic divergence is the process in which two or more populations of an ancestral species accumulate independent genetic changes through time, often after the populations have become reproductively isolated for some period of time. In some cases, subpopulations living in ecologically distinct peripheral environments can exhibit genetic divergence from the remainder of a population, especially where the range of a population is very large. The genetic differences among divergent populations can involve silent mutations (that have no effect on the phenotype) or give rise to significant morphological and/or physiological changes. Genetic divergence will always accompany reproductive isolation, either due to novel adaptations via selection and/or due to genetic drift, and is the principal mechanism underlying speciation.
Genetic drift or allelic drift is the change in the frequency of a gene variant ( allele ) in a population due to random sampling. The alleles in the offspring are a sample of those in the parents, and chance has a role in determining whether a given individual survives and reproduces. A population’s allele frequency is the fraction of the copies of one gene that share a particular form. Genetic drift may cause gene variants to disappear completely and thereby reduce genetic variation. When there are few copies of an allele, the effect of genetic drift is larger, and when there are many copies the effect is smaller. These changes in gene frequency can contribute to divergence.
Divergent evolution is usually a result of diffusion of the same species to different and isolated environments, which blocks the gene flow among the distinct populations allowing differentiated fixation of characteristics through genetic drift and natural selection.Divergent evolution can also be applied to molecular biology characteristics. This could apply to a pathway in two or more organisms or cell types. This can apply to genes and proteins, such as nucleotide sequences or protein sequences that are derived from two or more homologous genes. Both orthologous genes (resulting from a speciation event) and paralogous genes (resulting from gene duplication within a population) can be said to display divergent evolution.
Key Points
• Ectopic recombination occurs when there is an unequal crossing-over and the product of this recombination are a duplication at the site of the exchange and a reciprocal deletion.
• Gene duplications do not always result in detrimental mutations; they can contribute to divergent evolution, which causes genetic differences between groups to develop and eventually form new species.
• Replication slippage can occur when there is an error during DNA replication and duplications of short genetic sequences are produced.
• Retrotranspositions occur when a retrovirus copies their genome by reverse transcribing RNA to DNA and aberrantly attach to cellular mRNA and reverse transcribe copies of genes to create retrogenes.
• Aneuploidy can occur when there is a nondisjunction even at a single chromosome thus, the result is an abnormal number of chromosomes.
• Genetic divergence can occur by mechanisms such as genetic drift which contibute to the accumulation of independent genetic changes of two or more populations derived from a common ancestor.
Key Terms
• paralogous: having a similar structure indicating divergence from a common ancestral gene
• nondisjunction: the failure of chromosome pairs to separate properly during meiosis
• retrogene: a DNA gene copied back from RNA by reverse transcription
• genetic drift: an overall shift of allele distribution in an isolated population, due to random fluctuations in the frequencies of individual alleles of the genes | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/22%3A_The_Origin_of_Species/22.01%3A_The_Nature_of_Species_and_the_Biological_Species_Concept/22.1.04%3A_Evolution_of_Genomes/22.1.4D%3A_Gene_Duplications_a.txt |
Noncoding DNA are sequences of DNA that do not encode protein sequences but can be transcribed to produce important regulatory molecules.
Learning Objectives
• Summarize the importance of noncoding DNA
Key Points
• In the human genome, over 98% of DNA is classified as noncoding DNA and can be transcribed to regulatory noncoding RNAs (i.e. tRNAs, rRNAs), origins of DNA replication, centromeres, telomeres and scaffold attachment regions (SARs).
• Noncoding regions are most commonly referred to as ‘junk DNA’, however, this term is misleading as noncoding DNA does have functional importance.
• The proportion of coding and noncoding DNA within organisms varies and the amount of noncoding DNA typically correlates with organism complexity, though there are many notable exceptions.
Key Terms
• intergenic: describing the noncoding sections of nucleic acid between genes
• noncoding: DNA which does not code for protein
• intron: a portion of a split gene that is included in pre-RNA transcripts but is removed during RNA processing and rapidly degraded
Noncoding DNA
In genomics and related disciplines, noncoding DNA sequences are components of an organism’s DNA that do not encode protein sequences. Some noncoding DNA is transcribed into functional noncoding RNA molecules (e.g. transfer RNA, ribosomal RNA, and regulatory RNAs), while others are not transcribed or give rise to RNA transcripts of unknown function. The amount of noncoding DNA varies greatly among species. For example, over 98% of the human genome is noncoding DNA, while only about 2% of a typical bacterial genome is noncoding DNA.
Initially, a large proportion of noncoding DNA had no known biological function and was therefore sometimes referred to as “junk DNA”, particularly in the lay press. However, many types of noncoding DNA sequences do have important biological functions, including the transcriptional and translational regulation of protein-coding sequences, origins of DNA replication, centromeres, telomeres, scaffold attachment regions (SARs), genes for functional RNAs, and many others. Other noncoding sequences have likely, but as-yet undetermined, functions. Some sequences may have no biological function for the organism, such as endogenous retroviruses.
Genomic Variation between Organisms
The amount of total genomic DNA varies widely between organisms, and the proportion of coding and noncoding DNA within these genomes varies greatly as well. More than 98% of the human genome does not encode protein sequences, including most sequences within introns and most intergenic DNA. While overall genome size, and by extension the amount of noncoding DNA, are correlated to organism complexity, there are many exceptions. For example, the genome of the unicellular Polychaos dubium (formerly known as Amoeba dubia) has been reported to contain more than 200 times the amount of DNA in humans. The pufferfish Takifugu rubripes genome is only about one eighth the size of the human genome, yet seems to have a comparable number of genes; approximately 90% of the Takifugu genome is noncoding DNA.
In 2013, a new “record” for most efficient genome was discovered. Utricularia gibba, a bladderwort plant, has only 3% noncoding DNA. The extensive variation in nuclear genome size among eukaryotic species is known as the C-value enigma or C-value paradox. Most of the genome size difference appears to lie in the noncoding DNA. About 80 percent of the nucleotide bases in the human genome may be transcribed, but transcription does not necessarily imply function. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/22%3A_The_Origin_of_Species/22.01%3A_The_Nature_of_Species_and_the_Biological_Species_Concept/22.1.04%3A_Evolution_of_Genomes/22.1.4E%3A_Noncoding_DNA.txt |
The genome size does not always correlate with the complexity of the organism and, in fact, shows great variation in size and gene number.
Learning Objectives
• Describe how variations in the size and number of genes can arise through evolutionary mechanisms
Key Points
• Harmless mutations and sexual recombination of chromosomes may allow the evolution of new characteristics.
• Genome size can be affected by various events, including duplication, insertion, recombination, deletion and polyploidization events.
• Genome size can be affected by evolution of an organism and result is an increased or decreased need for specific genes for survival based on behavior.
• The human genome exemplifies the concept that complexity does not always correlate with an increase in genome size; there are fewer protein coding genes present than expected relative to the genome size.
Key Terms
• polyploidization: hybridization that leads to polyploidy
• pseudogene: a segment of DNA that is part of the genome of an organism, and which is similar to a gene but does not code for a gene product
• genome: the cell’s complete genetic information packaged as a double-stranded DNA molecule
Variations in Size and Number of Genes
Genetic diversity refers to any variation in the nucleotides, genes, chromosomes, or whole genomes of organisms. Genetic diversity at its most elementary level is represented by differences in the sequences of nucleotides (adenine, cytosine, guanine, and thymine) that form the DNA (deoxyribonucleic acid) within the cells of the organism. The DNA is contained in the chromosomes present within the cell; some chromosomes are contained within specific organelles in the cell (for example, the chromosomes of mitochondria and chloroplast). Nucleotide variation is measured for discrete sections of the chromosomes, called genes. Thus, each gene compromises a hereditary section of DNA that occupies a specific place of the chromosome, and controls a particular characteristic of an organism.
Chromosomes
Most organisms are diploid, having two sets of chromosomes, and therefore two copies (called alleles ) of each gene. However, some organisms can be haploid, triploid, or tetraploid (having one, three, or four sets of chromosomes respectively). Within any single organism, there may be variation between the two (or more) alleles for each gene. This variation is introduced either through mutation of one of the alleles, or as a result of sexual reproduction.
During sexual reproduction, offspring inherit alleles from both parents and these alleles might be slightly different, especially if there has been migration or hybridization of organisms, so that the parents may come from different populations and gene pools. Also, when the offspring’s chromosomes are copied after fertilization, genes can be exchanged in a process called sexual recombination. Harmless mutations and sexual recombination may allow the evolution of new characteristics.
Genome Size and Number
Genome size is usually measured in base pairs (or bases in single-stranded DNA or RNA). The C-value is another measure of genome size. The C-value refers to the amount, in picograms, of DNA contained within a haploid nucleus (e.g. a gamete) or one half the amount in a diploid somatic cell of a eukaryotic organism. In some cases (notably among diploid organisms), the terms C-value and genome size are used interchangeably, however in polyploids the C-value may represent two or more genomes contained within the same nucleus.
Different species can have different numbers of genes within the entire DNA or genome of the organism. However, a greater total number of genes might not correspond with a greater observable complexity in the anatomy and physiology of the organism (i.e. greater phenotypic complexity). For example, the predicted size of the human genome is not much larger than the genomes of some invertebrates and plants, and may even be smaller than the Indian rice genome. In humans, more proteins are encoded per gene than in other species. In prokaryotic genomes, research has shown that there is a significant positive correlation between the C-value of prokaryotes and the amount of genes that compose the genome. This indicates that gene number is the main factor influencing the size of the prokaryotic genome.
Genes vs Genome Size
In eukaryotic organisms, there is a paradox observed, namely that the number of genes that make up the genome does not correlate with genome size. In other words, the genome size is much larger than would be expected given the total number of protein coding genes. Genome size can increase by duplication, insertion, or polyploidization and the process of recombination can lead to both DNA loss or gain. It is also possible that genomes can shrink due to deletions.
A famous example for such gene decay is the genome of Mycobacterium leprae, the causative agent of leprosy. M.leprae has lost many once-functional genes over time due to the formation of pseudogenes. This is evident in looking at its closest ancestor Mycobacterium tuberculosis. M. leprae lives inside and replicates inside of a host and due to this arrangement it does not have a need for many of the genes it once carried which allowed it to live and prosper outside of the host. Thus over time these genes have lost their function through mechanisms such as mutation causing them to become pseudogenes. It is beneficial to an organism to rid itself of non-essential genes because it makes replicating its DNA much faster and more energy-efficient.
An example of increasing genome size over time is seen in filamentous plant pathogens. These plant pathogen genomes have been growing larger over the years due to repeat-driven expansion. The repeat-rich regions contain genes coding for host interaction proteins. With the addition of more and more repeats to these regions the plants increase the possibility of developing new virulence factors through mutation and other forms of genetic recombination. In this way it is beneficial for these plant pathogens to have larger genomes.
Contributions and Attributions
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Fossils tell us when organisms lived, as well as provide evidence for the progression and evolution of life on earth over millions of years.
Learning Objectives
• Synthesize the contributions of the fossil record to our understanding of evolution
Key Points
• Fossils are the preserved remains or traces of animals, plants, and other organisms from the past.
• Fossils are important evidence for evolution because they show that life on earth was once different from life found on earth today.
• Usually only a portion of an organism is preserved as a fossil, such as body fossils (bones and exoskeletons ), trace fossils (feces and footprints), and chemofossils (biochemical signals).
• Paleontologists can determine the age of fossils using methods like radiometric dating and categorize them to determine the evolutionary relationships between organisms.
Key Terms
• biomarker: A substance used as an indicator of a biological state, most commonly disease.
• trace fossil: A type of fossil reflecting the reworking of sediments and hard substrates by organisms including structures like burrows, trails, and impressions.
• fossil record: All discovered and undiscovered fossils and their placement in rock formations and sedimentary layers.
• strata: Layers of sedimentary rock.
• fossiliferous: Containing fossils.
What Fossils Tell Us
Fossils are the preserved remains or traces of animals, plants, and other organisms from the past. Fossils range in age from 10,000 to 3.48 billion years old. The observation that certain fossils were associated with certain rock strata led 19th century geologists to recognize a geological timescale. Like extant organisms, fossils vary in size from microscopic, like single-celled bacteria, to gigantic, like dinosaurs and trees.
Permineralization
Permineralization is a process of fossilization that occurs when an organism is buried. The empty spaces within an organism (spaces filled with liquid or gas during life) become filled with mineral-rich groundwater. Minerals precipitate from the groundwater, occupying the empty spaces. This process can occur in very small spaces, such as within the cell wall of a plant cell. Small-scale permineralization can produce very detailed fossils. For permineralization to occur, the organism must be covered by sediment soon after death, or soon after the initial decay process.
The degree to which the remains are decayed when covered determines the later details of the fossil. Fossils usually consist of the portion of the organisms that was partially mineralized during life, such as the bones and teeth of vertebrates or the chitinous or calcareous exoskeletons of invertebrates. However, other fossils contain traces of skin, feathers or even soft tissues.
Trace Fossils
Fossils may also consist of the marks left behind by the organism while it was alive, such as footprints or feces. These types of fossils are called trace fossils, or ichnofossils, as opposed to body fossils. Past life may also leave some markers that cannot be seen but can be detected in the form of biochemical signals; these are known as chemofossils or biomarkers.
The Fossil Record
The totality of fossils, both discovered and undiscovered, and their placement in fossiliferous (fossil-containing) rock formations and sedimentary layers (strata) is known as the fossil record. The fossil record was one of the early sources of data underlying the study of evolution and continues to be relevant to the history of life on Earth. The development of radiometric dating techniques in the early 20th century allowed geologists to determine the numerical or “absolute” age of various strata and their included fossils.
Evidence for Evolution
Fossils provide solid evidence that organisms from the past are not the same as those found today; fossils show a progression of evolution. Fossils, along with the comparative anatomy of present-day organisms, constitute the morphological, or anatomical, record. By comparing the anatomies of both modern and extinct species, paleontologists can infer the lineages of those species. This approach is most successful for organisms that had hard body parts, such as shells, bones or teeth. The resulting fossil record tells the story of the past and shows the evolution of form over millions of years. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/22%3A_The_Origin_of_Species/22.01%3A_The_Nature_of_Species_and_the_Biological_Species_Concept/22.1.05%3A_Evidence_of_Evolution/22.1.5A%3A_The_Fossil_Record_.txt |
Fossils can form under ideal conditions by preservation, permineralization, molding (casting), replacement, or compression.
Learning Objectives
• Predict the conditions suitable to fossil formation
Key Points
• Preservation of remains in amber or other substances is the rarest from of fossilization; this mechanism allows scientists to study the skin, hair, and organs of ancient creatures.
• Permineralization, where minerals like silica fill the empty spaces of shells, is the most common form of fossilization.
• Molds form when shells or bones dissolve, leaving behind an empty depression; a cast is then formed when the depression is filled by sediment.
• Replacement occurs when the original shell or bone dissolves away and is replaced by a different mineral; when this occurs with permineralization, it is called petrification.
• In compression, the most common form of fossilization of leaves and ferns, a dark imprint of the fossil remains.
• Decay, chemical weathering, erosion, and predators are factors that deter fossilization.
• Fossilization of soft body parts is rare, and hard parts are better preserved when buried.
Key Terms
• amber: a hard, generally yellow to brown translucent fossil resin
• permineralization: form of fossilization in which minerals are deposited in the pores of bone and similar hard animal parts
• petrification: process by which organic material is converted into stone through the replacement of the original material and the filling of the original pore spaces with minerals
Fossil Formation
The process of a once living organism becoming a fossil is called fossilization. Fossilization is a very rare process, and of all the organisms that have lived on Earth, only a tiny percentage of them ever become fossils. To see why, imagine an antelope that dies on the African plain. Most of its body is quickly eaten by scavengers, and the remaining flesh is soon eaten by insects and bacteria, leaving behind only scattered bones. As the years go by, the bones are scattered and fragmented into small pieces, eventually turning into dust and returning their nutrients to the soil. As a result, it would be rare for any of the antelope’s remains to actually be preserved as a fossil.
Fossilization can occur in many ways. Most fossils are preserved in one of five processes:
• preserved remains
• permineralization
• molds and casts
• replacement
• compression
Preserved Remains
The rarest form of fossilization is the preservation of original skeletal material and even soft tissue. For example, some insects have been preserved perfectly in amber, which is ancient tree sap. In addition, several mammoths and even a Neanderthal hunter have been discovered frozen in glaciers. These preserved remains allow scientists the rare opportunity to examine the skin, hair, and organs of ancient creatures. Scientists have collected DNA from these remains and compared the DNA sequences to those of modern creatures.
Permineralization
The most common method of fossilization is permineralization. After a bone, wood fragment, or shell is buried in sediment, it may be exposed to mineral-rich water that moves through the sediment. This water will deposit minerals, typically silica, into empty spaces, producing a fossil. Fossilized dinosaur bones, petrified wood, and many marine fossils were formed by permineralization.
Molds and Casts
In some cases, the original bone or shell dissolves away, leaving behind an empty space in the shape of the shell or bone. This depression is called a mold. Later, the space may be filled with other sediments to form a matching cast in the shape of the original organism. Many mollusks (bivalves, snails, and squid) are commonly found as molds and casts because their shells dissolve easily.
Replacement
In some cases, the original shell or bone dissolves away and is replaced by a different mineral. For example, shells that were originally calcite may be replaced by dolomite, quartz, or pyrite. If quartz fossils are surrounded by a calcite matrix, the calcite can be dissolved away by acid, leaving behind an exquisitely preserved quartz fossil. When permineralization and replacement occur together, the organism is said to have undergone petrification, the process of turning organic material into stone. However, replacement can occur without permineralization and vice versa.
Compression
Some fossils form when their remains are compressed by high pressure. This can leave behind a dark imprint of the fossil. Compression is most common for fossils of leaves and ferns but also can occur with other organisms.
Conditions for Fossilization
Following the death of an organism, several forces contribute to the dissolution of its remains. Decay, predators, or scavengers will typically rapidly remove the flesh. The hard parts, if they are separable at all, can be dispersed by predators, scavengers, or currents. The individual hard parts are subject to chemical weathering and erosion, as well as to splintering by predators or scavengers, which will crunch up bones for marrow and shells to extract the flesh inside. Also, an animal swallowed whole by a predator, such as a mouse swallowed by a snake, will have not just its flesh but some, and perhaps all, its bones destroyed by the gastric juices of the predator.
It would not be an exaggeration to say that the typical vertebrate fossil consists of a single bone, or tooth, or fish scale. The preservation of an intact skeleton with the bones in the relative positions they had in life requires a remarkable circumstances, such as burial in volcanic ash, burial in aeolian sand due to the sudden slumping of a sand dune, burial in a mudslide, burial by a turbidity current, and so forth. The mineralization of soft parts is even less common and is seen only in exceptionally rare chemical and biological conditions. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/22%3A_The_Origin_of_Species/22.01%3A_The_Nature_of_Species_and_the_Biological_Species_Concept/22.1.05%3A_Evidence_of_Evolution/22.1.5B%3A_Fossil_Formation.txt |
Because not all animals have bodies which fossilize easily, the fossil record is considered incomplete.
Learning Objectives
• Explain the gap in the fossil record
Key Points
• The number of species known about through fossils is less than 1% of all species that have ever lived.
• Because hard body parts are more easily preserved than soft body parts, there are more fossils of animals with hard body parts, such as vertebrates, echinoderms, brachiopods, and some groups of arthropods.
• Very few fossils have been found in the period from 360 to 345 million years ago, known as Romer’s gap. Theories to explain this include the period’s geochemistry, errors in excavation, and limited vertebrate diversity.
Key Terms
• transitional fossil: Fossilized remains of a life form that exhibits traits common to both an ancestral group and its derived descendant group.
• Romer’s gap: A period in the tetrapod fossil record (360 to 345 million years ago) from which excavators have not yet found relevant fossils.
Incompleteness of the Fossil Record
Each fossil discovery represents a snapshot of the process of evolution. Because of the specialized and rare conditions required for a biological structure to fossilize, many important species or groups may never leave fossils at all. Even if they do leave fossils, humans may never find them—for example, if they are buried under hundreds of feet of ice in Antarctica. The number of species known about through the fossil record is less than 5% of the number of species alive today. Fossilized species may represent less than 1% of all the species that have ever lived.
Types of Fossils in the Fossil Record
The fossil record is very uneven and is mostly comprised of fossils of organisms with hard body parts, leaving most groups of soft-bodied organisms with little to no fossil record. Groups considered to have a good fossil record, including transitional fossils between these groups, are the vertebrates, the echinoderms, the brachiopods, and some groups of arthropods. Their hard bones and shells fossilize easily, unlike the bodies of organisms like cephalopods or jellyfish.
Romer’s Gap
Romer’s gap is an example of an apparent gap in the tetrapod fossil record used in the study of evolutionary biology. These gaps represent periods from which no relevant fossils have been found. Romer’s gap is named after paleontologist Alfred Romer, who first recognized it. Romer’s gap spanned from approximately 360 to 345 million years ago, corresponding to the first 15 million years of the Carboniferous Period.
There has been much debate over why there are so few fossils from this time period. Some scientists have suggested that the geochemistry of the time period caused bad conditions for fossil formation, so few organisms were fossilized. Another theory suggests that scientists have simply not yet discovered an excavation site for these fossils, due to inaccessibility or random chance.
22.1.5D: Carbon Dating and
The age of fossils can be determined using stratigraphy, biostratigraphy, and radiocarbon dating.
Learning Objectives
• Summarize the available methods for dating fossils
Key Points
• Determining the ages of fossils is an important step in mapping out how life evolved across geologic time.
• The study of stratigraphy enables scientists to determine the age of a fossil if they know the age of layers of rock that surround it.
• Biostratigraphy enables scientists to match rocks with particular fossils to other rocks with those fossils to determine age.
• Paleontology seeks to map out how life evolved across geologic time. A substantial hurdle is the difficulty of working out fossil ages.
• Scientists use carbon dating when determining the age of fossils that are less than 60,000 years old, and that are composed of organic materials such as wood or leather.
Key Terms
• half-life: The time required for half of the nuclei in a sample of a specific isotope to undergo radioactive decay.
• stratigraphy: The study of rock layers and the layering process.
• radiocarbon dating: A method of estimating the age of an artifact or biological vestige based on the relative amounts of various isotopes of carbon present in a sample.
Determining Fossil Ages
Paleontology seeks to map out how life evolved across geologic time. A substantial hurdle is the difficulty of working out fossil ages. There are several different methods for estimating the ages of fossils, including:
1. stratigraphy
2. biostratigraphy
3. carbon dating
Stratigraphy
Paleontologists rely on stratigraphy to date fossils. Stratigraphy is the science of understanding the strata, or layers, that form the sedimentary record. Strata are differentiated from each other by their different colors or compositions and are exposed in cliffs, quarries, and river banks. These rocks normally form relatively horizontal, parallel layers, with younger layers forming on top.
If a fossil is found between two layers of rock whose ages are known, the fossil’s age is thought to be between those two known ages. Because rock sequences are not continuous, but may be broken up by faults or periods of erosion, it is difficult to match up rock beds that are not directly adjacent.
Biostratigraphy
Fossils of species that survived for a relatively short time can be used to match isolated rocks: this technique is called biostratigraphy. For instance, the extinct chordate Eoplacognathus pseudoplanus is thought to have existed during a short range in the Middle Ordovician period. If rocks of unknown age have traces of E. pseudoplanus, they have a mid-Ordovician age. Such index fossils must be distinctive, globally distributed, and occupy a short time range to be useful. Misleading results can occur if the index fossils are incorrectly dated.
Relative Dating
Stratigraphy and biostratigraphy can in general provide only relative dating (A was before B), which is often sufficient for studying evolution. This is difficult for some time periods, however, because of the barriers involved in matching rocks of the same age across continents. Family-tree relationships can help to narrow down the date when lineages first appeared. For example, if fossils of B date to X million years ago and the calculated “family tree” says A was an ancestor of B, then A must have evolved earlier.
It is also possible to estimate how long ago two living branches of a family tree diverged by assuming that DNA mutations accumulate at a constant rate. However, these “molecular clocks” are sometimes inaccurate and provide only approximate timing. For example, they are not sufficiently precise and reliable for estimating when the groups that feature in the Cambrian explosion first evolved, and estimates produced by different approaches to this method may vary as well.
Carbon Dating
Together with stratigraphic principles, radiometric dating methods are used in geochronology to establish the geological time scale. Beds that preserve fossils typically lack the radioactive elements needed for radiometric dating (” radiocarbon dating ” or simply “carbon dating”). The principle of radiocarbon dating is simple: the rates at which various radioactive elements decay are known, and the ratio of the radioactive element to its decay products shows how long the radioactive element has existed in the rock. This rate is represented by the half-life, which is the time it takes for half of a sample to decay.
The half-life of carbon-14 is 5,730 years, so carbon dating is only relevant for dating fossils less than 60,000 years old. Radioactive elements are common only in rocks with a volcanic origin, so the only fossil-bearing rocks that can be dated radiometrically are volcanic ash layers. Carbon dating uses the decay of carbon-14 to estimate the age of organic materials, such as wood and leather. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/22%3A_The_Origin_of_Species/22.01%3A_The_Nature_of_Species_and_the_Biological_Species_Concept/22.1.05%3A_Evidence_of_Evolution/22.1.5C%3A_Gaps_in_the_Fossil.txt |
Learning Objectives
• Analyze the fossil record to understand the evolution of horses
Fossils provide evidence that organisms from the past are not the same as those found today, and demonstrate a progression of evolution. Scientists date and categorize fossils to determine when the organisms lived relative to each other. The resulting fossil record tells the story of the past and shows the evolution of forms over millions of years.
Case Study: Evolution of the Modern Horse
Highly detailed fossil records have been recovered for sequences in the evolution of modern horses. The fossil record of horses in North America is especially rich and contains transition fossils: fossils that show intermediate stages between earlier and later forms. The fossil record extends back to a dog-like ancestor some 55 million years ago, which gave rise to the first horse-like species 55 to 42 million years ago in the genus Eohippus.
The first equid fossil was found in the gypsum quarries in Montmartre, Paris in the 1820s. The tooth was sent to the Paris Conservatory, where Georges Cuvier identified it as a browsing equine related to the tapir. His sketch of the entire animal matched later skeletons found at the site. During the H.M.S. Beagle survey expedition, Charles Darwin had remarkable success with fossil hunting in Patagonia. In 1833 in Santa Fe, Argentina, he was “filled with astonishment” when he found a horse’s tooth in the same stratum as fossils of giant armadillos and wondered if it might have been washed down from a later layer, but concluded this was “not very probable.” In 1836, the anatomist Richard Owen confirmed the tooth was from an extinct species, which he subsequently named Equus curvidens.
The original sequence of species believed to have evolved into the horse was based on fossils discovered in North America in the 1870s by paleontologist Othniel Charles Marsh. The sequence, from Eohippus to the modern horse (Equus), was popularized by Thomas Huxley and became one of the most widely known examples of a clear evolutionary progression. The sequence of transitional fossils was assembled by the American Museum of Natural History into an exhibit that emphasized the gradual, “straight-line” evolution of the horse.
Since then, as the number of equid fossils has increased, the actual evolutionary progression from Eohippus to Equus has been discovered to be much more complex and multibranched than was initially supposed. Detailed fossil information on the rate and distribution of new equid species has also revealed that the progression between species was not as smooth and consistent as was once believed.
Although some transitions were indeed gradual progressions, a number of others were relatively abrupt in geologic time, taking place over only a few million years. Both anagenesis, a gradual change in an entire population ‘s gene frequency, and cladogenesis, a population “splitting” into two distinct evolutionary branches, occurred, and many species coexisted with “ancestor” species at various times.
Adaptation for Grazing
The series of fossils tracks the change in anatomy resulting from a gradual drying trend that changed the landscape from a forested habitat to a prairie habitat. Early horse ancestors were originally specialized for tropical forests, while modern horses are now adapted to life on drier land. Successive fossils show the evolution of teeth shapes and foot and leg anatomy to a grazing habit with adaptations for escaping predators.
The horse belongs to the order Perissodactyla (odd-toed ungulates), the members of which all share hoofed feet and an odd number of toes on each foot, as well as mobile upper lips and a similar tooth structure. This means that horses share a common ancestry with tapirs and rhinoceroses. Later species showed gains in size, such as those of Hipparion, which existed from about 23 to 2 million years ago. The fossil record shows several adaptive radiations in the horse lineage, which is now much reduced to only one genus, Equus, with several species. Paleozoologists have been able to piece together a more complete outline of the modern horse’s evolutionary lineage than that of any other animal.
Key Points
• A dog-like organism gave rise to the first horse ancestors 55-42 million years ago.
• The fossil record shows modern horses moved from tropical forests to prairie habitats, developed teeth, and grew in size.
• The first equid fossil was a tooth from the extinct species Equus curvidens found in Paris in the 1820s.
• Thomas Huxley popularized the evolutionary sequence of horses, which became one of the most common examples of clear evolutionary progression.
• Horse evolution was previously believed to be a linear progress, but after more fossils were discovered, it was determined the evolution of horses was more complex and multi-branched.
• Horses have evolved from gradual change ( anagenesis ) as well as abrupt progression and division ( cladogenesis ).
Key Terms
• cladogenesis: An evolutionary splitting event in which each branch and its smaller branches forms a clade.
• equid: A member of the horse family.
• anagenesis: Evolution of a new species through a large scale change in gene frequency so that the new species replaces the old, rather than branching to produce an additional species. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/22%3A_The_Origin_of_Species/22.01%3A_The_Nature_of_Species_and_the_Biological_Species_Concept/22.1.05%3A_Evidence_of_Evolution/22.1.5E%3A_The_Fossil_Record_.txt |
Homologous structures are similar structures that evolved from a common ancestor.
Learning Objectives
• Describe the connection between evolution and the appearance of homologous structures
Key Points
• Homology is a relationship defined between structures or DNA derived from a common ancestor and illustrates descent from a common ancestor.
• Analogous structures are physically (but not genetically) similar structures that were not present the last common ancestor.
• Homology can also be partial; new structures can evolve through the combination or parts of developmental pathways.
• Analogy may also be referred to as homoplasy, which is further divided into parallelism, reversal, and convergence.
Key Terms
• homology: A correspondence of structures in two life forms with a common evolutionary origin, such as flippers and hands.
• analogy: The relationship between characteristics that are apparently similar but did not develop from the same structure
• homoplasy: A correspondence between the parts or organs of different species acquired as the result of parallel evolution or convergence.
Homologous Structures
Homology is the relationship between structures or DNA derived from the most recent common ancestor. A common example of homologous structures in evolutionary biology are the wings of bats and the arms of primates. Although these two structures do not look similar or have the same function, genetically, they come from the same structure of the last common ancestor. Homologous traits of organisms are therefore explained by descent from a common ancestor.
It’s important to note that defining two structures as homologous depends on what ancestor is being described as the common ancestor. If we go all the way back to the beginning of life, all structures are homologous!
In genetics, homology is measured by comparing protein or DNA sequences. Homologous gene sequences share a high similarity, supporting the hypothesis that they share a common ancestor.
Homology can also be partial: new structures can evolve through the combination of developmental pathways or parts of them. As a result, hybrid or mosaic structures can evolve that exhibit partial homologies. For example, certain compound leaves of flowering plants are partially homologous both to leaves and shoots because they combine some traits of leaves and some of shoots.
Paralogous Structures
Homologous sequences are considered paralogous if they were separated by a gene duplication event; if a gene in an organism is duplicated to occupy two different positions in the same genome, then the two copies are paralogous.
A set of sequences that are paralogous are called paralogs of each other. Paralogs typically have the same or similar function, but sometimes do not. It is considered that due to lack of the original selective pressure upon one copy of the duplicated gene, this copy is free to mutate and acquire new functions.
Paralogous genes often belong to the same species, but not always. For example, the hemoglobin gene of humans and the myoglobin gene of chimpanzees are considered paralogs. This is a common problem in bioinformatics; when genomes of different species have been sequenced and homologous genes have been found, one can not immediately conclude that these genes have the same or similar function, as they could be paralogs whose function has diverged.
Analogous Structures
The opposite of homologous structures are analogous structures, which are physically similar structures between two taxa that evolved separately (rather than being present in the last common ancestor). Bat wings and bird wings evolved independently and are considered analogous structures. Genetically, a bat wing and a bird wing have very little in common; the last common ancestor of bats and birds did not have wings like either bats or birds. Wings evolved independently in each lineage after diverging from ancestors with forelimbs that were not used as wings (terrestrial mammals and theropod dinosaurs, respectively).
It is important to distinguish between different hierarchical levels of homology in order to make informative biological comparisons. In the above example, the bird and bat wings are analogous as wings, but homologous as forelimbs because the organ served as a forearm (not a wing) in the last common ancestor of tetrapods.
Analogy is different than homology. Although analogous characteristics are superficially similar, they are not homologous because they are phylogenetically independent. The wings of a maple seed and the wings of an albatross are analogous but not homologous (they both allow the organism to travel on the wind, but they didn’t both develop from the same structure). Analogy is commonly also referred to as homoplasy. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/22%3A_The_Origin_of_Species/22.01%3A_The_Nature_of_Species_and_the_Biological_Species_Concept/22.1.05%3A_Evidence_of_Evolution/22.1.5F%3A_Homologous_Structu.txt |
Convergent evolution occurs in different species that have evolved similar traits independently of each other.
Learning Objectives
• Predict the circumstances supporting convergent evolution of two species
Key Points
• Examples of convergent evolution include the relationship between bat and insect wings, shark and dolphin bodies, and vertebrate and cephalopod eyes.
• Analogous structures arise from convergent evolution, but homologous structures do not.
• Convergent evolution is the opposite of divergent evolution, in which related species evolve different traits.
• Convergent evolution is similar to parallel evolution, in which two similar but independent species evolve in the same direction and independently acquire similar characteristics.
Key Terms
• parallel evolution: the development of a similar trait in related, but distinct, species descending from the same ancestor, but from different clades
• convergent evolution: a trait of evolution in which species not of similar recent origin acquire similar properties due to natural selection
• divergent evolution: the process by which a species with similar traits become groups that are tremendously different from each other over many generations
• morphology: the form and structure of an organism
Convergent Evolution
Sometimes, similar phenotypes evolve independently in distantly related species. For example, flight has evolved in both bats and insects, and they both have wings, which are adaptations to flight. However, the wings of bats and insects have evolved from very different original structures. This phenomenon is called convergent evolution, where similar traits evolve independently in species that do not share a recent common ancestry.
Examples of Convergent Evolution
Convergent evolution describes the independent evolution of similar features in species of different lineages. The two species came to the same function, flying, but did so separately from each other. They have “converged” on this useful trait. Both sharks and dolphins have similar body forms, yet are only distantly related: sharks are fish and dolphins are mammals. Such similarities are a result of both populations being exposed to the same selective pressures. Within both groups, changes that aid swimming have been favored. Thus, over time, they developed similar appearances (morphology), even though they are not closely related.
One of the most well-known examples of convergent evolution is the camera eye of cephalopods (e.g., octopus), vertebrates (e.g., mammals), and cnidaria (e.g., box jellies). Their last common ancestor had at most a very simple photoreceptive spot, but a range of processes led to the progressive refinement of this structure to the advanced camera eye. There is, however, one subtle difference: the cephalopod eye is “wired” in the opposite direction, with blood and nerve vessels entering from the back of the retina, rather than the front as in vertebrates.
Convergent evolution is similar to, but distinguishable from, the phenomenon of parallel evolution. Parallel evolution occurs when two independent but similar species evolve in the same direction and thus independently acquire similar characteristics; for example, gliding frogs have evolved in parallel from multiple types of tree frog.
Analogous Structures
Traits arising through convergent evolution are analogous structures, in contrast to homologous structures, which have a common origin, but not necessarily similar function. The British anatomist Richard Owen was the first scientist to recognize the fundamental difference between analogies and homologies. Bat and pterosaur wings are an example of analogous structures, while the bat wing is homologous to human and other mammal forearms, sharing an ancestral state despite serving different functions.
Divergent Evolution
The opposite of convergent evolution is divergent evolution, whereby related species evolve different traits. On a molecular level, this can happen due to random mutation unrelated to adaptive changes. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/22%3A_The_Origin_of_Species/22.01%3A_The_Nature_of_Species_and_the_Biological_Species_Concept/22.1.05%3A_Evidence_of_Evolution/22.1.5G%3A_Convergent_Evoluti.txt |
Vestigial structures have no function but may still be inherited to maintain fitness.
Learning Objectives
• Discuss the connection between evolution and the existence of vestigial structures
Key Points
• Structures that have no apparent function and appear to be residual parts from a past ancestor are called vestigial structures.
• Examples of vestigial structures include the human appendix, the pelvic bone of a snake, and the wings of flightless birds.
• Vestigial structures can become detrimental, but in most cases these structures are harmless; however, these structures, like any other structure, require extra energy and are at risk for disease.
• Vestigial structures, especially non-harmful ones, take a long time to be phased out since eliminating them would require major alterations that could result in negative side effects.
Key Terms
• vestigial structure: Genetically determined structures or attributes that have lost most or all of their ancestral function in a given species.
• adaptation: A modification of something or its parts that makes it more fit for existence under the conditions of its current environment.
What Are Vestigial Structures?
Some organisms possess structures with no apparent function which appear to be residual parts from a past ancestor. For example, some snakes have pelvic bones despite having no legs because they descended from reptiles that did have legs. Another example of a structure with no function is the human vermiform appendix. These unused structures without function are called vestigial structures. Other examples of vestigial structures are wings (which may have other functions) on flightless birds like the ostrich, leaves on some cacti, traces of pelvic bones in whales, and the sightless eyes of cave animals.
There are also several reflexes and behaviors that are considered to be vestigial. The formation of goose bumps in humans under stress is a vestigial reflex its function in human ancestors was to raise the body’s hair, making the ancestor appear larger and scaring off predators. The arrector pili muscle, which is a band of smooth muscle that connects the hair follicle to connective tissue, contracts and creates the goose bumps on skin.
Vestigial Structures in Evolution
Vestigial structures are often homologous to structures that function normally in other species. Therefore, vestigial structures can be considered evidence for evolution, the process by which beneficial heritable traits arise in populations over an extended period of time. The existence of vestigial traits can be attributed to changes in the environment and behavior patterns of the organism in question. As the function of the trait is no longer beneficial for survival, the likelihood that future offspring will inherit the “normal” form of it decreases. In some cases the structure becomes detrimental to the organism.
If there are no selection pressures actively lowering the fitness of the individual, the trait will persist in future generations unless the trait is eliminated through genetic drift or other random events.
Although in many cases the vestigial structure is of no direct harm, all structures require extra energy in terms of development, maintenance, and weight and are also a risk in terms of disease (e.g., infection, cancer). This provides some selective pressure for the removal of parts that do not contribute to an organism’s fitness, but a structure that is not directly harmful will take longer to be ‘phased out’ than one that is. Some vestigial structures persist due to limitations in development, such that complete loss of the structure could not occur without major alterations of the organism’s developmental pattern, and such alterations would likely produce numerous negative side-effects.
The vestigial versions of a structure can be compared to the original version of the structure in other species in order to determine the homology of the structure. Homologous structures indicate common ancestry with those organisms that have a functional version of the structure. Vestigial traits can still be considered adaptations because an adaptation is often defined as a trait that has been favored by natural selection. Adaptations, therefore, need not be adaptive, as long as they were at some point. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/22%3A_The_Origin_of_Species/22.01%3A_The_Nature_of_Species_and_the_Biological_Species_Concept/22.1.05%3A_Evidence_of_Evolution/22.1.5H%3A_Vestigial_Structur.txt |
The biological distribution of species is based on the movement of tectonic plates over a period of time.
Learning Objectives
• Relate biogeography and the distribution of species
Key Points
• Biogeography is the study of geological species distribution, which is influenced by both biotic and abiotic factors.
• Some species are endemic and are only found in a particular region, while others are generalists and are distributed worldwide.
• Species that evolved before the breakup of continents are distributed worldwide.
• Species that evolved after the breakup of continents are found in only certain regions of the planet.
Key Terms
• endemic: unique to a particular area or region; not found in other places
• generalist: species which can thrive in a wide variety of environmental conditions
• Pangaea: supercontinent that included all the landmasses of the earth before the Triassic period and that broke up into Laurasia and Gondwana
Distribution of Species
Biogeography is the study of the geographic distribution of living things and the abiotic factors that affect their distribution. Abiotic factors, such as temperature and rainfall, vary based on latitude and elevation, primarily. As these abiotic factors change, the composition of plant and animal communities also changes.
Patterns of Species Distribution
Ecologists who study biogeography examine patterns of species distribution. No species exists everywhere; for example, the Venus flytrap is endemic to a small area in North and South Carolina. An endemic species is one which is naturally found only in a specific geographic area that is usually restricted in size. Other species are generalists: species which live in a wide variety of geographic areas; the raccoon, for example, is native to most of North and Central America.
Since species distribution patterns are based on biotic and abiotic factors and their influences during the very long periods of time required for species evolution, early studies of biogeography were closely linked to the emergence of evolutionary thinking in the eighteenth century. Some of the most distinctive assemblages of plants and animals occur in regions that have been physically separated for millions of years by geographic barriers. Biologists estimate that Australia, for example, has between 600,000 and 700,000 species of plants and animals. Approximately 3/4 of living plant and mammal species are endemic species found solely in Australia.
The geographic distribution of organisms on the planet follows patterns that are best explained by evolution in conjunction with the movement of tectonic plates over geological time. Broad groups that evolved before the breakup of the supercontinent Pangaea (about 200 million years ago) are distributed worldwide. Groups that evolved since the breakup appear uniquely in regions of the planet, such as the unique flora and fauna of northern continents that formed from the supercontinent Laurasia and of the southern continents that formed from the supercontinent Gondwana. The presence of Proteaceae in Australia, southern Africa, and South America is best explained by the plant family’s presence there prior to the southern supercontinent Gondwana breaking up.
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One of the best definition os species is that of the evolutionary biologist Ernst Mayr: "A species is an actually or potentially interbreeding population that does not interbreed with other such populations when there is opportunity to do so." However, sometimes breeding may take place (as it can between a horse and a donkey) but if so, the offspring are not so fertile and/or well adapted as the parents (the mule produced is sterile).
Allopatric Speciation: the Role of Isolation in Speciation
The formation of two or more species often (some workers think always!) requires geographical isolation of subpopulations of the species. Only then can natural selection or perhaps genetic drift produce distinctive gene pools. It is no accident that the various races (or "subspecies") of animals almost never occupy the same territory. Their distribution is allopatric ("other country").
The seven distinct subspecies or races of the yellowthroat Geothlypis trichas (a warbler) in the continental U.S. would soon merge into a single homogeneous population if they occupied the same territory and bred with one another.
Darwin's Finches
As a young man of 26, Charles Darwin visited the Galapagos Islands off the coast of Ecuador. Among the animals he studied were what appeared to be 13 species* of finches found nowhere else on earth.
• Some have stout beaks for eating seeds of one size or another (#2, #3, #6).
• Others have beaks adapted for eating insects or nectar.
• One (#7) has a beak like a woodpecker's. It uses it to drill holes in wood, but lacking the long tongue of a true woodpecker, it uses a cactus spine held in its beak to dig the insect out.
• One (#12) looks more like a warbler than a finch, but its eggs, nest, and courtship behavior is like that of the other finches.
Darwin's finches. The finches numbered 1–7 are ground finches. They seek their food on the ground or in low shrubs. Those numbered 8–13 are tree finches. They live primarily on insects.
1. Large cactus finch (Geospiza conirostris)
2. Large ground finch (Geospiza magnirostris)
3. Medium ground finch (Geospiza fortis)
4. Cactus finch (Geospiza scandens)
5. Sharp-beaked ground finch (Geospiza difficilis)
6. Small ground finch (Geospiza fuliginosa)
7. Woodpecker finch (Cactospiza pallida)
8. Vegetarian tree finch (Platyspiza crassirostris)
9. Medium tree finch (Camarhynchus pauper)
10. Large tree finch (Camarhynchus psittacula)
11. Small tree finch (Camarhynchus parvulus)
12. Warbler finch (Certhidia olivacea)
13. Mangrove finch (Cactospiza heliobates)
(From BSCS, Biological Science: Molecules to Man, Houghton Mifflin Co., 1963)
* Genetic analysis provides evidence that:
• There are actually two species of warbler finch — Certhidia olivacea now called the green warbler finch and Certhidia fusca, the gray warbler finch.
• The various populations of Geospiza difficilis found on the different islands belong to one or another of three clades so genetically distinct that they deserve full species status.
Whether the number is 13 or 17, since Darwin's time, these birds have provided a case study of how a single species reaching the Galapagos from Central or South America could - over a few million years - give rise to the various species that live there today. Several factors have been identified that may contribute to speciation.
Ecological opportunity
When the ancestor of Darwin's finches reached the Galapagos, it found no predators (There were no mammals and few reptiles on the islands.) and few, if any, competitors. There were only a handful of other types of songbirds. In fact, if true warblers or woodpeckers had been present, their efficiency at exploiting their niches would surely have prevented the evolution of warblerlike and woodpeckerlike finches.
Geographical Isolation (allopatry)
The proximity of the various islands has permitted enough migration of Darwin's finches between them to enable distinct island populations to arise. But the distances between the islands is great enough to limit interbreeding between populations on different islands. This has made possible the formation of distinctive subspecies (= races) on the various islands.
The importance of geographical isolation is illuminated by a single, fourteenth, species of Darwin's finches that lives on Cocos Island, some 500 miles (800 km) to the northeast of the Galapagos. The first immigrants there must also have found relaxed selection pressures with few predators or competitors. How different the outcome, though. Where one immigrant species gave rise to at least 13 on the scattered Galapagos Islands, no such divergence has occurred on the single, isolated Cocos Island.
Evolutionary Change
In isolation, changes in the gene pool can occur through some combination of natural selection, genetic drift, and founder effect. These factors may produce distinct subpopulations on the different islands. So long as they remain separate (allopatric) we consider them races or subspecies. In fact, they might not be able to interbreed with other races but so long as we don't know, we assume that they could.
How much genetic change is needed to create a new species? Perhaps not as much as you might think. For example, changes at one or just a few gene loci might do the trick. For example, a single mutation altering flower color or petal shape could immediately prevent cross-pollination between the new and the parental types (a form of prezygotic isolating mechanism).
Reunion
The question of their status - subspecies or true species - is resolved if they ever do come to occupy the same territory again (become sympatric). If successful interbreeding occurs, the differences will gradually disappear, and a single population will be formed again. Speciation will not have occurred. If, on the other hand, two subspecies reunite but fail to resume breeding, speciation has occurred and they have become separate species.
An example: The medium tree finch Camarhynchus pauper is found only on Floreana Island. Its close relative, the large tree finch, Camarhynchus psittacula, is found on all the central islands including Floreana. Were it not for its presence on Floreana, both forms would be considered subspecies of the same species. Because they do coexist and maintain their separate identity on Floreana, we know that speciation has occurred.
Isolating Mechanisms
What might keep two subpopulations from interbreeding when reunited geographically? There are several mechanisms.
Prezygotic Isolating Mechanisms act before fertilization occurs. Sexual selection - a failure to elicit mating behavior. On Floreana, Camarhynchus psittacula has a longer beak than Camarhynchus pauper, and the research teams led by Peter and Rosemary Grant have demonstrated that beak size is an important criterion by which Darwin's finches choose their mates. Two subpopulations may occupy different habitats in the same area and thus fail to meet at breeding time. In plants, a shift in the time of flowering can prevent pollination between the two subpopulations. Structural differences in the sex organs may become an isolating mechanism. The sperm may fail to reach or fuse with the egg.
Postzygotic Isolating Mechanisms act even if fertilization does occur. Even if a zygote is formed, genetic differences may have become so great that the resulting hybrids are less viable or less fertile than the parental types. The sterile mule produced by mating a horse with a donkey is an example. Sterility in the males produced by hybridization is more common than in females. In fact, it is the most common postzygotic isolating mechanism. When Drosophila melanogaster attempts to mate with its relative Drosophila simulans, no viable males are even produced. Mutations in a single gene (encoding a component of the nuclear pore complex) are responsible.
Reinforcement
When two species that have separated in allopatry become reunited, their prezygotic and postzygotic isolating mechanisms may become more stringent than those between the same species existing apart from each other. This phenomenon is called reinforcement. It arises from natural selection working to favor individuals that avoid interspecific matings, which would produce less-fit hybrids, when the two species are first reunited.
Speciation by Hybridization
Hybridization between related angiosperms is sometimes followed by a doubling of the chromosome number. The resulting polyploids are now fully fertile with each other although unable to breed with either parental type - a new species has been created. This appears to have been a frequent mechanism of speciation in angiosperms. Even without forming a polyploid, interspecific hybridization can occasionally lead to a new species of angiosperm. Two species of sunflower, the "common sunflower", Helianthus annuus, and the "prairie sunflower", H. petiolaris, grow widely over the western half of the United States. They can interbreed, but only rarely are fertile offspring produced.
However, Rieseberg and colleagues have found evidence that successful hybridization between them has happened naturally in the past. They have shown that three other species of sunflower (each growing in a habitat too harsh for either parental type) are each the product of an ancient hybridization between Helianthus annuus and H. petiolaris. Although each of these species has the same diploid number of chromosomes as the parents (2n = 34), they each have a pattern of chromosome segments that have been derived, by genetic recombination, from both the parental genomes. They demonstrated this in several ways, notably by combining RFLP analysis with the polymerase chain reaction (PCR).
They even went on to produce (at a low frequency) annuus x petiolaris hybrids in the greenhouse that mimicked the phenotypes and genotypes of the natural hybrids. (These monumental studies were described in the 29 August 2003 issue of Science.)
Another example. In Pennsylvania, hybrids between a species of fruit fly (not Drosophila) that feeds on blueberries and another species (again, not Drosophila) that feeds on snowberries feed on honeysuckle where they neither encounter competition from their parental species nor have an opportunity to breed with them (no introgression). This study was published in the 28 July 2005 issue of Nature. So speciation can occur as a result of hybridization between two related species, if the hybrid
• receives a genome that enables it to breed with other such hybrids but not breed with either parental species,
• can escape to a habitat where it does not have to compete with either parent,
• is adapted to live under those new conditions.
Adaptive Radiation
The processes described in this page can occur over and over. In the case of Darwin's finches, they must have been repeated a number of times forming new species that gradually divided the available habitats between them. From the first arrival have come a variety of ground-feeding and tree-feeding finches as well as the warblerlike finch and the tool-using woodpeckerlike finch. The formation of a number of diverse species from a single ancestral one is called an adaptive radiation.
Speciateion in theHouse mice on the island of Madeira
A report in the 13 January 2000 issue of Nature describes a study of house mouse populations on the island of Madeira off the Northwest coast of Africa. These workers (Janice Britton-Davidian et al) examined the karyotypes of 143 house mice (Mus musculus domesticus) from various locations along the coast of this mountainous island.
Their findings:
• There are 6 distinct populations (shown by different colors)
• Each of these has a distinct karyotype, with a diploid number less than the "normal" (2n = 40).
• The reduction in chromosome number has occurred through Robertsonian fusions. Mouse chromosomes tend to be acrocentric; that is, the centromere connects one long and one very short arm. Acrocentric chromosomes are at risk of translocations that fuse the long arms of two different chromosomes with the loss of the short arms.
• The different populations are allopatric; isolated in different valleys leading down to the sea.
• The distinct and uniform karyotype found in each population probably arose from genetic drift rather than natural selection.
• The 6 different populations are technically described as races because there is no opportunity for them to attempt interbreeding.
• However, they surely meet the definition of true species. While hybrids would form easily (no prezygotic isolating mechanisms), these would probably be infertile as proper synapsis and segregation of such different chromosomes would be difficult when the hybrids attempted to form gametes by meiosis.
Sympatric Speciation
Sympatric speciation refers to the formation of two or more descendant species from a single ancestral species all occupying the same geographic location. Some evolutionary biologists don't believe that it ever occurs. They feel that interbreeding would soon eliminate any genetic differences that might appear. But there is some compelling (albeit indirect) evidence that sympatric speciation can occur.
Speciation in three-spined sticklebacks
The three-spined sticklebacks, freshwater fishes that have been studied by Dolph Schluter (who received his Ph.D. for his work on Darwin's finches with Peter Grant) and his current colleagues in British Columbia, provide an intriguing example that is best explained by sympatric speciation.
They have found:
• Two different species of three-spined sticklebacks in each of five different lakes.
• a large benthic species with a large mouth that feeds on large prey in the littoral zone
• a smaller limnetic species with a smaller mouth that feeds on the small plankton in open water.
• DNA analysis indicates that each lake was colonized independently, presumably by a marine ancestor, after the last ice age.
• DNA analysis also shows that the two species in each lake are more closely related to each other than they are to any of the species in the other lakes.
• Nevertheless, the two species in each lake are reproductively isolated; neither mates with the other.
• However, aquarium tests showed that
• The benthic species from one lake will spawn with the benthic species from the other lakes and likewise the limnetic species from the different lakes will spawn with each other.
• These benthic and limnetic species even display their mating preferences when presented with sticklebacks from Japanese lakes; that is, a Canadian benthic prefers a Japanese benthic over its close limnetic cousin from its own lake.
• Their conclusion: in each lake, what began as a single population faced such competition for limited resources that
• disruptive selection — competition favoring fishes at either extreme of body size and mouth size over those nearer the mean — coupled with
• assortative mating — each size preferred mates like it
favored a divergence into two subpopulations exploiting different food in different parts of the lake.
• The fact that this pattern of speciation occurred the same way on three separate occasions suggests strongly that ecological factors in a sympatric population can cause speciation.
Sympatric speciation driven by ecological factors may also account for the extraordinary diversity of crustaceans living in the depths of Siberia's Lake Baikal.
How many genes are needed to start down the path to sympatric speciation?
Perhaps not very many. The European corn borer, Ostrinia nubilalis, (which despite its common name is a major pest in the U.S. as well) exists as two distinct races designated Z and E. Both can be found in the same area; that is, they are sympatric. But in the field, they practice assortative mating - only breeding with mates of their own race.
The females of both races synthesize and release a pheromone that is a sex attractant for the males. Both races use the same substance but different isomers of it. Which isomer is produced is under the control of a single enzyme-encoding gene locus. The ability of the males to respond to one isomer or the other is controlled by 2 loci.
The Problem of Clines
There is another possible way for new species to arise in the absence of geographical barriers. If a population ranges over a large area and if the individuals in that population can disperse over only a small portion of this range, then gene flow across these great distances would be reduced. The occurrence of gradual phenotypic (and genotypic) differences in a population across a large geographical area is called a cline. Successful interbreeding occurs freely at every point along the cline, but individuals at the ends of the cline may not be able to interbreed. This can be tested in the laboratory.
And, on occasions, it is tested in nature. If a cline bends around so that the ends meet, and the populations reunited at the junction cannot interbreed, then the definition of separate species has been met. Such species are called ring species and this type of speciation is called parapatric speciation.
Two examples:
1. The Caribbean slipper spurge Euphorbia tithymaloides.
Genetic analysis shows that this wildflower originated in Central America where Mexico and Guatemala share a common boundary. From there it spread in two directions
• northeast through the Yucatan peninsula and then island-hopped through Jamaica, the Dominican Republic, Puerto Rico and into the Virgin Islands;
• south through Central America, on through Venezuela, and then north through Barbados and the other islands of the Lesser Antilles finally also reaching the Virgin Islands.
Reunited in the Virgin Islands, the two populations have diverged sufficiently that they retain their distinctive genotypic and phenotypic traits. Ongoing studies will determine to what degree they may be reproductively isolated.
2. The large-blotched salamander Ensatina eschscholtzii.
This animal is found in California where it occurs in a number of different subspecies or races. A single subspecies is found in Northern California, and it is thought to be the founder of all the others. Over time that original population spread southward in two directions:
• down the Sierra Nevada mountains east of the great central San Joaquin Valley and
• down the coast range of mountains west of the valley.
South of the valley, the eastern group has moved west and now meets the western group, closing the ring. Here the two populations fail to interbreed successfully, maintaining their distinct identities. But each subspecies interbreeds in an unbroken chain up the two paths their ancestors took.
Ring species present a difficult problem in assigning species designations. It is easy to say that the populations at the ends of the cline represent separate species, but where did one give rise to the other? At every point along the cline, interbreeding goes on successfully.
The same problem faces paleontologists examining the gradual phenotypic changes seen in an unbroken line of ever-younger fossils from what one presumes to be a single line of descent. If one could resurrect the ancestral species (A) and the descendant species (B) and they could not interbreed, then they meet the definition of separate species. But there was no moment in time when one could say that A became B. So the clines of today are a model in space of Darwin's descent with modification occurring over time.
Although clines present a problem for classifiers, they are a beautiful demonstration of Darwin's conviction that the accumulation of small inherited differences can lead to the formation of new species. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/22%3A_The_Origin_of_Species/22.02%3A_Natural_Selection_and_Reproductive_Isolation.txt |
Allopatric speciation occurs when a single species becomes geographically separated; each group evolves new and distinctive traits.
Learning Objectives
• Give examples of allopatric speciation
Key Points
• When a population is geographically continuous, the allele frequencies among its members are similar; however, when a population becomes separated, the allele frequencies between the two groups can begin to vary.
• If the separation between groups continues for a long period of time, the differences between their alleles can become more and more pronounced due to differences in climate, predation, food sources, and other factors, eventually leading to the formation of a new species.
• Geographic separation between populations can occur in many ways; the severity of the separation depends on the travel capabilities of the species.
• Allopatric speciation events can occur either by dispersal, when a few members of a species move to a new geographical area, or by vicariance, when a natural situation, such as the formation of a river or valley, physically divide organisms.
• When a population disperses throughout an area, into new, different and often isolated habitats, multiple speciation events can occur in which the single original species gives rise to many new species; this phenomenon is called adaptive radiation.
Key Terms
• vicariance: the separation of a group of organisms by a geographic barrier, resulting in differentiation of the original group into new varieties or species
• adaptive radiation: the diversification of species into separate forms that each adapt to occupy a specific environmental niche
• dispersal: the movement of a few members of a species to a new geographical area, resulting in differentiation of the original group into new varieties or species
Allopatric Speciation
A geographically-continuous population has a gene pool that is relatively homogeneous. Gene flow, the movement of alleles across the range of the species, is relatively free because individuals can move and then mate with individuals in their new location. Thus, the frequency of an allele at one end of a distribution will be similar to the frequency of the allele at the other end. When populations become geographically discontinuous, that free-flow of alleles is prevented. When that separation continues for a period of time, the two populations are able to evolve along different trajectories. This is known as allopatric speciation. Thus, their allele frequencies at numerous genetic loci gradually become more and more different as new alleles independently arise by mutation in each population. Typically, environmental conditions, such as climate, resources, predators, and competitors for the two populations will differ causing natural selection to favor divergent adaptations in each group.
Isolation of populations leading to allopatric speciation can occur in a variety of ways: a river forming a new branch, erosion forming a new valley, a group of organisms traveling to a new location without the ability to return, or seeds floating over the ocean to an island. The nature of the geographic separation necessary to isolate populations depends entirely on the biology of the organism and its potential for dispersal. If two flying insect populations took up residence in separate nearby valleys, chances are individuals from each population would fly back and forth, continuing gene flow. However, if two rodent populations became divided by the formation of a new lake, continued gene flow would be improbable; therefore, speciation would be probably occur.
Biologists group allopatric processes into two categories: dispersal and vicariance. Dispersal occurs when a few members of a species move to a new geographical area, while vicariance occurs when a natural situation arises to physically divide organisms.
Scientists have documented numerous cases of allopatric speciation. For example, along the west coast of the United States, two separate sub-species of spotted owls exist. The northern spotted owl has genetic and phenotypic differences from its close relative, the Mexican spotted owl, which lives in the south.
Additionally, scientists have found that the further the distance between two groups that once were the same species, the more probable it is that speciation will occur. This seems logical because as the distance increases, the various environmental factors would generally have less in common than locations in close proximity. Consider the two owls: in the north, the climate is cooler than in the south causing the types of organisms in each ecosystem differ, as do their behaviors and habits. Also, the hunting habits and prey choices of the southern owls vary from the northern owls. These variances can lead to evolved differences in the owls, resulting in speciation.
Adaptive Radiation
In some cases, a population of one species disperses throughout an area with each finding a distinct niche or isolated habitat. Over time, the varied demands of their new lifestyles lead to multiple speciation events originating from a single species. This is called adaptive radiation because many adaptations evolve from a single point of origin, causing the species to radiate into several new ones. Island archipelagos like the Hawaiian Islands provide an ideal context for adaptive radiation events because water surrounds each island which leads to geographical isolation for many organisms. The Hawaiian honeycreeper illustrates one example of adaptive radiation. From a single species, called the founder species, numerous species have evolved.
In Hawaiian honeycreepers, the response to natural selection based on specific food sources in each new habitat led to the evolution of a different beak suited to the specific food source. The seed-eating birds have a thicker, stronger beak which is suited to break hard nuts. The nectar-eating birds have long beaks to dip into flowers to reach the nectar. The insect-eating birds have beaks like swords, appropriate for stabbing and impaling insects.
22.03: The Role of Genetic Drift and Natural Selection in Speciation
Learning Objectives
• Explain the mechanisms of gene duplication and divergence
Gene Duplication
Gene duplication is the process by which a region of DNA coding for a gene is copied. Gene duplication can occur as the result of an error in recombination or through a retrotransposition event. Duplicate genes are often immune to the selective pressure under which genes normally exist. This can result in a large number of mutations accumulating in the duplicate gene code. This may render the gene non-functional or in some cases confer some benefit to the organism. There are multiple mechanisms by which gene duplication can occur.
Ectopic Recombination
Duplications can arise from unequal crossing-over that occurs during meiosis between misaligned homologous chromosomes. The product of this recombination is a duplication at the site of the exchange and a reciprocal deletion. Ectopic recombination is typically mediated by sequence similarity at the duplicate breakpoints, which form direct repeats. Repetitive genetic elements, such as transposable elements, offer one source of repetitive DNA that can facilitate recombination, and they are often found at duplication breakpoints in plants and mammals.
Replication Slippage
Replication slippage is an error in DNA replication, which can produce duplications of short genetic sequences. During replication, DNA polymerase begins to copy the DNA, and at some point during the replication process, the polymerase dissociates from the DNA and replication stalls. When the polymerase reattaches to the DNA strand, it aligns the replicating strand to an incorrect position and incidentally copies the same section more than once. Replication slippage is also often facilitated by repetitive sequence but requires only a few bases of similarity.
Retrotransposition
During cellular invasion by a replicating retroelement or retrovirus, viral proteins copy their genome by reverse transcribing RNA to DNA. If viral proteins attach irregularly to cellular mRNA, they can reverse-transcribe copies of genes to create retrogenes. Retrogenes usually lack intronic sequence and often contain poly A sequences that are also integrated into the genome. Many retrogenes display changes in gene regulation in comparison to their parental gene sequences, which sometimes results in novel functions.
Aneuploidy
Aneuploidy occurs when nondisjunction at a single chromosome results in an abnormal number of chromosomes. Aneuploidy is often harmful and in mammals regularly leads to spontaneous abortions. Some aneuploid individuals are viable. For example, trisomy 21 in humans leads to Down syndrome, but it is not fatal. Aneuploidy often alters gene dosage in ways that are detrimental to the organism and therefore, will not likely spread through populations.
Gene duplication as an evolutionary event
Gene duplications are an essential source of genetic novelty that can lead to evolutionary innovation. Duplication creates genetic redundancy and if one copy of a gene experiences a mutation that affects its original function, the second copy can serve as a ‘spare part’ and continue to function correctly. Thus, duplicate genes accumulate mutations faster than a functional single-copy gene, over generations of organisms, and it is possible for one of the two copies to develop a new and different function. This is an examples of neofunctionalization.
Gene duplication is believed to play a major role in evolution; this stance has been held by members of the scientific community for over 100 years. It has been argued that gene duplication is the most important evolutionary force since the emergence of the universal common ancestor.
Another possible fate for duplicate genes is that both copies are equally free to accumulate degenerative mutations, so long as any defects are complemented by the other copy. This leads to a neutral “subfunctionalization” model, in which the functionality of the original gene is distributed among the two copies. Neither gene can be lost, as both now perform important non-redundant functions, but ultimately neither is able to achieve novel functionality. Subfunctionalization can occur through neutral processes in which mutations accumulate with no detrimental or beneficial effects. However, in some cases subfunctionalization can occur with clear adaptive benefits. If an ancestral gene is pleiotropic and performs two functions, often times neither one of these two functions can be changed without affecting the other function. In this way, partitioning the ancestral functions into two separate genes can allow for adaptive specialization of subfunctions, thereby providing an adaptive benefit.
Divergence
Genetic divergence is the process in which two or more populations of an ancestral species accumulate independent genetic changes through time, often after the populations have become reproductively isolated for some period of time. In some cases, subpopulations living in ecologically distinct peripheral environments can exhibit genetic divergence from the remainder of a population, especially where the range of a population is very large. The genetic differences among divergent populations can involve silent mutations (that have no effect on the phenotype) or give rise to significant morphological and/or physiological changes. Genetic divergence will always accompany reproductive isolation, either due to novel adaptations via selection and/or due to genetic drift, and is the principal mechanism underlying speciation.
Genetic drift or allelic drift is the change in the frequency of a gene variant ( allele ) in a population due to random sampling. The alleles in the offspring are a sample of those in the parents, and chance has a role in determining whether a given individual survives and reproduces. A population’s allele frequency is the fraction of the copies of one gene that share a particular form. Genetic drift may cause gene variants to disappear completely and thereby reduce genetic variation. When there are few copies of an allele, the effect of genetic drift is larger, and when there are many copies the effect is smaller. These changes in gene frequency can contribute to divergence.
Divergent evolution is usually a result of diffusion of the same species to different and isolated environments, which blocks the gene flow among the distinct populations allowing differentiated fixation of characteristics through genetic drift and natural selection.Divergent evolution can also be applied to molecular biology characteristics. This could apply to a pathway in two or more organisms or cell types. This can apply to genes and proteins, such as nucleotide sequences or protein sequences that are derived from two or more homologous genes. Both orthologous genes (resulting from a speciation event) and paralogous genes (resulting from gene duplication within a population) can be said to display divergent evolution.
Key Points
• Ectopic recombination occurs when there is an unequal crossing-over and the product of this recombination are a duplication at the site of the exchange and a reciprocal deletion.
• Gene duplications do not always result in detrimental mutations; they can contribute to divergent evolution, which causes genetic differences between groups to develop and eventually form new species.
• Replication slippage can occur when there is an error during DNA replication and duplications of short genetic sequences are produced.
• Retrotranspositions occur when a retrovirus copies their genome by reverse transcribing RNA to DNA and aberrantly attach to cellular mRNA and reverse transcribe copies of genes to create retrogenes.
• Aneuploidy can occur when there is a nondisjunction even at a single chromosome thus, the result is an abnormal number of chromosomes.
• Genetic divergence can occur by mechanisms such as genetic drift which contibute to the accumulation of independent genetic changes of two or more populations derived from a common ancestor.
Key Terms
• paralogous: having a similar structure indicating divergence from a common ancestral gene
• nondisjunction: the failure of chromosome pairs to separate properly during meiosis
• retrogene: a DNA gene copied back from RNA by reverse transcription
• genetic drift: an overall shift of allele distribution in an isolated population, due to random fluctuations in the frequencies of individual alleles of the genes | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/22%3A_The_Origin_of_Species/22.03%3A_The_Role_of_Genetic_Drift_and_Natural_Selection_in_Speciation/22.3A%3A_Gene_Duplications_and_Divergence.txt |
One of the best definition os species is that of the evolutionary biologist Ernst Mayr: "A species is an actually or potentially interbreeding population that does not interbreed with other such populations when there is opportunity to do so." However, sometimes breeding may take place (as it can between a horse and a donkey) but if so, the offspring are not so fertile and/or well adapted as the parents (the mule produced is sterile).
Allopatric Speciation: the Role of Isolation in Speciation
The formation of two or more species often (some workers think always!) requires geographical isolation of subpopulations of the species. Only then can natural selection or perhaps genetic drift produce distinctive gene pools. It is no accident that the various races (or "subspecies") of animals almost never occupy the same territory. Their distribution is allopatric ("other country").
The seven distinct subspecies or races of the yellowthroat Geothlypis trichas (a warbler) in the continental U.S. would soon merge into a single homogeneous population if they occupied the same territory and bred with one another.
Darwin's Finches
As a young man of 26, Charles Darwin visited the Galapagos Islands off the coast of Ecuador. Among the animals he studied were what appeared to be 13 species* of finches found nowhere else on earth.
• Some have stout beaks for eating seeds of one size or another (#2, #3, #6).
• Others have beaks adapted for eating insects or nectar.
• One (#7) has a beak like a woodpecker's. It uses it to drill holes in wood, but lacking the long tongue of a true woodpecker, it uses a cactus spine held in its beak to dig the insect out.
• One (#12) looks more like a warbler than a finch, but its eggs, nest, and courtship behavior is like that of the other finches.
Darwin's finches. The finches numbered 1–7 are ground finches. They seek their food on the ground or in low shrubs. Those numbered 8–13 are tree finches. They live primarily on insects.
1. Large cactus finch (Geospiza conirostris)
2. Large ground finch (Geospiza magnirostris)
3. Medium ground finch (Geospiza fortis)
4. Cactus finch (Geospiza scandens)
5. Sharp-beaked ground finch (Geospiza difficilis)
6. Small ground finch (Geospiza fuliginosa)
7. Woodpecker finch (Cactospiza pallida)
8. Vegetarian tree finch (Platyspiza crassirostris)
9. Medium tree finch (Camarhynchus pauper)
10. Large tree finch (Camarhynchus psittacula)
11. Small tree finch (Camarhynchus parvulus)
12. Warbler finch (Certhidia olivacea)
13. Mangrove finch (Cactospiza heliobates)
(From BSCS, Biological Science: Molecules to Man, Houghton Mifflin Co., 1963)
* Genetic analysis provides evidence that:
• There are actually two species of warbler finch — Certhidia olivacea now called the green warbler finch and Certhidia fusca, the gray warbler finch.
• The various populations of Geospiza difficilis found on the different islands belong to one or another of three clades so genetically distinct that they deserve full species status.
Whether the number is 13 or 17, since Darwin's time, these birds have provided a case study of how a single species reaching the Galapagos from Central or South America could - over a few million years - give rise to the various species that live there today. Several factors have been identified that may contribute to speciation.
Ecological opportunity
When the ancestor of Darwin's finches reached the Galapagos, it found no predators (There were no mammals and few reptiles on the islands.) and few, if any, competitors. There were only a handful of other types of songbirds. In fact, if true warblers or woodpeckers had been present, their efficiency at exploiting their niches would surely have prevented the evolution of warblerlike and woodpeckerlike finches.
Geographical Isolation (allopatry)
The proximity of the various islands has permitted enough migration of Darwin's finches between them to enable distinct island populations to arise. But the distances between the islands is great enough to limit interbreeding between populations on different islands. This has made possible the formation of distinctive subspecies (= races) on the various islands.
The importance of geographical isolation is illuminated by a single, fourteenth, species of Darwin's finches that lives on Cocos Island, some 500 miles (800 km) to the northeast of the Galapagos. The first immigrants there must also have found relaxed selection pressures with few predators or competitors. How different the outcome, though. Where one immigrant species gave rise to at least 13 on the scattered Galapagos Islands, no such divergence has occurred on the single, isolated Cocos Island.
Evolutionary Change
In isolation, changes in the gene pool can occur through some combination of natural selection, genetic drift, and founder effect. These factors may produce distinct subpopulations on the different islands. So long as they remain separate (allopatric) we consider them races or subspecies. In fact, they might not be able to interbreed with other races but so long as we don't know, we assume that they could.
How much genetic change is needed to create a new species? Perhaps not as much as you might think. For example, changes at one or just a few gene loci might do the trick. For example, a single mutation altering flower color or petal shape could immediately prevent cross-pollination between the new and the parental types (a form of prezygotic isolating mechanism).
Reunion
The question of their status - subspecies or true species - is resolved if they ever do come to occupy the same territory again (become sympatric). If successful interbreeding occurs, the differences will gradually disappear, and a single population will be formed again. Speciation will not have occurred. If, on the other hand, two subspecies reunite but fail to resume breeding, speciation has occurred and they have become separate species.
An example: The medium tree finch Camarhynchus pauper is found only on Floreana Island. Its close relative, the large tree finch, Camarhynchus psittacula, is found on all the central islands including Floreana. Were it not for its presence on Floreana, both forms would be considered subspecies of the same species. Because they do coexist and maintain their separate identity on Floreana, we know that speciation has occurred.
Isolating Mechanisms
What might keep two subpopulations from interbreeding when reunited geographically? There are several mechanisms.
Prezygotic Isolating Mechanisms act before fertilization occurs. Sexual selection - a failure to elicit mating behavior. On Floreana, Camarhynchus psittacula has a longer beak than Camarhynchus pauper, and the research teams led by Peter and Rosemary Grant have demonstrated that beak size is an important criterion by which Darwin's finches choose their mates. Two subpopulations may occupy different habitats in the same area and thus fail to meet at breeding time. In plants, a shift in the time of flowering can prevent pollination between the two subpopulations. Structural differences in the sex organs may become an isolating mechanism. The sperm may fail to reach or fuse with the egg.
Postzygotic Isolating Mechanisms act even if fertilization does occur. Even if a zygote is formed, genetic differences may have become so great that the resulting hybrids are less viable or less fertile than the parental types. The sterile mule produced by mating a horse with a donkey is an example. Sterility in the males produced by hybridization is more common than in females. In fact, it is the most common postzygotic isolating mechanism. When Drosophila melanogaster attempts to mate with its relative Drosophila simulans, no viable males are even produced. Mutations in a single gene (encoding a component of the nuclear pore complex) are responsible.
Reinforcement
When two species that have separated in allopatry become reunited, their prezygotic and postzygotic isolating mechanisms may become more stringent than those between the same species existing apart from each other. This phenomenon is called reinforcement. It arises from natural selection working to favor individuals that avoid interspecific matings, which would produce less-fit hybrids, when the two species are first reunited.
Speciation by Hybridization
Hybridization between related angiosperms is sometimes followed by a doubling of the chromosome number. The resulting polyploids are now fully fertile with each other although unable to breed with either parental type - a new species has been created. This appears to have been a frequent mechanism of speciation in angiosperms. Even without forming a polyploid, interspecific hybridization can occasionally lead to a new species of angiosperm. Two species of sunflower, the "common sunflower", Helianthus annuus, and the "prairie sunflower", H. petiolaris, grow widely over the western half of the United States. They can interbreed, but only rarely are fertile offspring produced.
However, Rieseberg and colleagues have found evidence that successful hybridization between them has happened naturally in the past. They have shown that three other species of sunflower (each growing in a habitat too harsh for either parental type) are each the product of an ancient hybridization between Helianthus annuus and H. petiolaris. Although each of these species has the same diploid number of chromosomes as the parents (2n = 34), they each have a pattern of chromosome segments that have been derived, by genetic recombination, from both the parental genomes. They demonstrated this in several ways, notably by combining RFLP analysis with the polymerase chain reaction (PCR).
They even went on to produce (at a low frequency) annuus x petiolaris hybrids in the greenhouse that mimicked the phenotypes and genotypes of the natural hybrids. (These monumental studies were described in the 29 August 2003 issue of Science.)
Another example. In Pennsylvania, hybrids between a species of fruit fly (not Drosophila) that feeds on blueberries and another species (again, not Drosophila) that feeds on snowberries feed on honeysuckle where they neither encounter competition from their parental species nor have an opportunity to breed with them (no introgression). This study was published in the 28 July 2005 issue of Nature. So speciation can occur as a result of hybridization between two related species, if the hybrid
• receives a genome that enables it to breed with other such hybrids but not breed with either parental species,
• can escape to a habitat where it does not have to compete with either parent,
• is adapted to live under those new conditions.
Adaptive Radiation
The processes described in this page can occur over and over. In the case of Darwin's finches, they must have been repeated a number of times forming new species that gradually divided the available habitats between them. From the first arrival have come a variety of ground-feeding and tree-feeding finches as well as the warblerlike finch and the tool-using woodpeckerlike finch. The formation of a number of diverse species from a single ancestral one is called an adaptive radiation.
Speciateion in theHouse mice on the island of Madeira
A report in the 13 January 2000 issue of Nature describes a study of house mouse populations on the island of Madeira off the Northwest coast of Africa. These workers (Janice Britton-Davidian et al) examined the karyotypes of 143 house mice (Mus musculus domesticus) from various locations along the coast of this mountainous island.
Their findings:
• There are 6 distinct populations (shown by different colors)
• Each of these has a distinct karyotype, with a diploid number less than the "normal" (2n = 40).
• The reduction in chromosome number has occurred through Robertsonian fusions. Mouse chromosomes tend to be acrocentric; that is, the centromere connects one long and one very short arm. Acrocentric chromosomes are at risk of translocations that fuse the long arms of two different chromosomes with the loss of the short arms.
• The different populations are allopatric; isolated in different valleys leading down to the sea.
• The distinct and uniform karyotype found in each population probably arose from genetic drift rather than natural selection.
• The 6 different populations are technically described as races because there is no opportunity for them to attempt interbreeding.
• However, they surely meet the definition of true species. While hybrids would form easily (no prezygotic isolating mechanisms), these would probably be infertile as proper synapsis and segregation of such different chromosomes would be difficult when the hybrids attempted to form gametes by meiosis.
Sympatric Speciation
Sympatric speciation refers to the formation of two or more descendant species from a single ancestral species all occupying the same geographic location. Some evolutionary biologists don't believe that it ever occurs. They feel that interbreeding would soon eliminate any genetic differences that might appear. But there is some compelling (albeit indirect) evidence that sympatric speciation can occur.
Speciation in three-spined sticklebacks
The three-spined sticklebacks, freshwater fishes that have been studied by Dolph Schluter (who received his Ph.D. for his work on Darwin's finches with Peter Grant) and his current colleagues in British Columbia, provide an intriguing example that is best explained by sympatric speciation.
They have found:
• Two different species of three-spined sticklebacks in each of five different lakes.
• a large benthic species with a large mouth that feeds on large prey in the littoral zone
• a smaller limnetic species with a smaller mouth that feeds on the small plankton in open water.
• DNA analysis indicates that each lake was colonized independently, presumably by a marine ancestor, after the last ice age.
• DNA analysis also shows that the two species in each lake are more closely related to each other than they are to any of the species in the other lakes.
• Nevertheless, the two species in each lake are reproductively isolated; neither mates with the other.
• However, aquarium tests showed that
• The benthic species from one lake will spawn with the benthic species from the other lakes and likewise the limnetic species from the different lakes will spawn with each other.
• These benthic and limnetic species even display their mating preferences when presented with sticklebacks from Japanese lakes; that is, a Canadian benthic prefers a Japanese benthic over its close limnetic cousin from its own lake.
• Their conclusion: in each lake, what began as a single population faced such competition for limited resources that
• disruptive selection — competition favoring fishes at either extreme of body size and mouth size over those nearer the mean — coupled with
• assortative mating — each size preferred mates like it
favored a divergence into two subpopulations exploiting different food in different parts of the lake.
• The fact that this pattern of speciation occurred the same way on three separate occasions suggests strongly that ecological factors in a sympatric population can cause speciation.
Sympatric speciation driven by ecological factors may also account for the extraordinary diversity of crustaceans living in the depths of Siberia's Lake Baikal.
How many genes are needed to start down the path to sympatric speciation?
Perhaps not very many. The European corn borer, Ostrinia nubilalis, (which despite its common name is a major pest in the U.S. as well) exists as two distinct races designated Z and E. Both can be found in the same area; that is, they are sympatric. But in the field, they practice assortative mating - only breeding with mates of their own race.
The females of both races synthesize and release a pheromone that is a sex attractant for the males. Both races use the same substance but different isomers of it. Which isomer is produced is under the control of a single enzyme-encoding gene locus. The ability of the males to respond to one isomer or the other is controlled by 2 loci.
The Problem of Clines
There is another possible way for new species to arise in the absence of geographical barriers. If a population ranges over a large area and if the individuals in that population can disperse over only a small portion of this range, then gene flow across these great distances would be reduced. The occurrence of gradual phenotypic (and genotypic) differences in a population across a large geographical area is called a cline. Successful interbreeding occurs freely at every point along the cline, but individuals at the ends of the cline may not be able to interbreed. This can be tested in the laboratory.
And, on occasions, it is tested in nature. If a cline bends around so that the ends meet, and the populations reunited at the junction cannot interbreed, then the definition of separate species has been met. Such species are called ring species and this type of speciation is called parapatric speciation.
Two examples:
1. The Caribbean slipper spurge Euphorbia tithymaloides.
Genetic analysis shows that this wildflower originated in Central America where Mexico and Guatemala share a common boundary. From there it spread in two directions
• northeast through the Yucatan peninsula and then island-hopped through Jamaica, the Dominican Republic, Puerto Rico and into the Virgin Islands;
• south through Central America, on through Venezuela, and then north through Barbados and the other islands of the Lesser Antilles finally also reaching the Virgin Islands.
Reunited in the Virgin Islands, the two populations have diverged sufficiently that they retain their distinctive genotypic and phenotypic traits. Ongoing studies will determine to what degree they may be reproductively isolated.
2. The large-blotched salamander Ensatina eschscholtzii.
This animal is found in California where it occurs in a number of different subspecies or races. A single subspecies is found in Northern California, and it is thought to be the founder of all the others. Over time that original population spread southward in two directions:
• down the Sierra Nevada mountains east of the great central San Joaquin Valley and
• down the coast range of mountains west of the valley.
South of the valley, the eastern group has moved west and now meets the western group, closing the ring. Here the two populations fail to interbreed successfully, maintaining their distinct identities. But each subspecies interbreeds in an unbroken chain up the two paths their ancestors took.
Ring species present a difficult problem in assigning species designations. It is easy to say that the populations at the ends of the cline represent separate species, but where did one give rise to the other? At every point along the cline, interbreeding goes on successfully.
The same problem faces paleontologists examining the gradual phenotypic changes seen in an unbroken line of ever-younger fossils from what one presumes to be a single line of descent. If one could resurrect the ancestral species (A) and the descendant species (B) and they could not interbreed, then they meet the definition of separate species. But there was no moment in time when one could say that A became B. So the clines of today are a model in space of Darwin's descent with modification occurring over time.
Although clines present a problem for classifiers, they are a beautiful demonstration of Darwin's conviction that the accumulation of small inherited differences can lead to the formation of new species. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/22%3A_The_Origin_of_Species/22.04%3A_The_Geography_of_Speciation.txt |
The biological definition of species, which works for sexually reproducing organisms, is a group of actually or potentially interbreeding individuals. According to this definition, one species is distinguished from another by the possibility of matings between individuals from each species to produce fertile offspring. There are exceptions to this rule. Many species are similar enough that hybrid offspring are possible and may often occur in nature, but for the majority of species this rule generally holds. In fact, the presence of hybrids between similar species suggests that they may have descended from a single interbreeding species and that the speciation process may not yet be completed.
Given the extraordinary diversity of life on the planet there must be mechanisms for speciation: the formation of two species from one original species. Darwin envisioned this process as a branching event and diagrammed the process in the only illustration found in On the Origin of Species (Figure \(1\)a). For speciation to occur, two new populations must be formed from one original population, and they must evolve in such a way that it becomes impossible for individuals from the two new populations to interbreed. Biologists have proposed mechanisms by which this could occur that fall into two broad categories. Allopatric speciation, meaning speciation in “other homelands,” involves a geographic separation of populations from a parent species and subsequent evolution. Sympatric speciation, meaning speciation in the “same homeland,” involves speciation occurring within a parent species while remaining in one location.
Biologists think of speciation events as the splitting of one ancestral species into two descendant species. There is no reason why there might not be more than two species formed at one time except that it is less likely and such multiple events can also be conceptualized as single splits occurring close in time.
Speciation through Geographic Separation
A geographically continuous population has a gene pool that is relatively homogeneous. Gene flow, the movement of alleles across the range of the species, is relatively free because individuals can move and then mate with individuals in their new location. Thus, the frequency of an allele at one end of a distribution will be similar to the frequency of the allele at the other end. When populations become geographically discontinuous that free-flow of alleles is prevented. When that separation lasts for a period of time, the two populations are able to evolve along different trajectories. Thus, their allele frequencies at numerous genetic loci gradually become more and more different as new alleles independently arise by mutation in each population. Typically, environmental conditions, such as climate, resources, predators, and competitors, for the two populations will differ causing natural selection to favor divergent adaptations in each group. Different histories of genetic drift, enhanced because the populations are smaller than the parent population, will also lead to divergence.
Given enough time, the genetic and phenotypic divergence between populations will likely affect characters that influence reproduction enough that were individuals of the two populations brought together, mating would be less likely, or if a mating occurred, offspring would be non-viable or infertile. Many types of diverging characters may affect the reproductive isolation (inability to interbreed) of the two populations. These mechanisms of reproductive isolation can be divided into prezygotic mechanisms (those that operate before fertilization) and postzygotic mechanisms (those that operate after fertilization). Prezygotic mechanisms include traits that allow the individuals to find each other, such as the timing of mating, sensitivity to pheromones, or choice of mating sites. If individuals are able to encounter each other, character divergence may prevent courtship rituals from leading to a mating either because female preferences have changed or male behaviors have changed. Physiological changes may interfere with successful fertilization if mating is able to occur. Postzygotic mechanisms include genetic incompatibilities that prevent proper development of the offspring, or if the offspring live, they may be unable to produce viable gametes themselves as in the example of the mule, the infertile offspring of a female horse and a male donkey.
If the two isolated populations are brought back together and the hybrid offspring that formed from matings between individuals of the two populations have lower survivorship or reduced fertility, then selection will favor individuals that are able to discriminate between potential mates of their own population and the other population. This selection will enhance the reproductive isolation.
Isolation of populations leading to allopatric speciation can occur in a variety of ways: from a river forming a new branch, erosion forming a new valley, or a group of organisms traveling to a new location without the ability to return, such as seeds floating over the ocean to an island. The nature of the geographic separation necessary to isolate populations depends entirely on the biology of the organism and its potential for dispersal. If two flying insect populations took up residence in separate nearby valleys, chances are that individuals from each population would fly back and forth, continuing gene flow. However, if two rodent populations became divided by the formation of a new lake, continued gene flow would be unlikely; therefore, speciation would be more likely.
Biologists group allopatric processes into two categories. If a few members of a species move to a new geographical area, this is called dispersal. If a natural situation arises to physically divide organisms, this is called vicariance.
Scientists have documented numerous cases of allopatric speciation taking place. For example, along the west coast of the United States, two separate subspecies of spotted owls exist. The northern spotted owl has genetic and phenotypic differences from its close relative, the Mexican spotted owl, which lives in the south (Figure \(2\)). The cause of their initial separation is not clear, but it may have been caused by the glaciers of the ice age dividing an initial population into two.1
Additionally, scientists have found that the further the distance between two groups that once were the same species, the more likely for speciation to take place. This seems logical because as the distance increases, the various environmental factors would likely have less in common than locations in close proximity. Consider the two owls; in the north, the climate is cooler than in the south; the other types of organisms in each ecosystem differ, as do their behaviors and habits; also, the hunting habits and prey choices of the owls in the south vary from the northern ones. These variances can lead to evolved differences in the owls, and over time speciation will likely occur unless gene flow between the populations is restored.
In some cases, a population of one species disperses throughout an area, and each finds a distinct niche or isolated habitat. Over time, the varied demands of their new lifestyles lead to multiple speciation events originating from a single species, which is called adaptive radiation. From one point of origin, many adaptations evolve causing the species to radiate into several new ones. Island archipelagos like the Hawaiian Islands provide an ideal context for adaptive radiation events because water surrounds each island, which leads to geographical isolation for many organisms (Figure \(3\)). The Hawaiian honeycreeper illustrates one example of adaptive radiation. From a single species, called the founder species, numerous species have evolved, including the eight shown in Figure \(3\).
Notice the differences in the species’ beaks in Figure \(3\). Change in the genetic variation for beaks in response to natural selection based on specific food sources in each new habitat led to evolution of a different beak suited to the specific food source. The fruit and seed-eating birds have thicker, stronger beaks which are suited to break hard nuts. The nectar-eating birds have long beaks to dip into flowers to reach their nectar. The insect-eating birds have beaks like swords, appropriate for stabbing and impaling insects. Darwin’s finches are another well-studied example of adaptive radiation in an archipelago.
Speciation without Geographic Separation
Can divergence occur if no physical barriers are in place to separate individuals who continue to live and reproduce in the same habitat? A number of mechanisms for sympatric speciation have been proposed and studied.
One form of sympatric speciation can begin with a chromosomal error during meiosis or the formation of a hybrid individual with too many chromosomes. Polyploidy is a condition in which a cell, or organism, has an extra set, or sets, of chromosomes. Scientists have identified two main types of polyploidy that can lead to reproductive isolation of an individual in the polyploid state. In some cases a polyploid individual will have two or more complete sets of chromosomes from its own species in a condition called autopolyploidy (Figure \(4\)). The prefix “auto” means self, so the term means multiple chromosomes from one’s own species. Polyploidy results from an error in meiosis in which all of the chromosomes move into one cell instead of separating.
For example, if a plant species with 2n = 6 produces autopolyploid gametes that are also diploid (2n = 6, when they should be n = 3), the gametes now have twice as many chromosomes as they should have. These new gametes will be incompatible with the normal gametes produced by this plant species. But they could either self-pollinate or reproduce with other autopolyploid plants with gametes having the same diploid number. In this way, sympatric speciation can occur quickly by forming offspring with 4n called a tetraploid. These individuals would immediately be able to reproduce only with those of this new kind and not those of the ancestral species. The other form of polyploidy occurs when individuals of two different species reproduce to form a viable offspring called an allopolyploid. The prefix “allo” means “other” (recall from allopatric); therefore, an allopolyploid occurs when gametes from two different species combine. Figure \(5\) illustrates one possible way an allopolyploidy can form. Notice how it takes two generations, or two reproductive acts, before the viable fertile hybrid results.
The cultivated forms of wheat, cotton, and tobacco plants are all allopolyploids. Although polyploidy occurs occasionally in animals, most chromosomal abnormalities in animals are lethal; it takes place most commonly in plants. Scientists have discovered more than 1/2 of all plant species studied relate back to a species evolved through polyploidy.
Sympatric speciation may also take place in ways other than polyploidy. For example, imagine a species of fish that lived in a lake. As the population grew, competition for food also grew. Under pressure to find food, suppose that a group of these fish had the genetic flexibility to discover and feed off another resource that was unused by the other fish. What if this new food source was found at a different depth of the lake? Over time, those feeding on the second food source would interact more with each other than the other fish; therefore they would breed together as well. Offspring of these fish would likely behave as their parents and feed and live in the same area, keeping them separate from the original population. If this group of fish continued to remain separate from the first population, eventually sympatric speciation might occur as more genetic differences accumulated between them.
This scenario does play out in nature, as do others that lead to reproductive isolation. One such place is Lake Victoria in Africa, famous for its sympatric speciation of cichlid fish. Researchers have found hundreds of sympatric speciation events in these fish, which have not only happened in great number, but also over a short period of time. Figure \(6\) shows this type of speciation among a cichlid fish population in Nicaragua. In this locale, two types of cichlids live in the same geographic location; however, they have come to have different morphologies that allow them to eat various food sources.
Finally, a well-documented example of ongoing sympatric speciation occurred in the apple maggot fly, Rhagoletis pomonella, which arose as an isolated population sometime after the introduction of the apple into North America. The native population of flies fed on hawthorn species and is host-specific: it only infests hawthorn trees. Importantly, it also uses the trees as a location to meet for mating. It is hypothesized that either through mutation or a behavioral mistake, flies jumped hosts and met and mated in apple trees, subsequently laying their eggs in apple fruit. The offspring matured and kept their preference for the apple trees effectively dividing the original population into two new populations separated by host species, not by geography. The host jump took place in the nineteenth century, but there are now measureable differences between the two populations of fly. It seems likely that host specificity of parasites in general is a common cause of sympatric speciation.
Section Summary
Speciation occurs along two main pathways: geographic separation (allopatric speciation) and through mechanisms that occur within a shared habitat (sympatric speciation). Both pathways force reproductive isolation between populations. Sympatric speciation can occur through errors in meiosis that form gametes with extra chromosomes, called polyploidy. Autopolyploidy occurs within a single species, whereas allopolyploidy occurs because of a mating between closely related species. Once the populations are isolated, evolutionary divergence can take place leading to the evolution of reproductive isolating traits that prevent interbreeding should the two populations come together again. The reduced viability of hybrid offspring after a period of isolation is expected to select for stronger inherent isolating mechanisms.
Footnotes
1. 1 Courtney, S.P., et al, “Scientific Evaluation of the Status of the Northern Spotted Owl,” Sustainable Ecosystems Institute (2004), Portland, OR.
Glossary
adaptive radiation
a speciation when one species radiates out to form several other species
allopatric speciation
a speciation that occurs via a geographic separation
dispersal
an allopatric speciation that occurs when a few members of a species move to a new geographical area
speciation
a formation of a new species
sympatric speciation
a speciation that occurs in the same geographic space
vicariance
an allopatric speciation that occurs when something in the environment separates organisms of the same species into separate groups | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/22%3A_The_Origin_of_Species/22.05%3A_Adaptive_Radiation_and_Biological_Diversity.txt |
Two patterns are currently observed in the rates of speciation: gradual speciation and punctuated equilibrium.
Learning Objectives
• Explain how the interaction of an organism’s population size in association with environmental changes can lead to different rates of speciation
Key Points
• In the gradual speciation model, species diverge slowly over time in small steps while in the punctuated equilibrium model, a new species diverges rapidly from the parent species.
• The two key influencing factors on the change in speciation rate are the environmental conditions and the population size.
• Gradual speciation is most likely to occur in large populations that live in a stable environment, while the punctuation equilibrium model is more likely to occur in a small population with rapid environmental change.
Key Terms
• punctuated equilibrium: a theory of evolution holding that evolutionary change tends to be characterized by long periods of stability, with infrequent episodes of very fast development
• gradualism: in evolutionary biology, belief that evolution proceeds at a steady pace, without the sudden development of new species or biological features from one generation to the next
Varying Rates of Speciation
Scientists around the world study speciation, documenting observations both of living organisms and those found in the fossil record. As their ideas take shape and as research reveals new details about how life evolves, they develop models to help explain rates of speciation. In terms of how quickly speciation occurs, two patterns are currently observed: the gradual speciation model and the punctuated equilibrium model.
In the gradual speciation model, species diverge gradually over time in small steps. In the punctuated equilibrium model, a new species changes quickly from the parent species and then remains largely unchanged for long periods of time afterward. This early change model is called punctuated equilibrium, because it begins with a punctuated or periodic change and then remains in balance afterward. While punctuated equilibrium suggests a faster tempo, it does not necessarily exclude gradualism.
The primary influencing factor on changes in speciation rate is environmental conditions. Under some conditions, selection occurs quickly or radically. Consider a species of snails that had been living with the same basic form for many thousands of years. Layers of their fossils would appear similar for a long time. When a change in the environment takes place, such as a drop in the water level, a small number of organisms are separated from the rest in a brief period of time, essentially forming one large and one tiny population. The tiny population faces new environmental conditions. Because its gene pool quickly became so small, any variation that surfaces and that aids in surviving the new conditions becomes the predominant form.
22.07: Speciation and Extinction Through Time
History of life as revealed by the fossil record
With help from molecular phylogenies:
Eras Periods Epochs Aquatic Life Terrestrial Life
With approximate starting dates in millions of years ago in parentheses. Geologic features in green
Cenozoic (66)
The "Age of
Mammals"
Quaternary (2.6) Holocene Humans in the new world
Pleistocene Periodic glaciation First humans
Continental drift continues
Neogene (23) Pliocene Atmospheric oxygen reaches today's level (21%) Hominids
Miocene Adaptive radiation of birds, continued radiation of mammals
Paleogene (66) Oligocene All modern groups present
Eocene
Paleocene
Mesozoic (251)
The "Age
of Reptiles"
Cretaceous (146) Still attached: N. America & N. Europe; Australia & Antarctica; Mass extinction of both aquatic and terrestrial life at the end
Modern bony fishes Extinction of dinosaurs and pterosaurs; first snakes
Extinction of ammonites, plesiosaurs, ichthyosaurs Rise of angiosperms
Africa & S. America begin to drift apart
Jurassic (200) Plesiosaurs, ichthyosaurs abundant; first diatoms Archaeopteryx; dinosaurs dominant but mammals (Eutheria) begin to diversify
Ammonites again abundant First lizards
Skates, rays, and bony fishes abundant Adaptive radiation of dinosaurs
Pangaea splits into Laurasia and Gondwana; atmospheric oxygen drops to ~13%
Triassic (251) Mass extinctions at the end. Mass extinctions at the end.
First mammals
Adaptive radiation of reptiles: thecodonts, therapsids, turtles, crocodiles, first dinosaurs
Ammonites abundant at first
Rise of bony fishes
Paleozoic (542) Permian (299) Periodic glaciation and arid climate; atmospheric oxygen reaches ~30%. Volcanic eruptions killed off 90% of marine species at end.
Extinction of trilobites Reptiles abundant. Cycads, conifers, ginkgos
Pennsylvanian (320) Warm, humid climate
Together
the Pennsylvanian
and Mississippian
make up the
"Carboniferous";
also called the
"Age of Amphibians"
Ammonites, bony fishes First reptiles
Coal swamps
Mississippian (359) Adaptive radiation of sharks Forests of lycopsids, sphenopsids, and seed ferns
Amphibians abundant
Adaptive radiation of the insects (Hexapoda)
Atmospheric oxygen begins to rise as organic matter is buried, not respired
Devonian (416)
The "Age of Fishes"
Extensive inland seas Cartilaginous and bony fishes abundant. Ammonites, nautiloids, ostracoderms, eurypterids Ferns, lycopsids, and sphenopsids
First gymnosperms
First amphibians
Silurian (443) Mild climate; inland seas First bony fishes First myriapods and chelicerates
Ordovician (485) Mild climate, inland seas Trilobites abundant Fungi present
First plants (liverworts?) First insects
Cambrian (541) First vertebrates (jawless fishes). Eurypterids, crustaceans
mollusks, echinoderms, sponges, cnidarians, annelids, and tunicates present. Trilobites dominant.
No fossils of terrestrial eukaryotes, but phylogenetic trees suggest that lichens, mosses, perhaps even vascular plants were present.
Periodic glaciation
Proterozoic (2500) Ediacaran
(635)
Fossil evidence of multicellular algae, fungi, and bilaterian invertebrates
Evidence of eukaryotes
~1.8 x109 years ago
Archaean (3600) Evidence of archaea and bacteria
~3.5 x109 years ago
The Geologic and Evolutionary Record
A remarkable feature of the table above is how often evolutionary changes coincided with geologic changes on the earth. But consider that changes in geology (e.g., mountain formation or lowering of the sea level) cause changes in climate, and together these alter the habitats available for life. Two types of geologic change seem to have had especially dramatic effects on life: continental drift and the impact of asteroids
Continental Drift
A body of evidence, both geological and biological, supports the conclusion that 200 million years ago, at the start of the Mesozoic era, all the continents were attached to one another in a single land mass, which has been named Pangaea. This drawing of Pangaea (adapted from data of R. S. Dietz and J. C. Holden) is based on a computer-generated fit of the continents as they would look if the sea level were lowered by 6000 feet (~1800 meters). During the Triassic, Pangaea began to break up, first into two major land masses:
• Laurasia in the Northern Hemisphere
• Gondwana in the Southern Hemisphere.
The present continents separated at intervals throughout the remainder of the Mesozoic and through the Cenozoic, eventually reaching the positions they have today. Let us examine some of the evidence.
Shape of the Continents
The east coast of South America and the west coast of Africa and are strikingly complementary. This is even more dramatic when one tries to fit the continents together using the boundaries of the continental slopes, e.g., 6000 feet (~1800 meters) down, rather than the shorelines.
Geology
• In both mineral content and age, the rocks in a region on the east coast of Brazil match precisely those found in Ghana on the west coast of Africa.
• The low mountain ranges and rock types in New England and eastern Canada appear to be continued in parts of Great Britain, France, and Scandinavia.
• India and the southern part of Africa both show evidence of periodic glaciation during Paleozoic times (even though both are now close to the equator). The pattern of glacial deposits in the two regions not only match each other but also glacial deposits found in South America, Australia, and Antarctica.
Fossils
• Fossil reptiles found in South Africa are also found in Brazil and Argentina.
• Fossil amphibians and reptiles found in Antarctica are also found in South Africa, India, and China.
• Most of the marsupials alive today are confined to South America and Australia. But if these two continents were connected by Antarctica in the Mesozoic, one might expect to find fossil marsupials there. In March 1982, this prediction was fulfilled with the discovery in Antarctica of the remains of Polydolops, a 9-ft (2.7 m) marsupial.
The Impact Hypothesis
The Cretaceous period, the last period of the Mesozoic, marked the end of the Age of Reptiles. It was followed by the Cenozoic era, the Age of Mammals. Although extinctions have occurred throughout the history of life, an extraordinary number of them occurred in a relatively brief period at the end of the Cretaceous. Why?
The Alvarez Theory
Louis Alvarez, his son Walter, and their colleagues proposed that a giant asteroid or comet striking the earth some 66 million years ago caused the massive die-off at the end of the Cretaceous. Presumably, the impact generated so much dust and gases that skies were darkened all over the earth, photosynthesis declined, and worldwide temperatures dropped. The outcome was that as many as 75% of all species — including all dinosaurs — became extinct.
The key piece of evidence for the Alvarez hypothesis was the finding of thin deposits of clay containing the element iridium at the interface between the rocks of the Cretaceous and those of the Paleogene period (called the K-Pg boundary after the German word for Cretaceous). Iridium is a rare element on earth (although often discharged from volcanoes), but occurs in certain meteorites at concentrations thousands of times greater than in the earth's crust.
After languishing for many years, the Alvarez theory gained strong support from the discovery in the 1990s of the remains of a huge (180 km in diameter) crater in the Yucatan Peninsula that dated to 65 million years ago.
The abundance of sulfate-containing rock in the region suggests that the impact generated enormous amounts of sulfur dioxide (SO2), which later returned to earth as a bath of acid rain. A smaller crater in Iowa, formed at the same time, many have contributed to the devastation. Perhaps during this period the earth passed through a swarm of asteroids or a comet and the repeated impacts made the earth uninhabitable for so many creatures of the Mesozoic.
Other Impacts
A mass extinction of non-dinosaur reptiles occurred earlier, at the end of the Triassic. It was followed by a great expansion in the diversity of dinosaurs. The recent discovery of a layer enriched in iridium in rocks formed at the boundary between the Triassic and Jurassic suggests that impact from an asteroid or comet may have been responsible then just as it was at the K-Pg boundary.
The largest extinction of all time occurred still earlier at the end of the Permian period. There is evidence off the coast of Australia that a huge impact there may have contributed to the extinctions at the Permian-Triassic (P-T) boundary. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/22%3A_The_Origin_of_Species/22.06%3A_The_Pace_of_Evolution.txt |
Learning Objecctives
• Describe how microorganisms are classified and distinguished as unique species
• Compare historical and current systems of taxonomy used to classify microorganisms
Once microbes became visible to humans with the help of microscopes, scientists began to realize their enormous diversity. Microorganisms vary in all sorts of ways, including their size, their appearance, and their rates of reproduction. To study this incredibly diverse new array of organisms, researchers needed a way to systematically organize them.
The Science of Taxonomy
Taxonomy is the classification, description, identification, and naming of living organisms. Classification is the practice of organizing organisms into different groups based on their shared characteristics. The most famous early taxonomist was a Swedish botanist, zoologist, and physician named Carolus Linnaeus (1701–1778). In 1735, Linnaeus published Systema Naturae, an 11-page booklet in which he proposed the Linnaean taxonomy, a system of categorizing and naming organisms using a standard format so scientists could discuss organisms using consistent terminology. He continued to revise and add to the book, which grew into multiple volumes (Figure \(1\)).
In his taxonomy, Linnaeus divided the natural world into three kingdoms: animal, plant, and mineral (the mineral kingdom was later abandoned). Within the animal and plant kingdoms, he grouped organisms using a hierarchy of increasingly specific levels and sublevels based on their similarities. The names of the levels in Linnaeus’s original taxonomy were kingdom, class, order, family, genus (plural: genera), and species. Species was, and continues to be, the most specific and basic taxonomic unit.
Evolving Trees of Life (Phylogenies)
With advances in technology, other scientists gradually made refinements to the Linnaean system and eventually created new systems for classifying organisms. In the 1800s, there was a growing interest in developing taxonomies that took into account the evolutionary relationships, or phylogenies, of all different species of organisms on earth. One way to depict these relationships is via a diagram called a phylogenetic tree (or tree of life). In these diagrams, groups of organisms are arranged by how closely related they are thought to be. In early phylogenetic trees, the relatedness of organisms was inferred by their visible similarities, such as the presence or absence of hair or the number of limbs. Now, the analysis is more complicated. Today, phylogenic analyses include genetic, biochemical, and embryological comparisons, as will be discussed later in this chapter.
Linnaeus’s tree of life contained just two main branches for all living things: the animal and plant kingdoms. In 1866, Ernst Haeckel, a German biologist, philosopher, and physician, proposed another kingdom, Protista, for unicellular organisms (Figure \(2\)). He later proposed a fourth kingdom, Monera, for unicellular organisms whose cells lack nuclei, like bacteria.
Nearly 100 years later, in 1969, American ecologist Robert Whittaker (1920–1980) proposed adding another kingdom—Fungi—in his tree of life. Whittaker’s tree also contained a level of categorization above the kingdom level—the empire or superkingdom level—to distinguish between organisms that have membrane-bound nuclei in their cells (eukaryotes) and those that do not (prokaryotes). Empire Prokaryota contained just the Kingdom Monera. The Empire Eukaryota contained the other four kingdoms: Fungi, Protista, Plantae, and Animalia. Whittaker’s five-kingdom tree was considered the standard phylogeny for many years.
Figure \(3\) shows how the tree of life has changed over time. Note that viruses are not found in any of these trees. That is because they are not made up of cells and thus it is difficult to determine where they would fit into a tree of life.
Exercise \(1\)
Briefly summarize how our evolving understanding of microorganisms has contributed to changes in the way that organisms are classified.
Clinical Focus: Part 2
Antibiotic drugs are specifically designed to kill or inhibit the growth of bacteria. But after a couple of days on antibiotics, Cora shows no signs of improvement. Also, her CSF cultures came back from the lab negative. Since bacteria or fungi were not isolated from Cora’s CSF sample, her doctor rules out bacterial and fungal meningitis. Viral meningitis is still a possibility.
However, Cora now reports some troubling new symptoms. She is starting to have difficulty walking. Her muscle stiffness has spread from her neck to the rest of her body, and her limbs sometimes jerk involuntarily. In addition, Cora’s cognitive symptoms are worsening. At this point, Cora’s doctor becomes very concerned and orders more tests on the CSF samples.
Exercise \(2\)
What types of microorganisms could be causing Cora’s symptoms?
The Role of Genetics in Modern Taxonomy
Haeckel’s and Whittaker’s trees presented hypotheses about the phylogeny of different organisms based on readily observable characteristics. But the advent of molecular genetics in the late 20th century revealed other ways to organize phylogenetic trees. Genetic methods allow for a standardized way to compare all living organisms without relying on observable characteristics that can often be subjective. Modern taxonomy relies heavily on comparing the nucleic acids (deoxyribonucleic acid [DNA] or ribonucleic acid [RNA]) or proteins from different organisms. The more similar the nucleic acids and proteins are between two organisms, the more closely related they are considered to be.
In the 1970s, American microbiologist Carl Woese discovered what appeared to be a “living record” of the evolution of organisms. He and his collaborator George Fox created a genetics-based tree of life based on similarities and differences they observed in the small subunit ribosomal RNA (rRNA) of different organisms. In the process, they discovered that a certain type of bacteria, called archaebacteria (now known simply as archaea), were significantly different from other bacteria and eukaryotes in terms of the sequence of small subunit rRNA. To accommodate this difference, they created a tree with three Domains above the level of Kingdom: Archaea, Bacteria, and Eukarya (Figure \(4\)). Genetic analysis of the small subunit rRNA suggests archaea, bacteria, and eukaryotes all evolved from a common ancestral cell type. The tree is skewed to show a closer evolutionary relationship between Archaea and Eukarya than they have to Bacteria.
Exercise \(3\)
1. In modern taxonomy, how do scientists determine how closely two organisms are related?
2. Explain why the branches on the “tree of life” all originate from a single “trunk.”
Naming Microbes
In developing his taxonomy, Linnaeus used a system of binomial nomenclature, a two-word naming system for identifying organisms by genus and species. For example, modern humans are in the genus Homo and have the species name sapiens, so their scientific name in binomial nomenclature is Homo sapiens. In binomial nomenclature, the genus part of the name is always capitalized; it is followed by the species name, which is not capitalized. Both names are italicized.
Taxonomic names in the 18th through 20th centuries were typically derived from Latin, since that was the common language used by scientists when taxonomic systems were first created. Today, newly discovered organisms can be given names derived from Latin, Greek, or English. Sometimes these names reflect some distinctive trait of the organism; in other cases, microorganisms are named after the scientists who discovered them. The archaeon Haloquadratum walsbyi is an example of both of these naming schemes. The genus, Haloquadratum, describes the microorganism’s saltwater habitat (halo is derived from the Greek word for “salt”) as well as the arrangement of its square cells, which are arranged in square clusters of four cells (quadratum is Latin for “foursquare”). The species, walsbyi, is named after Anthony Edward Walsby, the microbiologist who discovered Haloquadratum walsbyi in in 1980. While it might seem easier to give an organism a common descriptive name—like a red-headed woodpecker—we can imagine how that could become problematic. What happens when another species of woodpecker with red head coloring is discovered? The systematic nomenclature scientists use eliminates this potential problem by assigning each organism a single, unique two-word name that is recognized by scientists all over the world.
In this text, we will typically abbreviate an organism’s genus and species after its first mention. The abbreviated form is simply the first initial of the genus, followed by a period and the full name of the species. For example, the bacterium Escherichia coli is shortened to E. coli in its abbreviated form. You will encounter this same convention in other scientific texts as well.
Bergey’s Manuals
Whether in a tree or a web, microbes can be difficult to identify and classify. Without easily observable macroscopic features like feathers, feet, or fur, scientists must capture, grow, and devise ways to study their biochemical properties to differentiate and classify microbes. Despite these hurdles, a group of microbiologists created and updated a set of manuals for identifying and classifying microorganisms. First published in 1923 and since updated many times, Bergey’s Manual of Determinative Bacteriology and Bergey’s Manual of Systematic Bacteriology are the standard references for identifying and classifying different prokaryotes. (Appendix D of this textbook is partly based on Bergey’s manuals; it shows how the organisms that appear in this textbook are classified.) Because so many bacteria look identical, methods based on nonvisual characteristics must be used to identify them. For example, biochemical tests can be used to identify chemicals unique to certain species. Likewise, serological tests can be used to identify specific antibodies that will react against the proteins found in certain species. Ultimately, DNA and rRNA sequencing can be used both for identifying a particular bacterial species and for classifying newly discovered species.
Exercise \(4\)
• What is binomial nomenclature and why is it a useful tool for naming organisms?
• Explain why a resource like one of Bergey’s manuals would be helpful in identifying a microorganism in a sample.
Same Name, Different Strain
Within one species of microorganism, there can be several subtypes called strains. While different strains may be nearly identical genetically, they can have very different attributes. The bacteriumEscherichia coli is infamous for causing food poisoning and traveler’s diarrhea. However, there are actually many different strains of E. coli, and they vary in their ability to cause disease.
One pathogenic (disease-causing) E. coli strain that you may have heard of is E. coli O157:H7. In humans, infection from E. coli O157:H7 can cause abdominal cramps and diarrhea. Infection usually originates from contaminated water or food, particularly raw vegetables and undercooked meat. In the 1990s, there were several large outbreaks of E. coli O157:H7 thought to have originated in undercooked hamburgers.
While E. coli O157:H7 and some other strains have given E. coli a bad name, most E. coli strains do not cause disease. In fact, some can be helpful. Different strains of E. coli found naturally in our gut help us digest our food, provide us with some needed chemicals, and fight against pathogenic microbes.
Summary
• Carolus Linnaeus developed a taxonomic system for categorizing organisms into related groups.
• Binomial nomenclature assigns organisms Latinized scientific names with a genus and species designation.
• A phylogenetic tree is a way of showing how different organisms are thought to be related to one another from an evolutionary standpoint.
• The first phylogenetic tree contained kingdoms for plants and animals; Ernst Haeckel proposed adding a kingdom for protists.
• Robert Whittaker’s tree contained five kingdoms: Animalia, Plantae, Protista, Fungi, and Monera.
• Carl Woese used small subunit ribosomal RNA to create a phylogenetic tree that groups organisms into three domains based on their genetic similarity.
• Bergey’s manuals of determinative and systemic bacteriology are the standard references for identifying and classifying bacteria, respectively.
• Bacteria can be identified through biochemical tests, DNA/RNA analysis, and serological testing methods.
Glossary
binomial nomenclature
a universal convention for the scientific naming of organisms using Latinized names for genus and species
eukaryote
an organism made up of one or more cells that contain a membrane-bound nucleus and organelles
phylogeny
the evolutionary history of a group of organisms
prokaryote
an organism whose cell structure does not include a membrane-bound nucleus
taxonomy
the classification, description, identification, and naming of living organisms | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/23%3A_Systematics_Phylogeny_and_Comparative_Biology/23.01%3A_Systematics.txt |
Scientists collect information that allows them to make evolutionary connections between organisms. Similar to detective work, scientists must use evidence to uncover the facts. In the case of phylogeny, evolutionary investigations focus on two types of evidence: morphologic (form and function) and genetic.
Two Measures of Similarity
Organisms that share similar physical features and genetic sequences tend to be more closely related than those that do not. Features that overlap both morphologically and genetically are referred to as homologous structures; the similarities stem from common evolutionary paths. For example, as shown in Figure \(1\), the bones in the wings of bats and birds, the arms of humans, and the foreleg of a horse are homologous structures. Notice the structure is not simply a single bone, but rather a grouping of several bones arranged in a similar way in each organism even though the elements of the structure may have changed shape and size.
Misleading Appearances
Some organisms may be very closely related, even though a minor genetic change caused a major morphological difference to make them look quite different. For example, chimpanzees and humans, the skulls of which are shown in Figure \(2\) are very similar genetically, sharing 99 percent1 of their genes. However, chimpanzees and humans show considerable anatomical differences, including the degree to which the jaw protrudes in the adult and the relative lengths of our arms and legs.
However, unrelated organisms may be distantly related yet appear very much alike, usually because common adaptations to similar environmental conditions evolved in both. An example is the streamlined body shapes, the shapes of fins and appendages, and the shape of the tails in fishes and whales, which are mammals. These structures bear superficial similarity because they are adaptations to moving and maneuvering in the same environment—water. When a characteristic that is similar occurs by adaptive convergence (convergent evolution), and not because of a close evolutionary relationship, it is called an analogous structure. In another example, insects use wings to fly like bats and birds. We call them both wings because they perform the same function and have a superficially similar form, but the embryonic origin of the two wings is completely different. The difference in the development, or embryogenesis, of the wings in each case is a signal that insects and bats or birds do not share a common ancestor that had a wing. The wing structures, shown in Figure \(3\) evolved independently in the two lineages.
Similar traits can be either homologous or analogous. Homologous traits share an evolutionary path that led to the development of that trait, and analogous traits do not. Scientists must determine which type of similarity a feature exhibits to decipher the phylogeny of the organisms being studied.
Molecular Comparisons
With the advancement of DNA technology, the area of molecular systematics, which describes the use of information on the molecular level including DNA sequencing, has blossomed. New analysis of molecular characters not only confirms many earlier classifications, but also uncovers previously made errors. Molecular characters can include differences in the amino-acid sequence of a protein, differences in the individual nucleotide sequence of a gene, or differences in the arrangements of genes. Phylogenies based on molecular characters assume that the more similar the sequences are in two organisms, the more closely related they are. Different genes change evolutionarily at different rates and this affects the level at which they are useful at identifying relationships. Rapidly evolving sequences are useful for determining the relationships among closely related species. More slowly evolving sequences are useful for determining the relationships between distantly related species. To determine the relationships between very different species such as Eukarya and Archaea, the genes used must be very ancient, slowly evolving genes that are present in both groups, such as the genes for ribosomal RNA. Comparing phylogenetic trees using different sequences and finding them similar helps to build confidence in the inferred relationships.
Sometimes two segments of DNA in distantly related organisms randomly share a high percentage of bases in the same locations, causing these organisms to appear closely related when they are not. For example, the fruit fly shares 60 percent of its DNA with humans.2 In this situation, computer-based statistical algorithms have been developed to help identify the actual relationships, and ultimately, the coupled use of both morphologic and molecular information is more effective in determining phylogeny.
EVOLUTION IN ACTION: Why Does Phylogeny Matter?
In addition to enhancing our understanding of the evolutionary history of species, our own included, phylogenetic analysis has numerous practical applications. Two of those applications include understanding the evolution and transmission of disease and making decisions about conservation efforts. A 2010 study3 of MRSA (methicillin-resistant Staphylococcus aureus), an antibiotic resistant pathogenic bacterium, traced the origin and spread of the strain throughout the past 40 years. The study uncovered the timing and patterns in which the resistant strain moved from its point of origin in Europe to centers of infection and evolution in South America, Asia, North America, and Australasia. The study suggested that introductions of the bacteria to new populations occurred very few times, perhaps only once, and then spread from that limited number of individuals. This is in contrast to the possibility that many individuals had carried the bacteria from one place to another. This result suggests that public health officials should concentrate on quickly identifying the contacts of individuals infected with a new strain of bacteria to control its spread.
A second area of usefulness for phylogenetic analysis is in conservation. Biologists have argued that it is important to protect species throughout a phylogenetic tree rather than just those from one branch of the tree. Doing this will preserve more of the variation produced by evolution. For example, conservation efforts should focus on a single species without sister species rather than another species that has a cluster of close sister species that recently evolved. If the single evolutionarily distinct species goes extinct a disproportionate amount of variation from the tree will be lost compared to one species in the cluster of closely related species. A study published in 20074 made recommendations for conservation of mammal species worldwide based on how evolutionarily distinct and at risk of extinction they are. The study found that their recommendations differed from priorities based on simply the level of extinction threat to the species. The study recommended protecting some threatened and valued large mammals such as the orangutans, the giant and lesser pandas, and the African and Asian elephants. But they also found that some much lesser known species should be protected based on how evolutionary distinct they are. These include a number of rodents, bats, shrews and hedgehogs. In addition there are some critically endangered species that did not rate as very important in evolutionary distinctiveness including species of deer mice and gerbils. While many criteria affect conservation decisions, preserving phylogenetic diversity provides an objective way to protect the full range of diversity generated by evolution.
Building Phylogenetic Trees
How do scientists construct phylogenetic trees? Presently, the most accepted method for constructing phylogenetic trees is a method called cladistics. This method sorts organisms into clades, groups of organisms that are most closely related to each other and the ancestor from which they descended. For example, in Figure \(4\), all of the organisms in the shaded region evolved from a single ancestor that had amniotic eggs. Consequently, all of these organisms also have amniotic eggs and make a single clade, also called a monophyletic group. Clades must include the ancestral species and all of the descendants from a branch point.
ART CONNECTION
Which animals in this figure belong to a clade that includes animals with hair? Which evolved first: hair or the amniotic egg?
Clades can vary in size depending on which branch point is being referenced. The important factor is that all of the organisms in the clade or monophyletic group stem from a single point on the tree. This can be remembered because monophyletic breaks down into “mono,” meaning one, and “phyletic,” meaning evolutionary relationship.
Shared Characteristics
Cladistics rests on three assumptions. The first is that living things are related by descent from a common ancestor, which is a general assumption of evolution. The second is that speciation occurs by splits of one species into two, never more than two at a time, and essentially at one point in time. This is somewhat controversial, but is acceptable to most biologists as a simplification. The third assumption is that traits change enough over time to be considered to be in a different state .It is also assumed that one can identify the actual direction of change for a state. In other words, we assume that an amniotic egg is a later character state than non-amniotic eggs. This is called the polarity of the character change. We know this by reference to a group outside the clade: for example, insects have non-amniotic eggs; therefore, this is the older or ancestral character state. Cladistics compares ingroups and outgroups. An ingroup (lizard, rabbit and human in our example) is the group of taxa being analyzed. An outgroup (lancelet, lamprey and fish in our example) is a species or group of species that diverged before the lineage containing the group(s) of interest. By comparing ingroup members to each other and to the outgroup members, we can determine which characteristics are evolutionary modifications determining the branch points of the ingroup’s phylogeny.
If a characteristic is found in all of the members of a group, it is a shared ancestral characterbecause there has been no change in the trait during the descent of each of the members of the clade. Although these traits appear interesting because they unify the clade, in cladistics they are considered not helpful when we are trying to determine the relationships of the members of the clade because every member is the same. In contrast, consider the amniotic egg characteristic of Figure \(4\). Only some of the organisms have this trait, and to those that do, it is called a shared derived character because this trait changed at some point during descent. This character does tell us about the relationships among the members of the clade; it tells us that lizards, rabbits, and humans group more closely together than any of these organisms do with fish, lampreys, and lancelets.
A sometimes confusing aspect of “ancestral” and “derived” characters is that these terms are relative. The same trait could be either ancestral or derived depending on the diagram being used and the organisms being compared. Scientists find these terms useful when distinguishing between clades during the building of phylogenetic trees, but it is important to remember that their meaning depends on context.
Choosing the Right Relationships
Constructing a phylogenetic tree, or cladogram, from the character data is a monumental task that is usually left up to a computer. The computer draws a tree such that all of the clades share the same list of derived characters. But there are other decisions to be made, for example, what if a species presence in a clade is supported by all of the shared derived characters for that clade except one? One conclusion is that the trait evolved in the ancestor, but then changed back in that one species. Also a character state that appears in two clades must be assumed to have evolved independently in those clades. These inconsistencies are common in trees drawn from character data and complicate the decision-making process about which tree most closely represents the real relationships among the taxa.
To aid in the tremendous task of choosing the best tree, scientists often use a concept called maximum parsimony, which means that events occurred in the simplest, most obvious way. This means that the “best” tree is the one with the fewest number of character reversals, the fewest number of independent character changes, and the fewest number of character changes throughout the tree. Computer programs search through all of the possible trees to find the small number of trees with the simplest evolutionary pathways. Starting with all of the homologous traits in a group of organisms, scientists can determine the order of evolutionary events of which those traits occurred that is the most obvious and simple.
CONCEPT IN ACTION
Practice Parsimony: Go to this website to learn how maximum parsimony is used to create phylogenetic trees (be sure to continue to the second page).
These tools and concepts are only a few of the strategies scientists use to tackle the task of revealing the evolutionary history of life on Earth. Recently, newer technologies have uncovered surprising discoveries with unexpected relationships, such as the fact that people seem to be more closely related to fungi than fungi are to plants. Sound unbelievable? As the information about DNA sequences grows, scientists will become closer to mapping the evolutionary history of all life on Earth.
Section Summary
To build phylogenetic trees, scientists must collect character information that allows them to make evolutionary connections between organisms. Using morphologic and molecular data, scientists work to identify homologous characteristics and genes. Similarities between organisms can stem either from shared evolutionary history (homologies) or from separate evolutionary paths (analogies). After homologous information is identified, scientists use cladistics to organize these events as a means to determine an evolutionary timeline. Scientists apply the concept of maximum parsimony, which states that the likeliest order of events is probably the simplest shortest path. For evolutionary events, this would be the path with the least number of major divergences that correlate with the evidence.
Art Connections
Figure \(3\): Which animals in this figure belong to a clade that includes animals with hair? Which evolved first: hair or the amniotic egg?
Answer
Rabbits and humans belong in the clade that includes animals with hair. The amniotic egg evolved before hair, because the Amniota clade branches off earlier than the clade that encompasses animals with hair.
Footnotes
1. 1 Gibbons, A. (2012, June 13). Science Now. Retrieved from news.sciencemag.org/scienceno...sequenced.html
2. 2 Background on comparative genomic analysis. (2002, December). Retrieved from http://www.genome.gov/10005835
3. 3 Harris, S.R. et al. 2010. Evolution of MRSA during hospital transmission and intercontinental spread. Science 327:469–474.
4. 4 Isaac NJ, Turvey ST, Collen B, Waterman C, Baillie JE (2007) Mammals on the EDGE: Conservation Priorities Based on Threat and Phylogeny. PLoS ONE 2(3): e296. doi:10.1371/journal.pone.0000296
Glossary
analogous structure
a character found in two taxa that looks similar because of convergent evolution, not because of descent from a common ancestor
clade
a group of taxa with the same set of shared derived characters, including an ancestral species and all its descendants
cladistics
a method used to organize homologous traits to describe phylogenies using common descendent as the primary criterion used to classify organisms
maximum parsimony
applying the simplest, most obvious way with the least number of steps
molecular systematics
the methods of using molecular evidence to identify phylogenetic relationships
monophyletic group
(also, clade) organisms that share a single ancestor
shared ancestral character
a character on a phylogenetic branch that is shared by a particular clade
shared derived character
a character on a phylogenetic tree that is shared only by a certain clade of organisms | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/23%3A_Systematics_Phylogeny_and_Comparative_Biology/23.02%3A_Cladistics.txt |
All life on Earth evolved from a common ancestor. Biologists map how organisms are related by constructing phylogenetic trees. In other words, a “tree of life” can be constructed to illustrate when different organisms evolved and to show the relationships among different organisms, as shown in Figure \(1\). Notice that from a single point, the three domains of Archaea, Bacteria, and Eukarya diverge and then branch repeatedly. The small branch that plants and animals (including humans) occupy in this diagram shows how recently these groups had their origin compared with other groups.
The phylogenetic tree in Figure \(1\) illustrates the pathway of evolutionary history. The pathway can be traced from the origin of life to any individual species by navigating through the evolutionary branches between the two points. Also, by starting with a single species and tracing backward to any branch point, the organisms related to it by various degrees of closeness can be identified.
A phylogeny is the evolutionary history and the relationships among a species or group of species. The study of organisms with the purpose of deriving their relationships is called systematics.
Many disciplines within the study of biology contribute to understanding how past and present life evolved over time, and together they contribute to building, updating, and maintaining the “tree of life.” Information gathered may include data collected from fossils, from studying morphology, from the structure of body parts, or from molecular structure, such as the sequence of amino acids in proteins or DNA nucleotides. By considering the trees generated by different sets of data scientists can put together the phylogeny of a species.
Scientists continue to discover new species of life on Earth as well as new character information, thus trees change as new data arrive.
The Levels of Classification
Taxonomy (which literally means “arrangement law”) is the science of naming and grouping species to construct an internationally shared classification system. The taxonomic classification system (also called the Linnaean system after its inventor, Carl Linnaeus, a Swedish naturalist) uses a hierarchical model. A hierarchical system has levels and each group at one of the levels includes groups at the next lowest level, so that at the lowest level each member belongs to a series of nested groups. An analogy is the nested series of directories on the main disk drive of a computer. For example, in the most inclusive grouping, scientists divide organisms into three domains: Bacteria, Archaea, and Eukarya. Within each domain is a second level called a kingdom. Each domain contains several kingdoms. Within kingdoms, the subsequent categories of increasing specificity are: phylum, class, order, family, genus, and species.
As an example, the classification levels for the domestic dog are shown in Figure \(2\). The group at each level is called a taxon (plural: taxa). In other words, for the dog, Carnivora is the taxon at the order level, Canidae is the taxon at the family level, and so forth. Organisms also have a common name that people typically use, such as domestic dog, or wolf. Each taxon name is capitalized except for species, and the genus and species names are italicized. Scientists refer to an organism by its genus and species names together, commonly called a scientific name, or Latin name. This two-name system is called binomial nomenclature. The scientific name of the wolf is therefore Canis lupus. Recent study of the DNA of domestic dogs and wolves suggest that the domestic dog is a subspecies of the wolf, not its own species, thus it is given an extra name to indicate its subspecies status, Canis lupus familiaris.
Figure \(2\) also shows how taxonomic levels move toward specificity. Notice how within the domain we find the dog grouped with the widest diversity of organisms. These include plants and other organisms not pictured, such as fungi and protists. At each sublevel, the organisms become more similar because they are more closely related. Before Darwin’s theory of evolution was developed, naturalists sometimes classified organisms using arbitrary similarities, but since the theory of evolution was proposed in the 19th century, biologists work to make the classification system reflect evolutionary relationships. This means that all of the members of a taxon should have a common ancestor and be more closely related to each other than to members of other taxa.
Recent genetic analysis and other advancements have found that some earlier taxonomic classifications do not reflect actual evolutionary relationships, and therefore, changes and updates must be made as new discoveries take place. One dramatic and recent example was the breaking apart of prokaryotic species, which until the 1970s were all classified as bacteria. Their division into Archaea and Bacteria came about after the recognition that their large genetic differences warranted their separation into two of three fundamental branches of life.
ART CONNECTION
In what levels are cats and dogs considered to be part of the same group?
CONCEPT IN ACTION
Visit this site to learn more about taxonomy.
Classification and Phylogeny
Scientists use a tool called a phylogenetic tree to show the evolutionary pathways and relationships between organisms. A phylogenetic tree is a diagram used to reflect evolutionary relationships among organisms or groups of organisms. The hierarchical classification of groups nested within more inclusive groups is reflected in diagrams. Scientists consider phylogenetic trees to be a hypothesis of the evolutionary past because one cannot go back through time to confirm the proposed relationships.
Unlike with a taxonomic classification, a phylogenetic tree can be read like a map of evolutionary history, as shown in Figure \(3\). Shared characteristics are used to construct phylogenetic trees. The point where a split occurs in a tree, called a branch point, represents where a single lineage evolved into distinct new ones. Many phylogenetic trees have a single branch point at the base representing a common ancestor of all the branches in the tree. Scientists call such trees rooted, which means there is a single ancestral taxon at the base of a phylogenetic tree to which all organisms represented in the diagram descend from. When two lineages stem from the same branch point, they are called sister taxa, for example the two species of orangutans. A branch point with more than two groups illustrates a situation for which scientists have not definitively determined relationships. An example is illustrated by the three branches leading to the gorilla subspecies; their exact relationships are not yet understood. It is important to note that sister taxa share an ancestor, which does not mean that one taxon evolved from the other. The branch point, or split, represents a common ancestor that existed in the past, but that no longer exists. Humans did not evolve from chimpanzees (nor did chimpanzees evolve from humans) although they are our closest living relatives. Both humans and chimpanzees evolved from a common ancestor that lived, scientists believe, six million years ago and looked different from both modern chimpanzees and modern humans.
The branch points and the branches in phylogenetic tree structure also imply evolutionary change. Sometimes the significant character changes are identified on a branch or branch point. For example, in Figure \(4\), the branch point that gives rise to the mammal and reptile lineage from the frog lineage shows the origin of the amniotic egg character. Also the branch point that gives rise to organisms with legs is indicated at the common ancestor of mammals, reptiles, amphibians, and jawed fishes.
Limitations of Phylogenetic Trees
It is easy to assume that more closely related organisms look more alike, and while this is often the case, it is not always true. If two closely related lineages evolved under significantly different surroundings or after the evolution of a major new adaptation, they may look quite different from each other, even more so than other groups that are not as closely related. For example, the phylogenetic tree in Figure \(4\) shows that lizards and rabbits both have amniotic eggs, whereas salamanders (within the frog lineage) do not; yet on the surface, lizards and salamanders appear more similar than the lizards and rabbits.
Another aspect of phylogenetic trees is that, unless otherwise indicated, the branches do not show length of time, they show only the order in time of evolutionary events. In other words, a long branch does not necessarily mean more time passed, nor does a short branch mean less time passed— unless specified on the diagram. For example, in Figure \(4\), the tree does not indicate how much time passed between the evolution of amniotic eggs and hair. What the tree does show is the order in which things took place. Again using Figure \(4\), the tree shows that the oldest trait is the vertebral column, followed by hinged jaws, and so forth. Remember that any phylogenetic tree is a part of the greater whole, and similar to a real tree, it does not grow in only one direction after a new branch develops. So, for the organisms in Figure \(4\), just because a vertebral column evolved does not mean that invertebrate evolution ceased, it only means that a new branch formed. Also, groups that are not closely related, but evolve under similar conditions, may appear more similar to each other than to a close relative.
Section Summary
Scientists continually obtain new information that helps to understand the evolutionary history of life on Earth. Each group of organisms went through its own evolutionary journey, called its phylogeny. Each organism shares relatedness with others, and based on morphologic and genetic evidence scientists attempt to map the evolutionary pathways of all life on Earth. Historically, organisms were organized into a taxonomic classification system. However, today many scientists build phylogenetic trees to illustrate evolutionary relationships and the taxonomic classification system is expected to reflect evolutionary relationships.
Art Connections
Figure \(2\): In what levels are cats and dogs considered to be part of the same group?
Answer
Cats and dogs are part of the same group at five levels: both are in the domain Eukarya, the kingdom Animalia, the phylum Chordata, the class Mammalia, and the order Carnivora.
Glossary
binomial nomenclature
a system of two-part scientific names for an organism, which includes genus and species names
branch point
a point on a phylogenetic tree where a single lineage splits to distinct new ones
class
the category in the taxonomic classification system that falls within phylum and includes orders
domain
the highest level category in the classification system and that includes all taxonomic classifications below it; it is the most inclusive taxon
family
the category in the taxonomic classification system that falls within order and includes genera
genus
the category in the taxonomic classification system that falls within family and includes species; the first part of the scientific name
kingdom
the category in the taxonomic classification system that falls within domain and includes phyla
order
the category in the taxonomic classification system that falls within class and includes families
phylogenetic tree
diagram used to reflect the evolutionary relationships between organisms or groups of organisms
phylogeny
evolutionary history and relationship of an organism or group of organisms
phylum
the category in the taxonomic classification system that falls within kingdom and includes classes
rooted
describing a phylogenetic tree with a single ancestral lineage to which all organisms represented in the diagram relate
sister taxa
two lineages that diverged from the same branch point
species
the most specific category of classification
systematics
the science of determining the evolutionary relationships of organisms
taxon
a single level in the taxonomic classification system
taxonomy
the science of classifying organisms | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/23%3A_Systematics_Phylogeny_and_Comparative_Biology/23.03%3A_Systematics_and_Classification.txt |
Learning Objectives
• Explain the difference between homologous and analogous structures
Two Options for Similarities
In general, organisms that share similar physical features and genomes tend to be more closely related than those that do not. Such features that overlap both morphologically (in form) and genetically are referred to as homologous structures; they stem from developmental similarities that are based on evolution. For example, the bones in the wings of bats and birds have homologous structures.
Notice it is not simply a single bone, but rather a grouping of several bones arranged in a similar way. The more complex the feature, the more probable that any overlap is due to a common evolutionary past. Imagine two people from different countries both inventing a car with all the same parts and in exactly the same arrangement without any previous or shared knowledge. That outcome would be highly improbable. However, if two people both invented a hammer, it would be reasonable to conclude that both could have the original idea without the help of the other. The same relationship between complexity and shared evolutionary history is true for homologous structures in organisms.
Misleading Appearances
Some organisms may be very closely related, even though a minor genetic change caused a major morphological difference to make them look quite different. Similarly, unrelated organisms may be distantly related, but appear very similar. This usually happens because both organisms developed common adaptations that evolved within similar environmental conditions. When similar characteristics occur because of environmental constraints and not due to a close evolutionary relationship, it is called an analogy or homoplasy. For example, insects use wings to fly like bats and birds, but the wing structure and embryonic origin is completely different. These are called analogous structures.
Similar traits can be either homologous or analogous. Homologous structures share a similar embryonic origin; analogous organs have a similar function. For example, the bones in the front flipper of a whale are homologous to the bones in the human arm. These structures are not analogous. The wings of a butterfly and the wings of a bird are analogous, but not homologous. Some structures are both analogous and homologous: the wings of a bird and the wings of a bat are both homologous and analogous. Scientists must determine which type of similarity a feature exhibits to decipher the phylogeny of the organisms being studied.
Molecular Comparisons
With the advancement of DNA technology, the area of molecular systematics, which describes the use of information on the molecular level including DNA analysis, has blossomed. New computer programs not only confirm many earlier classified organisms, but also uncover previously-made errors. As with physical characteristics, even the DNA sequence can be tricky to read in some cases. For some situations, two very closely-related organisms can appear unrelated if a mutation occurred that caused a shift in the genetic code. An insertion or deletion mutation would move each nucleotide base over one place, causing two similar codes to appear unrelated.
Sometimes two segments of DNA code in distantly-related organisms randomly share a high percentage of bases in the same locations, causing these organisms to appear closely related when they are not. For both of these situations, computer technologies have been developed to help identify the actual relationships. Ultimately, the coupled use of both morphologic and molecular information is more effective in determining phylogeny.
Key Points
• Organisms may be very closely related, even though they look quite different, due to a minor genetic change that caused a major morphological difference.
• Unrelated organisms may appear very similar because both organisms developed common adaptations that evolved within similar environmental conditions.
• To determine the phylogeny of an organism, scientists must determine whether a similarity is homologous or analogous.
• The advancement of DNA technology, the area of molecular systematics, describes the use of information on the molecular level, including DNA analysis.
Key Terms
• analogous: when similar similar physical features occur in organisms because of environmental constraints and not due to a close evolutionary relationship
• homologous: when similar physical features and genomes stem from developmental similarities that are based on evolution
• phylogeny: the evolutionary history of an organism
• molecular systematics: molecular phylogenetics is the analysis of hereditary molecular differences, mainly in DNA sequences, to gain information on an organism’s evolutionary relationships | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/23%3A_Systematics_Phylogeny_and_Comparative_Biology/23.04%3A_Phylogenetics_and_Comparative_Biology.txt |
Genomics is a field that studies the entire collection of an organism’s DNA or genome. It involves sequencing, analyzing, and comparing the information contained within genomes. Since sequencing has become much less expensive and more efficient, vast amounts of genomic information is now available about a wide variety of organisms, but particularly microbes, with their smaller genome size. In fact, the biggest bottleneck currently is not the lack of information but the lack of computing power to process the information!
Sequencing
Sequencing, or determining the base order of an organism’s DNA or RNA, is often one of the first steps to finding out detailed information about an organism. A bacterial genome can range from 130 kilobase pairs (kbp) to over 14 Megabase pairs (Mbp), while a viral genome ranges from 0.859 to 2473 kbp. For comparison, the human genome contains about 3 billion base pairs.
Shotgun sequencing
Shotgun sequencing initially involves construction of a genomic library, where the genome is broken into randomly sized fragments that are inserted into vectors to produce a library of clones. The fragments are sequenced and then analyzed by a computer, which searches for overlapping regions to form a longer stretch of sequence. Eventually all the sequences are aligned to give the complete genome sequence. Errors are reduced because many of the clones contain identical or near identical sequences, resulting in good “coverage” of the genome.
Shotgun Sequencing. By Commins, J., Toft, C., Fares, M. A. [CC BY-SA 2.5], via Wikimedia Commons
Second generation DNA sequencing
Second-generation DNA sequencing uses massively parallel methods, where multiple samples are sequenced side-by-side. DNA fragments of a few hundred bases each are amplified by PCR and then attached to small bead, so that each bead carries several copies of the same section of DNA. The beads are put into a plate containing more than a million wells, each with one bead, and the DNA fragments are sequenced.
Third- and fourth-generation DNA sequencing
Third-generation DNA sequencing involves the sequencing of single molecules of DNA. Fourth-generation DNA sequencing, also known as “post light sequencing,” utilizes methods other than optical detection for sequencing.
Bioinformatics
After sequencing, it is time to make sense of the information. The field of bioinformatics combines many fields together (i.e. biology, computer science, statistics) to use the power of computers to analyze information contained in the genomic sequence. Locating specific genes within a genome is referred to as genome annotation.
Open Reading Frames (ORFS)
An open reading frame or ORF denotes a possible protein-coding gene. For double-stranded DNA, there are six reading frames to be analyzed, since the DNA is read in sets of three bases at a time and there are two strands of DNA. An ORF typically has at least 100 codons before a stop codon, with 3’ terminator sequences. A functional ORF is one that is actually used by the organism to encode a protein. Computers are used to search the DNA sequence looking for ORFs, with those presumed to encode protein further analyzed by a bioinformaticist.
It is often helpful for the sequence to be compared against a database of sequences coding for known proteins. GenBank is a database of over 200 billion base pairs of sequences that scientists can access, to try and find matches to the sequence of interest. The database search tool BLAST (basic local alignment search tool) has programs for comparing both nucleotide sequences and amino acid sequences, providing a ranking of results in order of decreasing similarity.
BLAST Results.
Comparative Genomics
Once the sequences of organisms have been obtained, meaningful information can be gathered using comparative genomics. For this genomes are assessed for information regarding size, organization, and gene content.
Comparison of the genome of microbial strains has given scientists a better picture regarding the genes that organisms pick up. A group of multiple strains share a core genome, genes coding for essential cellular functions that they all have in common. The pan genome represents all the genes found in all the members of species, so provides a good idea of the diversity of a group. Most of these “extra” genes are probably picked up by horizontal gene transfer.
Comparative genomics also shows that many genes are derived as a result of gene duplication. Genes within a single organism that likely came about because of gene duplication are referred to as paralogs. In many cases one of the genes might be altered to take on a new function. It is also possible for gene duplication to be found in different organisms, as a result of acquiring the original gene from a common ancestor. These genes are called orthologs.
Functional Genomics
The sequence of a genome and the location of genes provide part of the picture, but in order to fully understand an organism we need an idea of what the cell is doing with its genes. In other words, what happens when the genes are expressed? This is where functional genomics comes in – placing the genomic information in context.
The first step in gene expression is transcription or the manufacture of RNA. Transcriptome refers to the entire complement of RNA that a cell can make from its genome, while proteome refers to all the proteins encoded by an organisms’ genome, in the final step of gene expression.
Microarrays
Microarrays or gene chips are solid supports upon which multiple spots of DNA are placed, in a grid-like fashion. Each spot of DNA represents a single gene or ORF. Known fragments of nucleic acid are labeled and used as probes, with a signal produced if binding occurs. Microarrays can be used to determine what genes might be turned on or off under particular conditions, such as comparing the growth of a bacterial pathogen inside the host versus outside of the host.
Proteomics
The study of the proteins of an organism (or the proteome) is referred to as proteomics. Much of the interest focuses on functional proteomics, which examines the functions of the cellular proteins and the ways in which they interact with one another.
One common technique used in the study of proteins is two-dimensional gel electrophoresis, which first separates proteins based on their isoelectric points. This is accomplished by using a pH gradient, which separates the proteins based on their amino acid content. The separated proteins are then run through a polyacrylamide gel, providing the second dimension as proteins are separated by size.
Structural proteomics focuses on the three-dimensional structure of proteins, which is often determined by protein modeling, using computer algorithms to predict the most likely folding of the protein based on amino acid information and known protein patterns.
Metabolomics
Metabolomics strives to identify the complete set of metabolic intermediates produced by an organism. This can be extremely complicated, since many metabolites are used by cells in multiple pathways.
Metagenomics
Metagenomics or environmental genomics refers to the extraction of pooled DNA directly from a specific environment, without the initial isolation and identification of organisms within that environment. Since many microbial species are difficult to culture in the laboratory, studying the metagenome of an environment allows scientists to consider all organisms that might be present. Taxa can even be identified in the absence of organism isolation using nucleic acid sequences alone, where the taxon is known as phylotype.
Key Words
genomics, sequencing, shotgun sequencing, genomic library, second generation DNA sequencing, massively parallel methods, third- and fourth-generation DNA sequencing, bioinformatics, genome annotation, open reading frame/ORF, functional ORF, GenBank, BLAST/basic local alignment search tool, comparative genomics, core genome, pan genome, paralog, ortholog, functional genomics, transcriptome, proteome, microarray/gene chips, probe, proteomics, functional proteomics, two-dimensional gel electrophoresis, structural proteomics, metabolomics, metagenomics/environmental genomics, metagenome, phylotype.
Study Questions
1. What does the field of genomics encompass?
2. What is shotgun sequencing and how does this allow for the complete sequencing of an organism’s genome?
3. What are the basic differences among 2nd, 3rd, and 4th generation sequencing?
4. What is an open reading frame and how can scientists use it to determine information about a genome and its products?
5. How does functional genomics differ from comparative genomics? What are the tools used in functional genomics and what information can be obtained from each? | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/24%3A_Genome_Evolution/24.01%3A_Comparative_Genomics.txt |
The genome of an organism is the complete set of genes specifying how its phenotype will develop (under a certain set of environmental conditions). In this sense, then, diploid organisms (like ourselves) contain two genomes, one inherited from our mother, the other from our father. The table below presents a selection of representative genome sizes from the rapidly-growing list of organisms whose genomes have been sequenced.
Table of Genome Sizes (haploid)
Base pairs Genes Notes
φX174 5,386 11 virus of E. coli
Human mitochondrion 16,569 37
Nasuia deltocephalinicola 112,091 137 smallest genome yet found in a bacterium. This β-proteobacterium lives in a mutualistic relationship within a special organ of an insect (a leaf hopper) which it supplies with essential amino acids.
Epstein-Barr virus (EBV) 172,282 80 causes mononucleosis
nucleomorph of Guillardia theta 551,264 511 all that remains of the nuclear genome of a red alga (a eukaryote) engulfed long ago by another eukaryote
Mycoplasma genitalium 580,073 525 two of the smallest true organisms
Mycoplasma pneumoniae 816,394 679
Rickettsia prowazekii 1,111,523 834 bacterium that causes epidemic typhus
Treponema pallidum 1,138,011 1,039 bacterium that causes syphilis
Pelagibacter ubique 1,308,759 1,354 smallest genome yet found in a free-living organism (marine α-proteobacterium)
Helicobacter pylori 1,667,867 1,589 chief cause of stomach ulcers (not stress and diet)
Methanocaldococcus jannaschii 1,664,970 1,783 These unicellular microbes look like typical bacteria but their genes are so different from those of either bacteria or eukaryotes that they are classified in a third kingdom: Archaea.
Aeropyrum pernix 1,669,695 1,885
Methanothermobacter thermoautotrophicus 1,751,377 2,008
Streptococcus pneumoniae 2,160,837 2,236 the pneumococcus
Pandoravirus 2,473,870 2556 A virus (of an amoeba) with a genome larger than that of the bacteria and archaea above and about the same as that of some parasitic eukaryotes.
Listeria monocytogenes 2,944,528 2,926 2,853 of these encode proteins; the rest RNAs
Synechocystis 3,573,470 4,003 a marine cyanobacterium ("blue-green alga")
E. coli K-12 4,639,221 4,377 4,290 of these genes encode proteins; the rest RNAs
E. coli O157:H7 5.44 x 106 5,416 strain that is pathogenic for humans; has 1,346 genes not found in E. coli K-12
Schizosaccharomyces pombe 12,462,637 4,929 Fission yeast. A eukaryote with fewer genes than the three bacteria below.
Agrobacterium tumefaciens 4,674,062 5,419 Useful vector for making transgenic plants; shares many genes with Sinorhizobium meliloti
Pseudomonas aeruginosa 6.3 x 106 5,570 Increasingly common cause of opportunistic infections in humans.
Sinorhizobium meliloti 6,691,694 6,204 The rhizobial symbiont of alfalfa. Genome consists of one chromosome and 2 large plasmids.
Saccharomyces cerevisiae 12,495,682 5,770 Budding yeast. A eukaryote.
Neurospora crassa 38,639,769 10,082 Plus 498 RNA genes.
Thalassiosira pseudonana 34.5 x 106 11,242 A diatom. Plus 144 chloroplast and 40 mitochondrial genes encoding proteins
Naegleria gruberi 41 x 106 15,727 This free-living unicellular organism lives as both an amoeboid and a flagellated form. 4,133 of its genes are also found in other eukaryotes suggesting that they were present in the common ancestor of all eukaryotes. The great variety of functions encoded by these genes also suggests that the common ancestor of all eukaryotes was itself as complex as many of the present-day unicellular members.
Drosophila melanogaster 122,653,977 ~17,000 the "fruit fly"
Caenorhabditis elegans 100,258,171 21,733
Humans 3.3 x 109 ~21,000
Tetraodon nigroviridis (a pufferfish) 3.42 x 108 27,918 Although Tetraodon seems to have more protein-encoding genes than we do, it has much less non-coding DNA so its total genome is about a tenth the size of ours.
Mouse 2.8 x 109 ~23,000
Amphibians 109–1011 ?
Arabidopsis thaliana 0.135 x 109 27,407 a flowering plant (angiosperm) with one of the smallest genomes known in the plant kingdom.
Picea abies 19.6 x 109 28,354 the Norway spruce, a conifer (gymnosperm). Even though it has only ~900 more genes than Arabidopsis, it has 145 times as much DNA. Most of this appears to be derived from transposons.
Psilotum nudum 2.5 x 1011 ?
Even though Psilotum nudum (sometimes called the "whisk fern") is a far simpler plant than Arabidopsis (it has no true leaves, flowers, or fruit), it has 3000 times as much DNA. No one knows why, but 80% or more of it is repetitive DNA containing no genetic information. This is also the case for some amphibians, which contain 30 times as much DNA as we do, but certainly are not 30 times as complex. The total amount of DNA in the haploid genome is called its C value. The lack of a consistent relationship between the C value and the complexity of an organism (e.g., amphibians vs. mammals) is called the C value paradox.
Not all genes are Indispensable
The scientists at The Institute for Genomic Research (now known as the J. Craig Venter Institute) who determined the Mycoplasma genitalium sequence have followed this work by systematically destroying its genes (by mutating them with insertions) to see which ones are essential to life and which are dispensable. Of the 485 protein-encoding genes, they have concluded that only 381 of them are essential to life. In other words, the loss of any one of the 381 is lethal; the loss of any one of the others is not. (This is not to say that all the organism needs are those 381 — see "A Minimal Genome?" below.)
Using similar techniques, three groups have recently found that only about 10% of the genes in the human genome (~2000 of them) must be present for human cells to grow successfully in culture. These genes encode proteins for such essential functions as controlling the cell cycle, DNA replication, DNA transcription and RNA translation. The cells can tolerate the loss of any one of the other ~18,000 genes. Thus the human genome appears to have redundant pathways that can often compensate for the loss of a single gene at least for cells growing in culture. Probably others will turn out to be essential for the development and functioning of the various types of differentiated cells in the intact body.
A Minimal Genome?
In March of 2016, workers at the J. Craig Venter Institute reported that they had created a strain of mycoplasma containing only 473 genes. This synthetic organism, which grows vigorously in culture, now holds the record for the smallest genome of a free-living organism. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/24%3A_Genome_Evolution/24.02%3A_Genome_Size.txt |
Skills to Develop
• Describe how a karyogram is created
• Explain how nondisjunction leads to disorders in chromosome number
• Compare disorders caused by aneuploidy
• Describe how errors in chromosome structure occur through inversions and translocations
Inherited disorders can arise when chromosomes behave abnormally during meiosis. Chromosome disorders can be divided into two categories: abnormalities in chromosome number and chromosomal structural rearrangements. Because even small segments of chromosomes can span many genes, chromosomal disorders are characteristically dramatic and often fatal.
Identification of Chromosomes
The isolation and microscopic observation of chromosomes forms the basis of cytogenetics and is the primary method by which clinicians detect chromosomal abnormalities in humans. A karyotype is the number and appearance of chromosomes, and includes their length, banding pattern, and centromere position. To obtain a view of an individual’s karyotype, cytologists photograph the chromosomes and then cut and paste each chromosome into a chart, or karyogram, also known as an ideogram (Figure \(1\)).
In a given species, chromosomes can be identified by their number, size, centromere position, and banding pattern. In a human karyotype, autosomes or “body chromosomes” (all of the non–sex chromosomes) are generally organized in approximate order of size from largest (chromosome 1) to smallest (chromosome 22). The X and Y chromosomes are not autosomes. However, chromosome 21 is actually shorter than chromosome 22. This was discovered after the naming of Down syndrome as trisomy 21, reflecting how this disease results from possessing one extra chromosome 21 (three total). Not wanting to change the name of this important disease, chromosome 21 retained its numbering, despite describing the shortest set of chromosomes. The chromosome “arms” projecting from either end of the centromere may be designated as short or long, depending on their relative lengths. The short arm is abbreviated p (for “petite”), whereas the long arm is abbreviated q (because it follows “p” alphabetically). Each arm is further subdivided and denoted by a number. Using this naming system, locations on chromosomes can be described consistently in the scientific literature.
Career Connection: Geneticists Use Karyograms to Identify Chromosomal Aberrations
Although Mendel is referred to as the “father of modern genetics,” he performed his experiments with none of the tools that the geneticists of today routinely employ. One such powerful cytological technique is karyotyping, a method in which traits characterized by chromosomal abnormalities can be identified from a single cell. To observe an individual’s karyotype, a person’s cells (like white blood cells) are first collected from a blood sample or other tissue. In the laboratory, the isolated cells are stimulated to begin actively dividing. A chemical called colchicine is then applied to cells to arrest condensed chromosomes in metaphase. Cells are then made to swell using a hypotonic solution so the chromosomes spread apart. Finally, the sample is preserved in a fixative and applied to a slide.
The geneticist then stains chromosomes with one of several dyes to better visualize the distinct and reproducible banding patterns of each chromosome pair. Following staining, the chromosomes are viewed using bright-field microscopy. A common stain choice is the Giemsa stain. Giemsa staining results in approximately 400–800 bands (of tightly coiled DNA and condensed proteins) arranged along all of the 23 chromosome pairs; an experienced geneticist can identify each band. In addition to the banding patterns, chromosomes are further identified on the basis of size and centromere location. To obtain the classic depiction of the karyotype in which homologous pairs of chromosomes are aligned in numerical order from longest to shortest, the geneticist obtains a digital image, identifies each chromosome, and manually arranges the chromosomes into this pattern (Figure \(1\)).
At its most basic, the karyogram may reveal genetic abnormalities in which an individual has too many or too few chromosomes per cell. Examples of this are Down Syndrome, which is identified by a third copy of chromosome 21, and Turner Syndrome, which is characterized by the presence of only one X chromosome in women instead of the normal two. Geneticists can also identify large deletions or insertions of DNA. For instance, Jacobsen Syndrome—which involves distinctive facial features as well as heart and bleeding defects—is identified by a deletion on chromosome 11. Finally, the karyotype can pinpoint translocations, which occur when a segment of genetic material breaks from one chromosome and reattaches to another chromosome or to a different part of the same chromosome. Translocations are implicated in certain cancers, including chronic myelogenous leukemia.
During Mendel’s lifetime, inheritance was an abstract concept that could only be inferred by performing crosses and observing the traits expressed by offspring. By observing a karyogram, today’s geneticists can actually visualize the chromosomal composition of an individual to confirm or predict genetic abnormalities in offspring, even before birth.
Disorders in Chromosome Number
Of all of the chromosomal disorders, abnormalities in chromosome number are the most obviously identifiable from a karyogram. Disorders of chromosome number include the duplication or loss of entire chromosomes, as well as changes in the number of complete sets of chromosomes. They are caused by nondisjunction, which occurs when pairs of homologous chromosomes or sister chromatids fail to separate during meiosis. Misaligned or incomplete synapsis, or a dysfunction of the spindle apparatus that facilitates chromosome migration, can cause nondisjunction. The risk of nondisjunction occurring increases with the age of the parents.
Nondisjunction can occur during either meiosis I or II, with differing results (Figure \(2\)). If homologous chromosomes fail to separate during meiosis I, the result is two gametes that lack that particular chromosome and two gametes with two copies of the chromosome. If sister chromatids fail to separate during meiosis II, the result is one gamete that lacks that chromosome, two normal gametes with one copy of the chromosome, and one gamete with two copies of the chromosome.
Art Connection
Which of the following statements about nondisjunction is true?
1. Nondisjunction only results in gametes with n+1 or n–1 chromosomes.
2. Nondisjunction occurring during meiosis II results in 50 percent normal gametes.
3. Nondisjunction during meiosis I results in 50 percent normal gametes.
4. Nondisjunction always results in four different kinds of gametes.
Aneuploidy
An individual with the appropriate number of chromosomes for their species is called euploid; in humans, euploidy corresponds to 22 pairs of autosomes and one pair of sex chromosomes. An individual with an error in chromosome number is described as aneuploid, a term that includes monosomy (loss of one chromosome) or trisomy (gain of an extraneous chromosome). Monosomic human zygotes missing any one copy of an autosome invariably fail to develop to birth because they lack essential genes. This underscores the importance of “gene dosage” in humans. Most autosomal trisomies also fail to develop to birth; however, duplications of some of the smaller chromosomes (13, 15, 18, 21, or 22) can result in offspring that survive for several weeks to many years. Trisomic individuals suffer from a different type of genetic imbalance: an excess in gene dose. Individuals with an extra chromosome may synthesize an abundance of the gene products encoded by that chromosome. This extra dose (150 percent) of specific genes can lead to a number of functional challenges and often precludes development. The most common trisomy among viable births is that of chromosome 21, which corresponds to Down Syndrome. Individuals with this inherited disorder are characterized by short stature and stunted digits, facial distinctions that include a broad skull and large tongue, and significant developmental delays. The incidence of Down syndrome is correlated with maternal age; older women are more likely to become pregnant with fetuses carrying the trisomy 21 genotype (Figure \(3\)).
Link to Learning
Visualize the addition of a chromosome that leads to Down syndrome in this video simulation.
Polyploidy
An individual with more than the correct number of chromosome sets (two for diploid species) is called polyploid. For instance, fertilization of an abnormal diploid egg with a normal haploid sperm would yield a triploid zygote. Polyploid animals are extremely rare, with only a few examples among the flatworms, crustaceans, amphibians, fish, and lizards. Polyploid animals are sterile because meiosis cannot proceed normally and instead produces mostly aneuploid daughter cells that cannot yield viable zygotes. Rarely, polyploid animals can reproduce asexually by haplodiploidy, in which an unfertilized egg divides mitotically to produce offspring. In contrast, polyploidy is very common in the plant kingdom, and polyploid plants tend to be larger and more robust than euploids of their species (Figure \(4\)).
Sex Chromosome Nondisjunction in Humans
Humans display dramatic deleterious effects with autosomal trisomies and monosomies. Therefore, it may seem counterintuitive that human females and males can function normally, despite carrying different numbers of the X chromosome. Rather than a gain or loss of autosomes, variations in the number of sex chromosomes are associated with relatively mild effects. In part, this occurs because of a molecular process called X inactivation. Early in development, when female mammalian embryos consist of just a few thousand cells (relative to trillions in the newborn), one X chromosome in each cell inactivates by tightly condensing into a quiescent (dormant) structure called a Barr body. The chance that an X chromosome (maternally or paternally derived) is inactivated in each cell is random, but once the inactivation occurs, all cells derived from that one will have the same inactive X chromosome or Barr body. By this process, females compensate for their double genetic dose of X chromosome. In so-called “tortoiseshell” cats, embryonic X inactivation is observed as color variegation (Figure \(5\)). Females that are heterozygous for an X-linked coat color gene will express one of two different coat colors over different regions of their body, corresponding to whichever X chromosome is inactivated in the embryonic cell progenitor of that region.
An individual carrying an abnormal number of X chromosomes will inactivate all but one X chromosome in each of her cells. However, even inactivated X chromosomes continue to express a few genes, and X chromosomes must reactivate for the proper maturation of female ovaries. As a result, X-chromosomal abnormalities are typically associated with mild mental and physical defects, as well as sterility. If the X chromosome is absent altogether, the individual will not develop in utero.
Several errors in sex chromosome number have been characterized. Individuals with three X chromosomes, called triplo-X, are phenotypically female but express developmental delays and reduced fertility. The XXY genotype, corresponding to one type of Klinefelter syndrome, corresponds to phenotypically male individuals with small testes, enlarged breasts, and reduced body hair. More complex types of Klinefelter syndrome exist in which the individual has as many as five X chromosomes. In all types, every X chromosome except one undergoes inactivation to compensate for the excess genetic dosage. This can be seen as several Barr bodies in each cell nucleus. Turner syndrome, characterized as an X0 genotype (i.e., only a single sex chromosome), corresponds to a phenotypically female individual with short stature, webbed skin in the neck region, hearing and cardiac impairments, and sterility.
Duplications and Deletions
In addition to the loss or gain of an entire chromosome, a chromosomal segment may be duplicated or lost. Duplications and deletions often produce offspring that survive but exhibit physical and mental abnormalities. Duplicated chromosomal segments may fuse to existing chromosomes or may be free in the nucleus. Cri-du-chat (from the French for “cry of the cat”) is a syndrome associated with nervous system abnormalities and identifiable physical features that result from a deletion of most of 5p (the small arm of chromosome 5) (Figure \(6\)). Infants with this genotype emit a characteristic high-pitched cry on which the disorder’s name is based.
Chromosomal Structural Rearrangements
Cytologists have characterized numerous structural rearrangements in chromosomes, but chromosome inversions and translocations are the most common. Both are identified during meiosis by the adaptive pairing of rearranged chromosomes with their former homologs to maintain appropriate gene alignment. If the genes carried on two homologs are not oriented correctly, a recombination event could result in the loss of genes from one chromosome and the gain of genes on the other. This would produce aneuploid gametes.
Chromosome Inversions
A chromosome inversion is the detachment, 180° rotation, and reinsertion of part of a chromosome. Inversions may occur in nature as a result of mechanical shear, or from the action of transposable elements (special DNA sequences capable of facilitating the rearrangement of chromosome segments with the help of enzymes that cut and paste DNA sequences). Unless they disrupt a gene sequence, inversions only change the orientation of genes and are likely to have more mild effects than aneuploid errors. However, altered gene orientation can result in functional changes because regulators of gene expression could be moved out of position with respect to their targets, causing aberrant levels of gene products.
An inversion can be pericentric and include the centromere, or paracentric and occur outside of the centromere (). A pericentric inversion that is asymmetric about the centromere can change the relative lengths of the chromosome arms, making these inversions easily identifiable.
When one homologous chromosome undergoes an inversion but the other does not, the individual is described as an inversion heterozygote. To maintain point-for-point synapsis during meiosis, one homolog must form a loop, and the other homolog must mold around it. Although this topology can ensure that the genes are correctly aligned, it also forces the homologs to stretch and can be associated with regions of imprecise synapsis (Figure \(8\)).
Evolution Connection: The Chromosome 18 Inversion
Not all structural rearrangements of chromosomes produce nonviable, impaired, or infertile individuals. In rare instances, such a change can result in the evolution of a new species. In fact, a pericentric inversion in chromosome 18 appears to have contributed to the evolution of humans. This inversion is not present in our closest genetic relatives, the chimpanzees. Humans and chimpanzees differ cytogenetically by pericentric inversions on several chromosomes and by the fusion of two separate chromosomes in chimpanzees that correspond to chromosome two in humans.
The pericentric chromosome 18 inversion is believed to have occurred in early humans following their divergence from a common ancestor with chimpanzees approximately five million years ago. Researchers characterizing this inversion have suggested that approximately 19,000 nucleotide bases were duplicated on 18p, and the duplicated region inverted and reinserted on chromosome 18 of an ancestral human.
A comparison of human and chimpanzee genes in the region of this inversion indicates that two genes—ROCK1 and USP14—that are adjacent on chimpanzee chromosome 17 (which corresponds to human chromosome 18) are more distantly positioned on human chromosome 18. This suggests that one of the inversion breakpoints occurred between these two genes. Interestingly, humans and chimpanzees express USP14 at distinct levels in specific cell types, including cortical cells and fibroblasts. Perhaps the chromosome 18 inversion in an ancestral human repositioned specific genes and reset their expression levels in a useful way. Because both ROCK1 and USP14 encode cellular enzymes, a change in their expression could alter cellular function. It is not known how this inversion contributed to hominid evolution, but it appears to be a significant factor in the divergence of humans from other primates.1
Translocations
A translocation occurs when a segment of a chromosome dissociates and reattaches to a different, nonhomologous chromosome. Translocations can be benign or have devastating effects depending on how the positions of genes are altered with respect to regulatory sequences. Notably, specific translocations have been associated with several cancers and with schizophrenia. Reciprocal translocations result from the exchange of chromosome segments between two nonhomologous chromosomes such that there is no gain or loss of genetic information (Figure \(9\)).
Summary
The number, size, shape, and banding pattern of chromosomes make them easily identifiable in a karyogram and allows for the assessment of many chromosomal abnormalities. Disorders in chromosome number, or aneuploidies, are typically lethal to the embryo, although a few trisomic genotypes are viable. Because of X inactivation, aberrations in sex chromosomes typically have milder phenotypic effects. Aneuploidies also include instances in which segments of a chromosome are duplicated or deleted. Chromosome structures may also be rearranged, for example by inversion or translocation. Both of these aberrations can result in problematic phenotypic effects. Because they force chromosomes to assume unnatural topologies during meiosis, inversions and translocations are often associated with reduced fertility because of the likelihood of nondisjunction.
Art Connections
Figure \(2\): Which of the following statements about nondisjunction is true?
1. Nondisjunction only results in gametes with n+1 or n–1 chromosomes.
2. Nondisjunction occurring during meiosis II results in 50 percent normal gametes.
3. Nondisjunction during meiosis I results in 50 percent normal gametes.
4. Nondisjunction always results in four different kinds of gametes.
Answer
B.
Footnotes
1. 1 Violaine Goidts et al., “Segmental duplication associated with the human-specific inversion of chromosome 18: a further example of the impact of segmental duplications on karyotype and genome evolution in primates,” Human Genetics. 115 (2004):116-122
Glossary
aneuploid
individual with an error in chromosome number; includes deletions and duplications of chromosome segments
autosome
any of the non-sex chromosomes
chromosome inversion
detachment, 180° rotation, and reinsertion of a chromosome arm
euploid
individual with the appropriate number of chromosomes for their species
karyogram
photographic image of a karyotype
karyotype
number and appearance of an individuals chromosomes; includes the size, banding patterns, and centromere position
monosomy
otherwise diploid genotype in which one chromosome is missing
nondisjunction
failure of synapsed homologs to completely separate and migrate to separate poles during the first cell division of meiosis
paracentric
inversion that occurs outside of the centromere
pericentric
inversion that involves the centromere
polyploid
individual with an incorrect number of chromosome sets
translocation
process by which one segment of a chromosome dissociates and reattaches to a different, nonhomologous chromosome
trisomy
otherwise diploid genotype in which one entire chromosome is duplicated
X inactivation
condensation of X chromosomes into Barr bodies during embryonic development in females to compensate for the double genetic dose
24.03: Evolution within Genomes
Skills to Develop
• List the steps in eukaryotic transcription
• Discuss the role of RNA polymerases in transcription
• Compare and contrast the three RNA polymerases
• Explain the significance of transcription factors
Prokaryotes and eukaryotes perform fundamentally the same process of transcription, with a few key differences. The most important difference between prokaryotes and eukaryotes is the latter’s membrane-bound nucleus and organelles. With the genes bound in a nucleus, the eukaryotic cell must be able to transport its mRNA to the cytoplasm and must protect its mRNA from degrading before it is translated. Eukaryotes also employ three different polymerases that each transcribe a different subset of genes. Eukaryotic mRNAs are usually monogenic, meaning that they specify a single protein.
Initiation of Transcription in Eukaryotes
Unlike the prokaryotic polymerase that can bind to a DNA template on its own, eukaryotes require several other proteins, called transcription factors, to first bind to the promoter region and then help recruit the appropriate polymerase.
The Three Eukaryotic RNA Polymerases
The features of eukaryotic mRNA synthesis are markedly more complex those of prokaryotes. Instead of a single polymerase comprising five subunits, the eukaryotes have three polymerases that are each made up of 10 subunits or more. Each eukaryotic polymerase also requires a distinct set of transcription factors to bring it to the DNA template.
RNA polymerase I is located in the nucleolus, a specialized nuclear substructure in which ribosomal RNA (rRNA) is transcribed, processed, and assembled into ribosomes (Table \(1\)). The rRNA molecules are considered structural RNAs because they have a cellular role but are not translated into protein. The rRNAs are components of the ribosome and are essential to the process of translation. RNA polymerase I synthesizes all of the rRNAs except for the 5S rRNA molecule. The “S” designation applies to “Svedberg” units, a nonadditive value that characterizes the speed at which a particle sediments during centrifugation.
Table \(1\): Locations, Products, and Sensitivities of the Three Eukaryotic RNA Polymerases
RNA Polymerase Cellular Compartment Product of Transcription α-Amanitin Sensitivity
I Nucleolus All rRNAs except 5S rRNA Insensitive
II Nucleus All protein-coding nuclear pre-mRNAs Extremely sensitive
III Nucleus 5S rRNA, tRNAs, and small nuclear RNAs Moderately sensitive
RNA polymerase II is located in the nucleus and synthesizes all protein-coding nuclear pre-mRNAs. Eukaryotic pre-mRNAs undergo extensive processing after transcription but before translation. For clarity, this module’s discussion of transcription and translation in eukaryotes will use the term “mRNAs” to describe only the mature, processed molecules that are ready to be translated. RNA polymerase II is responsible for transcribing the overwhelming majority of eukaryotic genes.
RNA polymerase III is also located in the nucleus. This polymerase transcribes a variety of structural RNAs that includes the 5S pre-rRNA, transfer pre-RNAs (pre-tRNAs), and small nuclear pre-RNAs. The tRNAs have a critical role in translation; they serve as the adaptor molecules between the mRNA template and the growing polypeptide chain. Small nuclear RNAs have a variety of functions, including “splicing” pre-mRNAs and regulating transcription factors.
A scientist characterizing a new gene can determine which polymerase transcribes it by testing whether the gene is expressed in the presence of a particular mushroom poison, α-amanitin (table above). Interestingly, α-amanitin produced by Amanita phalloides, the Death Cap mushroom, affects the three polymerases very differently. RNA polymerase I is completely insensitive to α-amanitin, meaning that the polymerase can transcribe DNA in vitro in the presence of this poison. In contrast, RNA polymerase II is extremely sensitive to α-amanitin, and RNA polymerase III is moderately sensitive. Knowing the transcribing polymerase can clue a researcher into the general function of the gene being studied. Because RNA polymerase II transcribes the vast majority of genes, we will focus on this polymerase in our subsequent discussions about eukaryotic transcription factors and promoters.
Structure of an RNA Polymerase II Promoter
Eukaryotic promoters are much larger and more complex than prokaryotic promoters, but both have a TATA box. For example, in the mouse thymidine kinase gene, the TATA box is located at approximately -30 relative to the initiation (+1) site (Figure \(1\)). For this gene, the exact TATA box sequence is TATAAAA, as read in the 5' to 3' direction on the nontemplate strand. This sequence is not identical to the E. coli TATA box, but it conserves the A–T rich element. The thermostability of A–T bonds is low and this helps the DNA template to locally unwind in preparation for transcription.
Art Connection
A scientist splices a eukaryotic promoter in front of a bacterial gene and inserts the gene in a bacterial chromosome. Would you expect the bacteria to transcribe the gene?
The mouse genome includes one gene and two pseudogenes for cytoplasmic thymidine kinase. Pseudogenes are genes that have lost their protein-coding ability or are no longer expressed by the cell. These pseudogenes are copied from mRNA and incorporated into the chromosome. For example, the mouse thymidine kinase promoter also has a conserved CAAT box (GGCCAATCT) at approximately -80. This sequence is essential and is involved in binding transcription factors. Further upstream of the TATA box, eukaryotic promoters may also contain one or more GC-rich boxes (GGCG) or octamer boxes (ATTTGCAT). These elements bind cellular factors that increase the efficiency of transcription initiation and are often identified in more “active” genes that are constantly being expressed by the cell.
Transcription Factors for RNA Polymerase II
The complexity of eukaryotic transcription does not end with the polymerases and promoters. An army of basal transcription factors, enhancers, and silencers also help to regulate the frequency with which pre-mRNA is synthesized from a gene. Enhancers and silencers affect the efficiency of transcription but are not necessary for transcription to proceed. Basal transcription factors are crucial in the formation of a preinitiation complex on the DNA template that subsequently recruits RNA polymerase II for transcription initiation.
The names of the basal transcription factors begin with “TFII” (this is the transcription factor for RNA polymerase II) and are specified with the letters A–J. The transcription factors systematically fall into place on the DNA template, with each one further stabilizing the preinitiation complex and contributing to the recruitment of RNA polymerase II.
The processes of bringing RNA polymerases I and III to the DNA template involve slightly less complex collections of transcription factors, but the general theme is the same. Eukaryotic transcription is a tightly regulated process that requires a variety of proteins to interact with each other and with the DNA strand. Although the process of transcription in eukaryotes involves a greater metabolic investment than in prokaryotes, it ensures that the cell transcribes precisely the pre-mRNAs that it needs for protein synthesis.
Evolution Connection: The Evolution of Promoters
The evolution of genes may be a familiar concept. Mutations can occur in genes during DNA replication, and the result may or may not be beneficial to the cell. By altering an enzyme, structural protein, or some other factor, the process of mutation can transform functions or physical features. However, eukaryotic promoters and other gene regulatory sequences may evolve as well. For instance, consider a gene that, over many generations, becomes more valuable to the cell. Maybe the gene encodes a structural protein that the cell needs to synthesize in abundance for a certain function. If this is the case, it would be beneficial to the cell for that gene’s promoter to recruit transcription factors more efficiently and increase gene expression.
Scientists examining the evolution of promoter sequences have reported varying results. In part, this is because it is difficult to infer exactly where a eukaryotic promoter begins and ends. Some promoters occur within genes; others are located very far upstream, or even downstream, of the genes they are regulating. However, when researchers limited their examination to human core promoter sequences that were defined experimentally as sequences that bind the preinitiation complex, they found that promoters evolve even faster than protein-coding genes.
It is still unclear how promoter evolution might correspond to the evolution of humans or other higher organisms. However, the evolution of a promoter to effectively make more or less of a given gene product is an intriguing alternative to the evolution of the genes themselves.1
Promoter Structures for RNA Polymerases I and III
In eukaryotes, the conserved promoter elements differ for genes transcribed by RNA polymerases I, II, and III. RNA polymerase I transcribes genes that have two GC-rich promoter sequences in the -45 to +20 region. These sequences alone are sufficient for transcription initiation to occur, but promoters with additional sequences in the region from -180 to -105 upstream of the initiation site will further enhance initiation. Genes that are transcribed by RNA polymerase III have upstream promoters or promoters that occur within the genes themselves.
Eukaryotic Elongation and Termination
Following the formation of the preinitiation complex, the polymerase is released from the other transcription factors, and elongation is allowed to proceed as it does in prokaryotes with the polymerase synthesizing pre-mRNA in the 5' to 3' direction. As discussed previously, RNA polymerase II transcribes the major share of eukaryotic genes, so this section will focus on how this polymerase accomplishes elongation and termination.
Although the enzymatic process of elongation is essentially the same in eukaryotes and prokaryotes, the DNA template is more complex. When eukaryotic cells are not dividing, their genes exist as a diffuse mass of DNA and proteins called chromatin. The DNA is tightly packaged around charged histone proteins at repeated intervals. These DNA–histone complexes, collectively called nucleosomes, are regularly spaced and include 146 nucleotides of DNA wound around eight histones like thread around a spool.
For polynucleotide synthesis to occur, the transcription machinery needs to move histones out of the way every time it encounters a nucleosome. This is accomplished by a special protein complex called FACT, which stands for “facilitates chromatin transcription.” This complex pulls histones away from the DNA template as the polymerase moves along it. Once the pre-mRNA is synthesized, the FACT complex replaces the histones to recreate the nucleosomes.
The termination of transcription is different for the different polymerases. Unlike in prokaryotes, elongation by RNA polymerase II in eukaryotes takes place 1,000–2,000 nucleotides beyond the end of the gene being transcribed. This pre-mRNA tail is subsequently removed by cleavage during mRNA processing. On the other hand, RNA polymerases I and III require termination signals. Genes transcribed by RNA polymerase I contain a specific 18-nucleotide sequence that is recognized by a termination protein. The process of termination in RNA polymerase III involves an mRNA hairpin similar to rho-independent termination of transcription in prokaryotes.
Summary
Transcription in eukaryotes involves one of three types of polymerases, depending on the gene being transcribed. RNA polymerase II transcribes all of the protein-coding genes, whereas RNA polymerase I transcribes rRNA genes, and RNA polymerase III transcribes rRNA, tRNA, and small nuclear RNA genes. The initiation of transcription in eukaryotes involves the binding of several transcription factors to complex promoter sequences that are usually located upstream of the gene being copied. The mRNA is synthesized in the 5' to 3' direction, and the FACT complex moves and reassembles nucleosomes as the polymerase passes by. Whereas RNA polymerases I and III terminate transcription by protein- or RNA hairpin-dependent methods, RNA polymerase II transcribes for 1,000 or more nucleotides beyond the gene template and cleaves the excess during pre-mRNA processing.
Art Connections
Figure \(2\): A scientist splices a eukaryotic promoter in front of a bacterial gene and inserts the gene in a bacterial chromosome. Would you expect the bacteria to transcribe the gene?
Answer
No. Prokaryotes use different promoters than eukaryotes.
Footnotes
1. 1 H Liang et al., “Fast evolution of core promoters in primate genomes,” Molecular Biology and Evolution 25 (2008): 1239–44.
Glossary
CAAT box
(GGCCAATCT) essential eukaryotic promoter sequence involved in binding transcription factors
FACT
complex that “facilitates chromatin transcription” by disassembling nucleosomes ahead of a transcribing RNA polymerase II and reassembling them after the polymerase passes by
GC-rich box
(GGCG) nonessential eukaryotic promoter sequence that binds cellular factors to increase the efficiency of transcription; may be present several times in a promoter
Octamer box
(ATTTGCAT) nonessential eukaryotic promoter sequence that binds cellular factors to increase the efficiency of transcription; may be present several times in a promoter
preinitiation complex
cluster of transcription factors and other proteins that recruit RNA polymerase II for transcription of a DNA template
small nuclear RNA
molecules synthesized by RNA polymerase III that have a variety of functions, including splicing pre-mRNAs and regulating transcription factors | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/24%3A_Genome_Evolution/24.03%3A_Evolution_within_Genomes/24.3.01%3A_Eukaryotic_Transcription.txt |
Skills to Develop
• Describe horizontal gene transfer
• Illustrate how prokaryotes and eukaryotes transfer genes horizontally
• Identify the web and ring models of phylogenetic relationships and describe how they differ from the original phylogenetic tree concept
The concepts of phylogenetic modeling are constantly changing. It is one of the most dynamic fields of study in all of biology. Over the last several decades, new research has challenged scientists’ ideas about how organisms are related. New models of these relationships have been proposed for consideration by the scientific community.
Many phylogenetic trees have been shown as models of the evolutionary relationship among species. Phylogenetic trees originated with Charles Darwin, who sketched the first phylogenetic tree in 1837 (Figure \(1\)a), which served as a pattern for subsequent studies for more than a century. The concept of a phylogenetic tree with a single trunk representing a common ancestor, with the branches representing the divergence of species from this ancestor, fits well with the structure of many common trees, such as the oak (Figure \(1\)b). However, evidence from modern DNA sequence analysis and newly developed computer algorithms has caused skepticism about the validity of the standard tree model in the scientific community.
Limitations to the Classic Model
Classical thinking about prokaryotic evolution, included in the classic tree model, is that species evolve clonally. That is, they produce offspring themselves with only random mutations causing the descent into the variety of modern-day and extinct species known to science. This view is somewhat complicated in eukaryotes that reproduce sexually, but the laws of Mendelian genetics explain the variation in offspring, again, to be a result of a mutation within the species. The concept of genes being transferred between unrelated species was not considered as a possibility until relatively recently. Horizontal gene transfer (HGT), also known as lateral gene transfer, is the transfer of genes between unrelated species. HGT has been shown to be an ever-present phenomenon, with many evolutionists postulating a major role for this process in evolution, thus complicating the simple tree model. Genes have been shown to be passed between species which are only distantly related using standard phylogeny, thus adding a layer of complexity to the understanding of phylogenetic relationships.
The various ways that HGT occurs in prokaryotes is important to understanding phylogenies. Although at present HGT is not viewed as important to eukaryotic evolution, HGT does occur in this domain as well. Finally, as an example of the ultimate gene transfer, theories of genome fusion between symbiotic or endosymbiotic organisms have been proposed to explain an event of great importance—the evolution of the first eukaryotic cell, without which humans could not have come into existence.
Horizontal Gene Transfer
Horizontal gene transfer (HGT) is the introduction of genetic material from one species to another species by mechanisms other than the vertical transmission from parent(s) to offspring. These transfers allow even distantly related species to share genes, influencing their phenotypes. It is thought that HGT is more prevalent in prokaryotes, but that only about 2% of the prokaryotic genome may be transferred by this process. Some researchers believe such estimates are premature: the actual importance of HGT to evolutionary processes must be viewed as a work in progress. As the phenomenon is investigated more thoroughly, it may be revealed to be more common. Many scientists believe that HGT and mutation appear to be (especially in prokaryotes) a significant source of genetic variation, which is the raw material for the process of natural selection. These transfers may occur between any two species that share an intimate relationship (Table \(1\)).
Table \(1\): Summary of Mechanisms of Prokaryotic and Eukaryotic HGT
Mechanism Mode of Transmission Example
Prokaryotes transformation DNA uptake many prokaryotes
transduction bacteriophage (virus) bacteria
conjugation pilus many prokaryotes
gene transfer agents phage-like particles purple non-sulfur bacteria
Eukaryotes from food organisms unknown aphid
jumping genes transposons rice and millet plants
epiphytes/parasites unknown yew tree fungi
from viral infections
HGT in Prokaryotes
The mechanism of HGT has been shown to be quite common in the prokaryotic domains of Bacteria and Archaea, significantly changing the way their evolution is viewed. The majority of evolutionary models, such as in the Endosymbiont Theory, propose that eukaryotes descended from multiple prokaryotes, which makes HGT all the more important to understanding the phylogenetic relationships of all extant and extinct species.
The fact that genes are transferred among common bacteria is well known to microbiology students. These gene transfers between species are the major mechanism whereby bacteria acquire resistance to antibiotics. Classically, this type of transfer has been thought to occur by three different mechanisms:
1. Transformation: naked DNA is taken up by a bacteria
2. Transduction: genes are transferred using a virus
3. Conjugation: the use of a hollow tube called a pilus to transfer genes between organisms
More recently, a fourth mechanism of gene transfer between prokaryotes has been discovered. Small, virus-like particles called gene transfer agents (GTAs) transfer random genomic segments from one species of prokaryote to another. GTAs have been shown to be responsible for genetic changes, sometimes at a very high frequency compared to other evolutionary processes. The first GTA was characterized in 1974 using purple, non-sulfur bacteria. These GTAs, which are thought to be bacteriophages that lost the ability to reproduce on their own, carry random pieces of DNA from one organism to another. The ability of GTAs to act with high frequency has been demonstrated in controlled studies using marine bacteria. Gene transfer events in marine prokaryotes, either by GTAs or by viruses, have been estimated to be as high as 1013 per year in the Mediterranean Sea alone. GTAs and viruses are thought to be efficient HGT vehicles with a major impact on prokaryotic evolution.
As a consequence of this modern DNA analysis, the idea that eukaryotes evolved directly from Archaea has fallen out of favor. While eukaryotes share many features that are absent in bacteria, such as the TATA box (found in the promoter region of many genes), the discovery that some eukaryotic genes were more homologous with bacterial DNA than Archaea DNA made this idea less tenable. Furthermore, the fusion of genomes from Archaea and Bacteria by endosymbiosis has been proposed as the ultimate event in eukaryotic evolution.
HGT in Eukaryotes
Although it is easy to see how prokaryotes exchange genetic material by HGT, it was initially thought that this process was absent in eukaryotes. After all, prokaryotes are but single cells exposed directly to their environment, whereas the sex cells of multicellular organisms are usually sequestered in protected parts of the body. It follows from this idea that the gene transfers between multicellular eukaryotes should be more difficult. Indeed, it is thought that this process is rarer in eukaryotes and has a much smaller evolutionary impact than in prokaryotes. In spite of this fact, HGT between distantly related organisms has been demonstrated in several eukaryotic species, and it is possible that more examples will be discovered in the future.
In plants, gene transfer has been observed in species that cannot cross-pollinate by normal means. Transposons or “jumping genes” have been shown to transfer between rice and millet plant species. Furthermore, fungal species feeding on yew trees, from which the anti-cancer drug TAXOL® is derived from the bark, have acquired the ability to make taxol themselves, a clear example of gene transfer.
In animals, a particularly interesting example of HGT occurs within the aphid species (Figure \(2\)). Aphids are insects that vary in color based on carotenoid content. Carotenoids are pigments made by a variety of plants, fungi, and microbes, and they serve a variety of functions in animals, who obtain these chemicals from their food. Humans require carotenoids to synthesize vitamin A, and we obtain them by eating orange fruits and vegetables: carrots, apricots, mangoes, and sweet potatoes. On the other hand, aphids have acquired the ability to make the carotenoids on their own. According to DNA analysis, this ability is due to the transfer of fungal genes into the insect by HGT, presumably as the insect consumed fungi for food. A carotenoid enzyme called a desaturase is responsible for the red coloration seen in certain aphids, and it has been further shown that when this gene is inactivated by mutation, the aphids revert back to their more common green color (Figure \(2\)).
Genome Fusion and the Evolution of Eukaryotes
Scientists believe the ultimate in HGT occurs through genome fusion between different species of prokaryotes when two symbiotic organisms become endosymbiotic. This occurs when one species is taken inside the cytoplasm of another species, which ultimately results in a genome consisting of genes from both the endosymbiont and the host. This mechanism is an aspect of the Endosymbiont Theory, which is accepted by a majority of biologists as the mechanism whereby eukaryotic cells obtained their mitochondria and chloroplasts. However, the role of endosymbiosis in the development of the nucleus is more controversial. Nuclear and mitochondrial DNA are thought to be of different (separate) evolutionary origin, with the mitochondrial DNA being derived from the circular genomes of bacteria that were engulfed by ancient prokaryotic cells. Mitochondrial DNA can be regarded as the smallest chromosome. Interestingly enough, mitochondrial DNA is inherited only from the mother. The mitochondrial DNA degrades in sperm when the sperm degrades in the fertilized egg or in other instances when the mitochondria located in the flagellum of the sperm fails to enter the egg.
Within the past decade, the process of genome fusion by endosymbiosis has been proposed by James Lake of the UCLA/NASA Astrobiology Institute to be responsible for the evolution of the first eukaryotic cells (Figure \(3\)a). Using DNA analysis and a new mathematical algorithm called conditioned reconstruction (CR), his laboratory proposed that eukaryotic cells developed from an endosymbiotic gene fusion between two species, one an Archaea and the other a Bacteria. As mentioned, some eukaryotic genes resemble those of Archaea, whereas others resemble those from Bacteria. An endosymbiotic fusion event, such as Lake has proposed, would clearly explain this observation. On the other hand, this work is new and the CR algorithm is relatively unsubstantiated, which causes many scientists to resist this hypothesis.
More recent work by Lake (Figure \(3\)b) proposes that gram-negative bacteria, which are unique within their domain in that they contain two lipid bilayer membranes, indeed resulted from an endosymbiotic fusion of archaeal and bacterial species. The double membrane would be a direct result of the endosymbiosis, with the endosymbiont picking up the second membrane from the host as it was internalized. This mechanism has also been used to explain the double membranes found in mitochondria and chloroplasts. Lake’s work is not without skepticism, and the ideas are still debated within the biological science community. In addition to Lake’s hypothesis, there are several other competing theories as to the origin of eukaryotes. How did the eukaryotic nucleus evolve? One theory is that the prokaryotic cells produced an additional membrane that surrounded the bacterial chromosome. Some bacteria have the DNA enclosed by two membranes; however, there is no evidence of a nucleolus or nuclear pores. Other proteobacteria also have membrane-bound chromosomes. If the eukaryotic nucleus evolved this way, we would expect one of the two types of prokaryotes to be more closely related to eukaryotes.
The nucleus-first hypothesis proposes that the nucleus evolved in prokaryotes first (Figure \(4\)a), followed by a later fusion of the new eukaryote with bacteria that became mitochondria. The mitochondria-first hypothesis proposes that mitochondria were first established in a prokaryotic host (Figure \(4\)b), which subsequently acquired a nucleus, by fusion or other mechanisms, to become the first eukaryotic cell. Most interestingly, the eukaryote-first hypothesis proposes that prokaryotes actually evolved from eukaryotes by losing genes and complexity (Figure \(4\)c). All of these hypotheses are testable. Only time and more experimentation will determine which hypothesis is best supported by data.
Web and Network Models
The recognition of the importance of HGT, especially in the evolution of prokaryotes, has caused some to propose abandoning the classic “tree of life” model. In 1999, W. Ford Doolittle proposed a phylogenetic model that resembles a web or a network more than a tree. The hypothesis is that eukaryotes evolved not from a single prokaryotic ancestor, but from a pool of many species that were sharing genes by HGT mechanisms. As shown in Figure \(5\)a, some individual prokaryotes were responsible for transferring the bacteria that caused mitochondrial development to the new eukaryotes, whereas other species transferred the bacteria that gave rise to chloroplasts. This model is often called the “web of life.” In an effort to save the tree analogy, some have proposed using the Ficus tree (Figure \(5\)b) with its multiple trunks as a phylogenetic to represent a diminished evolutionary role for HGT.
Ring of Life Models
Others have proposed abandoning any tree-like model of phylogeny in favor of a ring structure, the so-called “ring of life” (Figure \(6\)); a phylogenetic model where all three domains of life evolved from a pool of primitive prokaryotes. Lake, again using the conditioned reconstruction algorithm, proposes a ring-like model in which species of all three domains—Archaea, Bacteria, and Eukarya—evolved from a single pool of gene-swapping prokaryotes. His laboratory proposes that this structure is the best fit for data from extensive DNA analyses performed in his laboratory, and that the ring model is the only one that adequately takes HGT and genomic fusion into account. However, other phylogeneticists remain highly skeptical of this model.
In summary, the “tree of life” model proposed by Darwin must be modified to include HGT. Does this mean abandoning the tree model completely? Even Lake argues that all attempts should be made to discover some modification of the tree model to allow it to accurately fit his data, and only the inability to do so will sway people toward his ring proposal.
This doesn’t mean a tree, web, or a ring will correlate completely to an accurate description of phylogenetic relationships of life. A consequence of the new thinking about phylogenetic models is the idea that Darwin’s original conception of the phylogenetic tree is too simple, but made sense based on what was known at the time. However, the search for a more useful model moves on: each model serving as hypotheses to be tested with the possibility of developing new models. This is how science advances. These models are used as visualizations to help construct hypothetical evolutionary relationships and understand the massive amount of data being analyzed.
Summary
The phylogenetic tree, first used by Darwin, is the classic “tree of life” model describing phylogenetic relationships among species, and the most common model used today. New ideas about HGT and genome fusion have caused some to suggest revising the model to resemble webs or rings.
Glossary
eukaryote-first hypothesis
proposal that prokaryotes evolved from eukaryotes
gene transfer agent (GTA)
bacteriophage-like particle that transfers random genomic segments from one species of prokaryote to another
genome fusion
fusion of two prokaryotic genomes, presumably by endosymbiosis
horizontal gene transfer (HGT)
(also, lateral gene transfer) transfer of genes between unrelated species
mitochondria-first hypothesis
proposal that prokaryotes acquired a mitochondrion first, followed by nuclear development
nucleus-first hypothesis
proposal that prokaryotes acquired a nucleus first, and then the mitochondrion
ring of life
phylogenetic model where all three domains of life evolved from a pool of primitive prokaryotes
web of life
phylogenetic model that attempts to incorporate the effects of horizontal gene transfer on evolution | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/24%3A_Genome_Evolution/24.03%3A_Evolution_within_Genomes/24.3.02%3A_Perspectives_on_the_Phylogenetic_Tree.txt |
Learning Objectives
• Understand the concept of gene expression.
• Understand transcriptional regulation of gene expression.
• Understand epigenetic gene regulation.4
• Understand post-transcriptional regulation of gene expression (RNA level).
• Understand post-translational protein modification and regulation.
Introduction
Every cell in a plant contains the same genetic information, the same set of genes. Yet Therefore different sets of genes are required for the various functions of different cells or tissues, as well as for plant responses to environmental stimuli or stresses. This is achieved by regulating the activity of genes according to the physiological demands of a particular cell type, developmental stage, or environmental condition. This regulation of activity is known as gene expression.
The term expression can be used in different ways that are sometimes confusing. Typically, if a gene product is produced, the gene is considered “expressed”. However, it sometimes occurs that a transcript might be produced but not a protein, or that a protein is produced but it is in an inactive state. In such cases, although a gene product is produced, the biological activity encoded by that gene is not present. For the purposes of this section, the key point is how the biological activity encoded by a gene is regulated.
The expression of genes in specific plant cells, tissues, and organs and the timing of this expression require a precise level of regulation. Expression, or genetic function, can potentially be regulated at any of the steps from transcription, RNA processing, translation, through post-translational protein modification, as discussed in lesson 1. Regulation can be qualitative (i.e. gene expression is either “on” or “off”) or quantitative (i.e. expression levels can be modulated “up” or “down”). Fluctuations in the intensities of external stimuli coupled to changes that occur at the genomic level result in different developmental outcomes or physiological states. Regulation of gene expression at the level of transcription can be brought about through chromatin and histone modifications. Also, a gene sequence can be differentially spliced to produce mRNA products of variable lengths leading to new protein products with novel functions. Some genes do not encode proteins but short forms of RNAs with regulatory functions such as induction of flowering. Finally, proteins products can be subjected to modifications such as phosphorylation or dephosphorylation to alter their functions, or can be completely degraded to turn off a gene.
Transcriptional gene regulation
Since transcription is the first step in gene expression, it makes sense in terms of cellular economy, to regulate expression at this point, and in fact this is one of the most important regulatory points. We already described the involvement of RNA polymerase in the transcription process, but in fact there are other protein factors that are required. Proteins involved in transcriptional regulation are known as transcription factors. It is the interaction of these transcription factors with specific DNA sequences that regulate the process of gene transcription.
A. The concept of differential (regulated) gene expression
As just described, not every gene is expressed all the time. When a gene displays different levels of expression in different circumstances, this is known as differential expression. Circumstances that might apply include, but are not limited to, different plant tissues (root vs. leaf), different developmental stages (germination vs. reproductive development), or in response to different environmental stimuli (cold stress or pathogen attack).
The term differential expression can also be used to compare the expression of different genes. If two genes show different expression patterns (among plant tissues or in response to environmental stimuli), they are considered differentially expressed, whereas genes that showed very similar patterns of expression would be considered co-expressed.
B. Promoters
As mentioned, transcription is regulated through the interactions of proteins, transcription factors, with specific DNA sequences. Most regulatory DNA sequences governing gene transcription are located on the 5′ border of the transcribed region. This region is called the gene promoter.
Promoters contain a core, which is required for the binding of the “basal transcriptional machinery”, including RNA polymerase. The “TATA” box, with a consensus sequence TATAA, is located within the core promoter, usually 25-30 nucleotides upstream of the transcription initiation site. Promoters also contain regulatory sequences that determine when, where, and to what level genes are transcribed. Promoters can vary in length from a hundred to a few thousand nucleotides.
The full promoter sequences of different genes that are expressed in a similar manner may be different. However, such promoters often contain short sequence “motifs” that are similar, referred to as cis elements. Early work (Benfy and Chua, 1990) to understand the function of different promoter elements in regulating gene expression in plant cells and tissues revealed that various combinations of cis elements are able to be interpreted by the cell and control gene expression. Sometimes cis elements promote gene transcription and sometimes they function to restrict transcription of genes in particular cells and tissues.
Promoter analysis is facilitated through the use of reporter genes. The reporter gene produces effects that are easily identifiable and quantifiable, which can be used to determine the function of a regulatory region of another gene (promoter, promoter elements, or enhancers) in cells, tissues, or organs. Such analyses are critical to crop biotechnology where targeted expression of genes in particular tissues is often desirable. To test whether a promoter is effective in conferring the expression of a gene to a particular tissue, scientists fuse the putative promoter to a reporter gene and introduce the promoter-gene fusion into plants. An example of a reporter is the GUS gene, which encodes a GUS enzyme (beta-Glucuronidase) that, when expressed, produces a blue color upon addition of a substrate. Figure 1 shows an example of GUS expression in maize seed using two promoters that act either in the endosperm or the embryo.
C. Enhancers
Enhancers are DNA sequences that increase the rate of transcription of a gene when they are present, although alone they cannot cause transcription to occur. Enhancers are usually position and orientation independent. Although they are normally located upstream of the promoter, they can also be located on the 3’ region of the gene or even with the coding region. Enhancers can increase the transcription when added to genes that they are not normally associated with. This is a useful property for biotechnology, allowing promoters to be manipulated for increased levels of transcriptional regulation. Some enhancers function at all times in all cells and tissues and they are referred to as constitutive. Other enhancers function in specific tissues at specific developmental stages. Some are active only in response to environmental signals. The AACCA enhancer on the promoter of soybean β-conglycinin gene encoding a seed storage protein functions specifically in seeds. Enhancers are thought to interact with specific nuclear proteins involved in transcription. For example, enhancers might facilitate the binding of transcription factors and direct these factors along the DNA strand to the direction of the promoter. Alternatively, enhancers may facilitate changes in DNA structure such as modification of the chromatin structure.
The counterpart of an enhancer is a silencer. Silencers have all the properties just described for enhancers, except they function to dampen, or decrease, the levels of transcription controlled by a promoter.
D. Transcription factors
RNA polymerase binds the promoter at the TATA box and in cooperation with other proteins drives gene transcription. The proteins that interact with RNA polymerase to facilitate its binding to the promoter and to regulate its activity are known as transcription factors. Some transcription factors, known as “basal transcription factors” are fundamental to RNA polymerase binding and function, and are expressed in all living cells.
Other transcription factors bind to cis regulatory DNA sequences of promoters, enhancers or silencers. These proteins interact in complex ways with the basal transcription machinery, to regulate the activity of RNA polymerase, and therefore gene transcription. Thus, transcription factors regulate when or where individual genes are expressed, and to what level.
Transcription factors can function as either positive or negative regulators. That is, they can either function to induce (increase) gene transcription or to repress it. The consequence of many transcription factors depends on their interactions with other proteins. Two factors together may be required for gene activity, and exclusion of one of the factors in space and time offers a mechanism for differential gene expression. Some transcription factors might function as a positive regulator in one context but as a negative regulator in another context, depending on what other cis elements and/or transcription factors might be present.
Epigenetic regulation
A. Chromatin structure and histone modification
At the molecular level chromatin is a product of an ordered and tight packaging of the double stranded DNA around nucleosomes (a core of proteins named histones), and an association with additional proteins.
Transcriptional regulation often involves modification of chromatin structure mediated by post-translational regulation (changes in acetylation and methylation) of histones. Histone acetylation involves the addition of acetyl groups and when histones are heavily acetylated the DNA is less tightly associated with them. This often correlates with increased transcriptional activity of specific genes. The idea is that when DNA is loosely associated with histones, it is more accessible to transcription factors that require interaction with the DNA to initiate transcription. Consequently, histone deacetylation (removal of acetyl groups) by histone deacetylase enzymes (for example, FLD, p462) stabilizes nucleosomes and represses transcription. On the other hand, histone acetylation by histone ecetyltransferase destabilizes nucleosomes and promotes transcription.
As described in the text, another form of histone modification is the addition of methyl groups to histone proteins, which similarly regulates chromatin condensation or decondensation.
B. DNA methylation
The nucleotide bases of DNA can be modified by the attachment of methyl groups at various locations. The addition of these methyl groups happens after the DNA has been synthesized and is controlled by enzymes that add methyl moieties to specific regions of DNA. The most common modified nucleotide base is C5 methylcytosine (m5C) due the activity of the enzyme DNA (cytosine-5) methyltransferase (MET). MET recognizes the unmethylated newly-replicated DNA strand and incorporates a methyl group if the template strand was methylated (hemimethylated).
Methylation status is correlated with gene expression (Figure 5) as demonstrated by the low level of methylation in regions of the genome undergoing active transcription.
Studies have shown that altering a plant’s overall DNA methylation status can affect growth and development. For example, cold treatment (vernalization) induces flowering in biannuals such as Arabidopsis and winter wheat, and lowers the level of methylation of particular genes. Also, treating plants with the drug 5 azacytidine prevents methylation at the 5 position of cytosine and stimulates flowering. Recent studies also suggest a relationship between epigenetic gene regulation and heterosis, with hybrids showing higher global levels of transcription, higher histone acetylation levels and lower DNA methylation levels (reviewed in He et al., 2011).
RNA-level regulation
Regulation of gene expression occurs at many levels, including post-transcriptionally. From the standpoint of the expression level for a given gene, a critical factor is the level of fully processed, mature mRNA. When we consider the level of the mature form a particular transcript at any given time reflects the steady state balance between synthesis, processing and degradation. The Post-transcriptional regulation of RNA occurs through several mechanisms.
RNA stability and degradation
The control of mRNA degradation rate, or turnover, is an important regulatory mechanism in gene expression. As mentioned, the level of a particular transcript at any given time reflects the steady state balance between synthesis and degradation. Thus, even though a gene may be transcribed at a high rate, a high rate of RNA turnover could effectively shut off the gene. The stability of mRNA can be regulated globally, to affect all or most transcripts, or it can be very specific to a particular mRNA. Regulated mRNA turnover may be particularly important in plants, since plants cannot move to avoid harsh environmental conditions and stresses are known to induce specific changes in RNA stability. Other factors such as light and plant hormones are also known to regulate mRNA stability.
The degradation of mRNA is catalyzed by enzymes called ribonucleases. Ribonucleases include exonucleases, which degrade only from one end of the transcript, and endonucleases, which can attack the mRNA molecule internally.
Therefore, controlling ribonuclease access to the mRNA substrate is an important regulatory mechanism in gene expression. This control is achieved through various mechanisms including, controlling the amount of nucleases present, regulating the activity of the nuclease, sequestering the nuclease to particular cellular locations to restrict its access to RNA, and to control the stability of the mRNA by decreasing accessibility to nuclease.
Four regions of an mRNA are important for its overall stability. These include, the 5′ untranslated region and the cap, coding region, 3’ untranslated region, and the poly(A) tail.
The cap at the 5′ end protects the mRNA from exonucleases that degrade RNA from the 5′ to the 3′ direction.
The 3′ untranslated region may contain short sequences that influence mRNA stability. For example, the repetition of the sequence AUUUA in the 3′ untranslated region of many animal and plant genes is associated with mRNAs with short half-lives (the time it takes for half the RNA to be degraded, after transcription is stopped).
The poly(A) tail increases mRNA stability but is not sufficient alone. It only provides stability when bound by proteins such as poly(A) binding protein (PABP). Test-tube experiments have shown that, removing PABP from a stable mRNA destabilizes it, while adding back purified PABP restores stability.
Translational regulation
As described, for most genes it is the protein product that performs the biological function. As such, regulating the amount of protein production effectively regulates gene expression. There are several known mechanisms by which the process of translation is known to be regulated. A detailed consideration of these mechanisms is beyond the scope of this course, but in general it is important to bear in mind their importance. For example, under certain stress conditions, “normal” translation is halted and only mRNAs related to stress tolerance are selectively permitted to be translated into proteins. This selective translation is important to allow plants to quickly respond to stress and to conserve energy under stress conditions.
Translation of mRNAs can play an important role in determining their overall stability. Mutations that add premature stop codons often lead to rapid degradation of the mRNA. Ribonucleases (figure 9) or other factors involved in degradation may recognize the number or spacing of ribosomes on an mRNA, and degrade those that are not produced properly. This may help prevent synthesis of proteins with incorrect functions which will negatively impact cellular processes. Errors during transcription could add or omit nucleotides which would alter the proper codon sequence creating mutant proteins.
Protein-level regulation
After translation, proteins are subject to a variety of modifications that can regulate their activity. There are many different ways by which proteins can potentially be modified and thereby regulated, and only a few of the basic mechanisms will be considered here.
Common types of post-translational modifications
The first mechanism is covalent modification by the addition of various chemical groups. A wide variety of groups can be involved, including small organic groups (methylation, acetylation) lipids (myristoylation, farnesylation, palmitylation), carbohydrates (glycosylation, glucosylation), small proteins (ubiquitination, sumoylation) and inorganic molecules (phosphorylation, sulfation). Such covalent modifications are generally accomplished by the activity of enzymes specialized to perform these modifications. Many of these modifications are also reversible; that is these groups can be added to a protein and subsequently removed. Phosphorylation is a particularly noteworthy reversible modification that is common in the regulation of many proteins. Enzymes that add phosphate groups to other proteins are called protein kinases, and those that remove phosphates are called phosphatases. As such, protein kinases and phosphatases are central to many cellular regulatory systems.
A second common mechanism of protein modification is through proteolytic cleavage. Proteolysis occurs as part of the general turnover of cellular proteins, which is required to eliminate damaged proteins and recycle amino acids. Proteolysis is important for the processing of certain proteins, for example in the removal of the signal peptide of proteins targeted to specific cellular compartments. It can also occur in a highly specific manner whereby particular proteins are targeted for degradation or for cleavage at a specific site within the protein. Proteolytic modifications are non-reversible.
Proteins can undergo modification through complex formation. Such complexes can occur among proteins or between a protein and a cofactor.
Proteins can also be modified according to conditions of the cellular environment. The redox state can result in oxidation or reduction of proteins, particularly of sulfhydryl side groups. Cellular pH can affect the charge of ionizable side groups.
Common types of protein regulation
All of the above mentioned types of protein modification can alter protein conformations and thus have regulatory consequences on protein function or activity. Protein regulation is highly complex and there are a myriad of different ways by which this occurs. Again we will just briefly consider a few of the more common mechanisms.
One major way protein modification can regulate protein function is by altering their activity. This can be true for many types of proteins including, but not limited to, enzymes, transcription factors, signaling proteins, and structural proteins.
Cells are compartmentalized into several membrane bound organelles, including the nucleus, chloroplasts, mitochondria, peroxisomes, endoplasmic reticulum (ER), golgi, and vacuoles. Each of these compartments performs unique metabolic functions that require a set of proteins. Compartmentation is regulated for some proteins. For example, upon exposure to light the phytochrome protein moves into the nucleus where it affects the expression of light-regulated genes.
Proteolytic processing is involved in several important regulatory processes. Many proteins are synthesized in an inactive form that requires proteolytic cleavage for activation. The full-length translation product before processing is often called the precursor, or a preprotein. As mentioned, cells contain membrane-bound compartments. Since membranes are impermeable to most proteins, an active mechanism is necessary to move a protein across a membrane. For proper delivery to their organellar destinations, specific amino acid sequences, called target signals must be present in a protein (to serve as an “address”). For example, entry into the chloroplast is achieved by the presence of a target signal called the transit peptide. This is at the amino terminal end of the protein and is proteolytically cleaved during import.
Another example of proteolytic processing is seen in a plant defense response in members of the solanaceae (for example, tomato and potato). An 18-amino acid peptide hormone called systemin is secreted by plant cells that are damaged by insects or mechanical wounding. Systemin production by wounded cells is required to induce the synthesis of proteins involved in defense. Systemin induces defense responses in wounded cells, and throughout the plant. Analogous to animal peptide hormones (e.g., insulin), systemin is initially synthesized as a much larger (200 amino acids) precursor called pro-systemin. Pro-system is inactive; however, upon wounding it undergoes proteolytic cleavage to produce activated systemin.
Targeted protein degradation
The amount of protein present in a cell or tissue is determined by both its rate of synthesis and its rate of degradation. Therefore, protein degradation is an important mechanism by which the plant can regulate biological activity (i.e., a genetic function). For example, one way to shut down a metabolic pathway is by degrading one of the key enzymes controlling the rate of the entire pathway. Therefore, protein degradation is an essential component of gene regulation to meet cellular demands for growth, development, and defense.
Protein degradation must be carefully controlled to fine tune gene expression to allow plants to adapt to new environmental conditions. Often, cells will adopt several complex mechanisms for proteolytic degradation of proteins. Enzymes that cleave or degrade proteins are referred to as proteases. For example, plant vacuoles are rich in proteases that play a similar function in protein degradation as that of lysosomes in animal cells. Protease activity must be tightly regulated to prevent accidental degradation of essential proteins. Sequestering proteases in particular organelles like the vacuole separates them from other organelles and is one of to control their activity.
An important mechanism by which specific proteins are targeted for degradation is through ubiquitin-mediated proteasomal degradation. The proteasome is a large complex of multiple protein subunits that have a protease activity to degrade proteins. Proteins get marked for proteasomal degradation with a small protein called ubiquitin. Ubiquitin is covalently attached to specific proteins in response to environmental or developmental signals. This allows plants to quickly adapt to changing conditions by eliminating proteins whose functions are not advantageous under the new conditions. For example, the photoreceptor phytochrome mentioned above becomes targeted for degradation when light is no longer available. This allows plants to change their physiological functions going from daylight to night conditions. Protein degradation by the proteasome system is also an important regulatory mechanism for plant hormone signaling, for example the signaling of the defense hormone jasmonic acid, and growth hormone gibberellic acid.
Proteins have lifetimes that range from a few minutes to weeks or more. Cells continuously make proteins from and break them down to amino acids. One of the functions of protein degradation is to eliminate aberrant or damaged proteins which could harm the cell. The second function is to facilitate the recycling of amino acids. For example, most of the amino acids required for growth of the seedling are derived from the degradation of seed storage proteins. Conversely, in annual crop plants, many of the amino acids in seed storage proteins are derived from proteins degraded in leaves and other plant parts during senescence.
Lesson Summary
The expression of genes in specific plant cells, tissues, and organs and the timing of this expression require a precise level of regulation. A single promoter may not be sufficient to regulate the expression of such gene(s) in space and time. Therefore, coding regions with the same function may have different promoters, and such genes are referred to as differentially regulated. Most regulatory sequences governing gene expression are located on the 5’ border of the coding region. Transcription is often initiated between 20 and 60 nucleotides upstream of the ATG start site. Enhancers are usually position and orientation independent. Although they are normally located upstream of the promoter, they can also be located on the 3’ region of the gene or even with the coding region. Enhancers can increase the transcription when added to genes that they are not associated with. RNA polymerase binds the promoter at the TATA box and in cooperation with other proteins drives gene transcription. The proteins that interact with RNA polymerase bind to regulatory sequences upstream and downstream of the transcription site.
Transcription factors can play a regulatory role by determining where individual genes are expressed. Transcriptional regulation often involves modification of chromatin by changes in acetylation and methylation of histone. The nucleotide bases of DNA can be modified by the attachment of methyl groups at various locations. Methylation status is correlated with gene expression. Alternative splicing describes an alternative mechanism of pre-mRNA processing to generate mRNAs that have different combinations of exons. The control of mRNA degradation rate, or turnover, is an important regulatory mechanism in gene expression. RNA interference (RNAi) is a post-transcriptional process involving the degradation of mRNA initiated by the formation of double-stranded RNA (dsRNA) of the target mRNA. Translation of mRNAs can play an important role in determining their overall stability. Mutations that add premature stop codons often lead to rapid degradation of the mRNA. Protein degradation is an essential component of gene regulation to meet cellular demands for growth, development, and defense. The plant can alter the activity of a metabolic pathway, by degrading one of the key enzymes controlling the rate of the entire pathway.
Exercises
1a. Which of the following could alter gene regulation
1. Deleting a promoter
2. Altering fertilizer application rate
3. Raising the temperature of the greenhouse
4. Herbicide application
5. Reduce irrigation frequency
1b. The detection of a gene product, for example, RNA or protein at any one moment is a reflection of the “steady state” of the product. Describe the term “steady state” in this context.
2. You are studying expression of a gene responsible for resistance to a pathogen. You cloned the gene and made antibody to detect the protein it encodes by a procedure called Western blot analysis, and the mRNA by a procedure called reverse transcription PCR. Explain the type of regulation from the scenarios in the table.
Scenarios
Not treated with pathogen
Treated with pathogen
mRNA
Protein
mRNA
Protein
1
Absent
Absent
Present
Present
2
Present
Absent
Present
Present
3
Present
Present
Absent
Absent
4
Present
Present
Present
Absent
5
Present
Present
Present
Present
3. You are studying the expression of a gene controlling height in your crop species. You have cloned the gene and are interested in determining its expression in different parts of the plant. You use the RT-PCR procedure as in the previous problem. After the PCR part, you load products on a gel and observe the following pattern. Explain your results in the context of gene regulation. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/24%3A_Genome_Evolution/24.04%3A_Gene_Function_and_Expression_Patterns.txt |
Recall that every cell in a plant contains the same genetic information. The genetic information of a cell constitutes its genome. Therefore, a genome is made up of genes and their regulatory elements. The genome size varies in different species of animals and plants. For example, the human genome is 3.2 Gb while that of hexaploid wheat is 16 Gb. Certainly, a human is very different from a wheat plant. Despite having a smaller genome, a human can think and move but a wheat plant cannot. What then brings about such stark differences? To answer this question we need to compare the genomes of these two organisms for features such as gene content, organization, and function. This type of research is referred to as comparative genomics. Using bioinformatics programs, genome sequences are aligned and the alignments are examined for their evolutionary relationship. Are they homologous, or do they share a common ancestor? Comparative analysis can also be done for genomes of different strains of a species or species that are distantly related. Differences of genomes can therefore be linked to functional consequences, or phenotypes.
Learning Objectives
• Understand the difference between genetic and physical maps
• Familiarize with comparative genomics tools
• Understand the challenges in comparative genomics
• Familiarize with the application of comparative mapping
Introduction to Structural Genomics
Overview
To conduct comparative genomics we need to know the structure of the genomes we wish to compare. We also need tools/approaches to perform such an analysis. The following sections describe mapping concepts and the fundamentals of comparative genomics.
Genetic Maps
The purpose of genetic maps (also called linkage maps) is to report the length of chromosome intervals, chromosomes, and whole genomes. Genetic maps are based on the rate of recombination. Thus, genetic distances reflect the number of crossover events “observed” for the region, chromosome, or genome of interest. Figure 2 is an example of a genetic map in tomato. Compare the linkage map of molecular markers with the classical genetic map. Molecular markers are super abundance and a single cross allows mapping thousands of markers. Classical maps based on morphological markers are less dense and require integration of maps developed from many crosses. Compare the molecular map with the cytological map on the right. The markers are highly dense in the heterochromatic regions containing the centromeres. This is because of the reduced or suppressed recombination rates in the heterochromatic regions.
Physical Maps
While a genetic map is based on the rates of crossing over and is arbitrary, physical maps provide physical locations of markers. Fluorescence in situ hybridization (FISH) mapping of genetic markers on the pachytene chromosomes can allow us to develop a physical map that corresponds to a genetic map (Fig. 2). Note that in Fig. 2, certain regions are expanded in the genetic map due to higher rates of recombination. The reverse is true for the heterochromatic regions including the centromeres due to reduced recombination rates. Thus, crossover events are not evenly distributed across the chromosomes. Crossover events tend to be suppressed in centromeres and repetitive DNA-rich heterochromatic regions, whereas they are enhanced generally in gene-rich, euchromatic regions. With the sequencing of the entire genomes of crop species, one can now have physical maps of individual chromosomes based on nucleotide sequence. Genome browsers (e.g., Phytozome for soybean) can allow us to navigate the physical maps for gene sequences or molecular markers to the nucleotide level.
Restriction Mapping
Restriction mapping can also allow us to generate a physical map of small DNA fragments cloned in a plasmid vector or larger fragments cloned in BAC (bacterial artificial chromosome) or YAC (yeast artificial chromosome) vectors. This requires determination of the positions of restriction sites on DNA. Consider a piece of linear DNA of 28 kb. The DNA was cut first by HindIII alone, then by PstI alone, and, finally, by both HindIII and PstI together. The following results were obtained:
Using these results, draw a map of the HindIII and PstI restriction site on this 28-kb piece of DNA, indicating the relative positions of the restriction sites and the distances between them.
Physical Maps and Genome Sequencing
With progress in sequencing technology, an increased number of plant genomes have been sequenced. As a result, physical maps have gained importance. The assembly of the whole-genome sequence relies on both genetic and physical maps for aligning sequenced fragments. Recall in Lesson 5 that BAC and YAC clones are used to prepare genomic libraries for sequencing. The cloned DNA fragments in a YAC or BAC are aligned to form continuous stretches of DNA for subsequent sequencing processes (Fig. 4).
Comparative Mapping
Description
Comparative mapping is a study how the genomes relate across species and genera and even families. The concept started with comparative mapping experiments using RFLP markers between two species that led to the discovery of conserved linear orders of marker loci across related species.
Colinearity and Synteny
The terms synteny and colinearity have been broadly used to describe the presence of conserved gene orders on chromosomes across species, genera or families. Colinearity describes the conservation of the gene order within a chromosomal segment between different species (Fig. 7). The term colinearity is used to explain conservation of loci at the chromosome level, and micro-colinearity at the locus level (Fig. 8). Synteny was originally used to describe the physical mapping without the linkage assumption. Now the term is used to define chromosomal segments or to gene loci in different organisms located on a chromosomal region originating from a common ancestor (Keller and Feuillet 2000). Genetic loci that arose from a common ancestor are defined as orthologous loci; whereas, paralogous loci are evolved through tandem duplication within a species and located side by side in a chromosomal segment. The examples of colinearity and micro-colinearity are shown in Figures 7 and 8, respectively.
Orthology Example
The eggplant chromosome E4 combines two segments (E4a and E4b) orthologous to tomato T4 and T10 respectively, indicating a translocation between the two genomes. The breakpoint is located between markers TG386 and T677 (highlighted in red), and the region is indicated by a black bar beside E4. Orthologous marker pairs are connected by lines. A dash line indicates a marker of low mapping confidence on either or both maps that is not used for deduction of inversions. Vertical arrows beside E4 depict inversions in E4 with respect to T10.
Micro-Colinearity Example
The genetic map of bread wheat (Triticum aestivum) is used to analyze micro-colinearity of the Q locus of T. monococcum, Brachypodium sylvaticum, and rice (Oryza sativa). Genes are shown as colored boxes along the physical maps of each species.
Orthology and Mapping
Comparative mapping is the alignment of chromosomes of related species based on genetic mapping of common DNA markers. Thus, comparative mapping involves the development of linkage maps (Fig. 1). The construction of comparative maps depends on orthology predictions to identify gene pairs of two species. Orthologous loci are loci in different species originating from the same ancestral locus. In contrast, paralagous loci are loci in different (or the same) species that arose due to a duplication of an ancestral locus.
Once the gene pairs have been established, blocks of conserved syteny are established using the positions of each gene in their respective map. The comparative studies in Solanaceae species revealed a modest and consistent rate of chromosomal changes across the family (0.03 ~ 0.12 rearrangements per chromosome per million years). Closely related species showed more conservation of gene orders than the distantly related species. For example, a high conservation of marker orders was observed between tomato and eggplant or tomato and potato than between tomato and pepper. Also, hot spots of chromosomal breakages were identified to suggest that breakpoints are not randomly distributed across the genome. In general, a higher frequency of inversions than translocations was observed among the Solaneaceous species.
Grass Genome Map
Early research to evaluate synteny in grass species suggested the grouping of grasses of the Poaceae families as a single genetic system (Bennetzen and Freeling, 1993). This early synteny work revealed that a large degree of colinearity exists among diverse grasses. For instance, a high conservation across grass species was observed in regions ranging from 5-10 cM. Also, most genes are homologous across species, i.e. all species have essentially the same genes. Additional fine structure mapping revealed insertions of repeated sequences among grass genomes. Overall, these efforts led to the development of the circular grass genome map.
Linear Comparative Map
The average conserved segments between Arabidopsis and B. nigra was estimated to be ~8 cMs (Fig. 11). This estimate correspondsto ~90 rearrangements since divergence of the two species; much higher than other species.
Soybean and Arabidopsis Linkage
The majority of the comparative mapping studies were based on conservation of nucleotide sequences among closely related species. In 2000, synteny between soybean and Arabidopsis chromosomes was observed when linear orders of predicted protein sequences of genes were compared between the two species (Figure 12). This study also showed that Arabidopsis contains large scale duplicated genomic regions (Grant et al. 2000).
Web-Based Mapping Tools
Web-based applications are available for mapping purposes. For example, the Comparative Map Viewer (CMap) available from GRAMENE (Fig. 13) allows comparisons of different maps.
Try This: NCBI MapViewer
1. In the “Introduction to Bioinformatics” module, you learned about bioinformatics web tools. Go to NCBI and access MapViewer within Genomes & Maps.
2. In “Introduction to Bioinformatics” module, you learned about bioinformatic webtools. Go to NCBI and access MapViewer within Genomes & Maps.
3. Search for plants, and select Phaseolus vulgaris (kidney bean).
How many chromosomes does kidney bean have?
4. Select chromosome 1, and answer the following:
• How many maps are available for chromosome 1?
• Are the maps physical or genetic? What is the estimated length for each map?
• List the types of markers used to develop each map?
• Try the zoom-in function in the left corner – what do you see?
Comparative Genomics
With the advent of nextgen sequencing, there has been a continuous supply of genome sequence data in the literature. Now the concept of comparing genome maps looking for linear order of genes or synteny has been changed to comparative genomics. It is now feasible to compare related or distant species or genera at the genome level with the aid of available genome sequences. Comparative genomics will have an impact on advancing our knowledge not only in the evolution of crop species, but also in answering biological questions. For example, traditional studies on domestication traits were focused on dozens of loci involved in a variety of functions. Many of the traits were not amenable to study using conventional mapping approaches. Through comparative genomics, it is now known that about 24% of loci in the maize genome were involved in either domestication or subsequent improvement. Through comparative genomics studies, it is now known that in both maize and sunflowers there some loci related to amino acid biosynthesis are enriched. Selection of genes for amino acid biosynthesis during domestication may suggest that protein metabolism has an important role in heterosis. In barley, allelic variation at a flowering time locus in European cultivars appears to have arisen by introgression from barley that was independently domesticated in Central Asia.
Gene Prediction
The availability of genome sequence information makes it possible to apply comparative genomics for identification of genes. Gene prediction by comparative analysis involves identification of local similarities by sequence alignment programs in pairs of closely or distantly related genomes. For example, the mouse genome helped increase the accuracy of predicting human genes (Parra et al. 2003).
Try This: Arabidopsis Analysis
1. Go to the Arabidopsis Information Resource and search for a gene called JAR1.
2. What is the function of JAR1 (AT2G46370)?
3. Go to NCBI and search for nucleotide sequence for JAR1 (NM_001202828.1).
4. Within NCBI, perform a BLAST search for sequences similar to JAR1 (remember to exclude Arabidopsis thaliana in your query). After obtaining sequences producing significant alignments evaluate the four top sequences (maximum identity of 85-99 %). Use your results to answer the following:
• Give the name of the organism from which the sequence was obtained
• Provide the title of the research and the name of the Journal that published the research
• List GenBank id or NCBI reference sequence number of each hit
Detecting Copy Number Variations
The traditional view of comparative genomics was the analysis of synteny (gene order) and sequence comparisons among related species. With the emergence of powerful computational approaches, the examination of the genomic distribution of large insertions and deletions (indels) and copy number variants (CNVs) are becoming the norm.
Copy number variations may result from deletions, causing some individuals to contain only a single copy of a DNA sequence, or may be due to duplications, having certain individuals with more than two copies.
Comparative Genomic Hybridization
Detecting DNA Copy Number Variations
Comparative genomic hybridization (CGH) is a method for genome-wide screening for DNA copy number variations. CGH uses two genomes, a test and a control, which are labeled differentially with fluorescence probes and allowed to competitively hybridize to metaphase chromosomes. The fluorescence signal intensity from test samples compared to controls is plotted across each chromosome, allowing detection of copy number variation. Array-based CGH does not use metaphase chromosomes. Instead, synthetic oligonucleotide probes, or fragments from genomic clones such as BAC or YAC clones are arrayed onto glass slides. The basic method for aCGH is shown in Fig. 18.
Gene Cloning
After predicting gene location, the next step is to predict the function of the gene. One of the approaches is to clone the gene using recombinant DNA approaches. Tests for gene function may involve in vitro biochemical analyses for the activity of an enzyme, or complementation of a mutant phenotype by the wild type allele. One can use information from comparative analysis of a species with a simple genome to clone genes from a species with a complex genome. For example, the isolation of the R3a blight resistance gene in potato utilized genomic information from tomato (Huang et al., 2005).
Analysis of Genome Evolution
Evolution of a species is a result of numerous processes including gene duplication and loss, whole genome duplication, variation in ploidy level, retrotransposon activity, and genome rearrangements. Genome evolution describes how the genome has been rearranged through time. Thus, to understand the evolution of a species we need to analyze genome evolution. Genome analysis involves construction of a map in one species and comparison of the map with maps from closely related species by the means of common markers (or common single gene traits).
An understanding of crop origins has long been held as central to the identification of useful genetic resources for crop improvement. The number of times that a species has been domesticated influences the genetic architecture of agronomic traits and the levels of genetic diversity in crop genomes. Domestication shapes the genetic variation that is available to modern breeders as it influences levels of nucleotide diversity and patterns of LD (linkage disequilibrium) genome-wide. The demographic history of domestication also informs our expectations of the genetic architecture of traits and thus our ability to identify causal genetic variants for crop improvement.
Genome Evolution: Details
There is evidence for both single domestications (such as maize and soybeans) and multiple domestications (such as avocados, common beans and barley); but for most crops it is not known whether single or multiple domestication events were involved. Following domestication, extensive admixture with wild relatives may occur; and this may be one explanation for the continued controversy regarding the origins of the domesticated indica and japonica rice.
Isolation of genes encoding domestication traits bears evolutionary importance. Until recently, traits that facilitated domestication, i.e. ‘domestication syndrome’ including decreased dispersal, reduced branching, loss of seed dormancy, reduced natural defenses and increased size of certain morphological features were investigated using mapping strategies. Thus, the study was limited to only a handful traits or loci. Whole-genome data of crops and their wild relatives will facilitate identification of complex demographic histories of many crops. Population genetic approaches, e.g. genome wide association studies (GWAS) will help identify loci that have no known phenotypes; e.g., 2-4% of loci in the maize were affected by artificial selection during domestication. Also, Nextgen sequencing will reveal genome-wide polymorphisms among the accessions leading to discovering demographic history and geographic origins of crop plants.
Domestication and Heterosis
Analysis of Genome Evolution
Comparative genetic mapping studies between species suggested some similarity in the genetic basis of domestication syndrome traits (orthology). Comparative genomics studies in both maize and sunflowers suggest selection on genes for amino acid biosynthesis (unknowingly) during domestication contributes to heterosis.
Challenges: Large Genomes
Most genome tools were not developed for plant genomics studies. First generation molecular markers were isozyme markers that were available in the late 1960s for mapping plant genomes. But such markers are limited in number, and DNA markers paved the way towards construction of high-density molecular maps in 1990s.
Despite the availability of DNA markers, large size of plant genomes remains the greatest challenge in plant comparative genomics.
Challenges: Transposable Content
Large genome sizes for plant species are a result of amplification of retrotransposable elements (Fig. 21). In addition, plants genomes contain multi-gene families and paralogous genes that are tandem-duplicated; for example, plant disease resistance genes.
Challenges: Map Assembly: Scenario 1
Duplicated and paralogous sequences, and transposable elements are difficult to assemble during the process of building a genome map (Fig. 22). In Fig. 22 colored shapes represent transposable elements or genes; genes X are a pair of paralogous genes. Short sequence reads are shown directly above where they would map to the reference.
Challenges: Map Assembly: Scenario 2
Duplicated and paralogous sequences, and transposable elements are difficult to assemble during the process of building a genome map (Fig. 23). In Fig. 23 colored shapes represent transposable elements or genes; genes X are a pair of paralogous genes. Short sequence reads are shown directly above where they would map to the reference.
Challenges: Map Assembly: Scenario 3
Duplicated and paralogous sequences, and transposable elements are difficult to assemble during the process of building a genome map (Fig. 24). In Fig. 24 colored shapes represent transposable elements or genes; genes X are a pair of paralogous genes. Short sequence reads are shown directly above where they would map to the reference.
Challenges: Map Assembly: Scenario 4
Duplicated and paralogous sequences, and transposable elements are difficult to assemble during the process of building a genome map (Fig. 25). In Fig. 25 colored shapes represent transposable elements or genes; genes X are a pair of paralogous genes. Short sequence reads are shown directly above where they would map to the reference.
Challenges: Map Assembly: Scenario 5
Duplicated and paralogous sequences, and transposable elements are difficult to assemble during the process of building a genome map (Fig. 26). In Fig. 26 colored shapes represent transposable elements or genes; genes X are a pair of paralogous genes. Short sequence reads are shown directly above where they would map to the reference.
Sequences
High proportion of repeated sequences also makes it difficult to conduct reference genome-based SNP identification and genome-wide association studies. Therefore, regardless of the emerging high throughput sequencing technologies, it remains challenging to achieve sufficient genome coverage for assembling short read sequences and paralogous sequences. Consequently, fewer crop species with large genomes have been sequenced so far. Improvement in sequence read length by nextgen approaches will reduce this problem allowing detection of local patterns of LD for identifying paralogous reads in complex crop genomes.
Summary
Comparative genomics is a field of research focusing on determining the evolutionary relationships of genomes and link differences to functional consequences, or phenotypes. With progress in sequencing technology, an increased number of plant genomes have been sequenced making it possible to construct comparative maps and predict gene pairs of two species. To understand how genomes evolve, a genome map is constructed in one species and compared with maps from closely related species by the means of common markers. The majority of the comparative mapping studies are based on conservation of nucleotide sequences among closely related species. Comparative genomics is also useful for the identification of genes. Following prediction of gene location by comparative analysis, target genes may be isolated and characterized to determine their function. However, one of the greatest challenges in plant comparative genomics is the large size of plant genomes. Consequently, fewer crop species with large genomes have currently been sequenced. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/24%3A_Genome_Evolution/24.05%3A_Applying_Comparative_Genomics.txt |
• 25.1: Deep Time
Evolutionary changes coincide with geologic changes on the earth. But consider that changes in geology (e.g., mountain formation or lowering of the sea level) cause changes in climate, and together these alter the habitats available for life. Two types of geologic change seem to have had especially dramatic effects on life: continental drift and the impact of asteroids
• 25.2: Origins of Life
To account for the origin of life on our earth requires solving several problems: How the organic molecules that define life, e.g. amino acids, nucleotides, were created. How these were assembled into macromolecules, e.g. proteins and nucleic acids, - a process requiring catalysts. How these were able to reproduce themselves. How these were assembled into a system delimited from its surroundings (i.e., a cell). A number of theories address each of these problems.
• 25.3: Evidence for Early Life
• 25.4: Earth's Changing System
Evolution by natural selection describes a mechanism for how species change over time. That species change had been suggested and debated well before Darwin began to explore this idea. The view that species were static and unchanging was grounded in the writings of Plato, yet there were also ancient Greeks who expressed evolutionary ideas.
• 25.5: Ever-Changing Life on Earth
Evolution by natural selection describes a mechanism for how species change over time. That species change had been suggested and debated well before Darwin began to explore this idea. The view that species were static and unchanging was grounded in the writings of Plato, yet there were also ancient Greeks who expressed evolutionary ideas.
25: The Origin and Diversity of Life
History of life as revealed by the fossil record
With help from molecular phylogenies:
Eras Periods Epochs Aquatic Life Terrestrial Life
With approximate starting dates in millions of years ago in parentheses. Geologic features in green
Cenozoic (66)
The "Age of
Mammals"
Quaternary (2.6) Holocene Humans in the new world
Pleistocene Periodic glaciation First humans
Continental drift continues
Neogene (23) Pliocene Atmospheric oxygen reaches today's level (21%) Hominids
Miocene Adaptive radiation of birds, continued radiation of mammals
Paleogene (66) Oligocene All modern groups present
Eocene
Paleocene
Mesozoic (251)
The "Age
of Reptiles"
Cretaceous (146) Still attached: N. America & N. Europe; Australia & Antarctica; Mass extinction of both aquatic and terrestrial life at the end
Modern bony fishes Extinction of dinosaurs and pterosaurs; first snakes
Extinction of ammonites, plesiosaurs, ichthyosaurs Rise of angiosperms
Africa & S. America begin to drift apart
Jurassic (200) Plesiosaurs, ichthyosaurs abundant; first diatoms Archaeopteryx; dinosaurs dominant but mammals (Eutheria) begin to diversify
Ammonites again abundant First lizards
Skates, rays, and bony fishes abundant Adaptive radiation of dinosaurs
Pangaea splits into Laurasia and Gondwana; atmospheric oxygen drops to ~13%
Triassic (251) Mass extinctions at the end. Mass extinctions at the end.
First mammals
Adaptive radiation of reptiles: thecodonts, therapsids, turtles, crocodiles, first dinosaurs
Ammonites abundant at first
Rise of bony fishes
Paleozoic (542) Permian (299) Periodic glaciation and arid climate; atmospheric oxygen reaches ~30%. Volcanic eruptions killed off 90% of marine species at end.
Extinction of trilobites Reptiles abundant. Cycads, conifers, ginkgos
Pennsylvanian (320) Warm, humid climate
Together
the Pennsylvanian
and Mississippian
make up the
"Carboniferous";
also called the
"Age of Amphibians"
Ammonites, bony fishes First reptiles
Coal swamps
Mississippian (359) Adaptive radiation of sharks Forests of lycopsids, sphenopsids, and seed ferns
Amphibians abundant
Adaptive radiation of the insects (Hexapoda)
Atmospheric oxygen begins to rise as organic matter is buried, not respired
Devonian (416)
The "Age of Fishes"
Extensive inland seas Cartilaginous and bony fishes abundant. Ammonites, nautiloids, ostracoderms, eurypterids Ferns, lycopsids, and sphenopsids
First gymnosperms
First amphibians
Silurian (443) Mild climate; inland seas First bony fishes First myriapods and chelicerates
Ordovician (485) Mild climate, inland seas Trilobites abundant Fungi present
First plants (liverworts?) First insects
Cambrian (541) First vertebrates (jawless fishes). Eurypterids, crustaceans
mollusks, echinoderms, sponges, cnidarians, annelids, and tunicates present. Trilobites dominant.
No fossils of terrestrial eukaryotes, but phylogenetic trees suggest that lichens, mosses, perhaps even vascular plants were present.
Periodic glaciation
Proterozoic (2500) Ediacaran
(635)
Fossil evidence of multicellular algae, fungi, and bilaterian invertebrates
Evidence of eukaryotes
~1.8 x109 years ago
Archaean (3600) Evidence of archaea and bacteria
~3.5 x109 years ago
The Geologic and Evolutionary Record
A remarkable feature of the table above is how often evolutionary changes coincided with geologic changes on the earth. But consider that changes in geology (e.g., mountain formation or lowering of the sea level) cause changes in climate, and together these alter the habitats available for life. Two types of geologic change seem to have had especially dramatic effects on life: continental drift and the impact of asteroids
Continental Drift
A body of evidence, both geological and biological, supports the conclusion that 200 million years ago, at the start of the Mesozoic era, all the continents were attached to one another in a single land mass, which has been named Pangaea. This drawing of Pangaea (adapted from data of R. S. Dietz and J. C. Holden) is based on a computer-generated fit of the continents as they would look if the sea level were lowered by 6000 feet (~1800 meters). During the Triassic, Pangaea began to break up, first into two major land masses:
• Laurasia in the Northern Hemisphere
• Gondwana in the Southern Hemisphere.
The present continents separated at intervals throughout the remainder of the Mesozoic and through the Cenozoic, eventually reaching the positions they have today. Let us examine some of the evidence.
Shape of the Continents
The east coast of South America and the west coast of Africa and are strikingly complementary. This is even more dramatic when one tries to fit the continents together using the boundaries of the continental slopes, e.g., 6000 feet (~1800 meters) down, rather than the shorelines.
Geology
• In both mineral content and age, the rocks in a region on the east coast of Brazil match precisely those found in Ghana on the west coast of Africa.
• The low mountain ranges and rock types in New England and eastern Canada appear to be continued in parts of Great Britain, France, and Scandinavia.
• India and the southern part of Africa both show evidence of periodic glaciation during Paleozoic times (even though both are now close to the equator). The pattern of glacial deposits in the two regions not only match each other but also glacial deposits found in South America, Australia, and Antarctica.
Fossils
• Fossil reptiles found in South Africa are also found in Brazil and Argentina.
• Fossil amphibians and reptiles found in Antarctica are also found in South Africa, India, and China.
• Most of the marsupials alive today are confined to South America and Australia. But if these two continents were connected by Antarctica in the Mesozoic, one might expect to find fossil marsupials there. In March 1982, this prediction was fulfilled with the discovery in Antarctica of the remains of Polydolops, a 9-ft (2.7 m) marsupial.
The Impact Hypothesis
The Cretaceous period, the last period of the Mesozoic, marked the end of the Age of Reptiles. It was followed by the Cenozoic era, the Age of Mammals. Although extinctions have occurred throughout the history of life, an extraordinary number of them occurred in a relatively brief period at the end of the Cretaceous. Why?
The Alvarez Theory
Louis Alvarez, his son Walter, and their colleagues proposed that a giant asteroid or comet striking the earth some 66 million years ago caused the massive die-off at the end of the Cretaceous. Presumably, the impact generated so much dust and gases that skies were darkened all over the earth, photosynthesis declined, and worldwide temperatures dropped. The outcome was that as many as 75% of all species — including all dinosaurs — became extinct.
The key piece of evidence for the Alvarez hypothesis was the finding of thin deposits of clay containing the element iridium at the interface between the rocks of the Cretaceous and those of the Paleogene period (called the K-Pg boundary after the German word for Cretaceous). Iridium is a rare element on earth (although often discharged from volcanoes), but occurs in certain meteorites at concentrations thousands of times greater than in the earth's crust.
After languishing for many years, the Alvarez theory gained strong support from the discovery in the 1990s of the remains of a huge (180 km in diameter) crater in the Yucatan Peninsula that dated to 65 million years ago.
The abundance of sulfate-containing rock in the region suggests that the impact generated enormous amounts of sulfur dioxide (SO2), which later returned to earth as a bath of acid rain. A smaller crater in Iowa, formed at the same time, many have contributed to the devastation. Perhaps during this period the earth passed through a swarm of asteroids or a comet and the repeated impacts made the earth uninhabitable for so many creatures of the Mesozoic.
Other Impacts
A mass extinction of non-dinosaur reptiles occurred earlier, at the end of the Triassic. It was followed by a great expansion in the diversity of dinosaurs. The recent discovery of a layer enriched in iridium in rocks formed at the boundary between the Triassic and Jurassic suggests that impact from an asteroid or comet may have been responsible then just as it was at the K-Pg boundary.
The largest extinction of all time occurred still earlier at the end of the Permian period. There is evidence off the coast of Australia that a huge impact there may have contributed to the extinctions at the Permian-Triassic (P-T) boundary. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/25%3A_The_Origin_and_Diversity_of_Life/25.01%3A_Deep_Time.txt |
To account for the origin of life on our earth requires solving several problems:
• How the organic molecules that define life, e.g. amino acids, nucleotides, were created.
• How these were assembled into macromolecules, e.g. proteins and nucleic acids, - a process requiring catalysts.
• How these were able to reproduce themselves.
• How these were assembled into a system delimited from its surroundings (i.e., a cell).
A number of theories address each of these problems. As for the first problem, four scenarios have been proposed. Organic molecules:
1. were synthesized from inorganic compounds in the atmosphere,
2. rained down on earth from outer space,
3. were synthesized at hydrothermal vents on the ocean floor,
4. were synthesized when comets or asteroids struck the early earth.
Scenario 1: Miller's Experiment
Stanley Miller, a graduate student in biochemistry, built the apparatus shown in Figure \(1\). He filled it with water (H2O), methane (CH4), ammonia (NH3) and hydrogen (H2), but no oxygen. He hypothesized that this mixture resembled the atmosphere of the early earth. The mixture was kept circulating by continuously boiling and then condensing the water. The gases passed through a chamber containing two electrodes with a spark passing between them.
At the end of a week, Miller used paper chromatography to show that the flask now contained several amino acids as well as some other organic molecules. However, it is now thought that the atmosphere of the early earth was not rich in methane and ammonia - essential ingredients in Miller's experiments. In the years since Miller's work, many variants of his procedure have been tried. Virtually all the small molecules that are associated with life have been formed:
• 17 of the 20 amino acids used in protein synthesis, and all the purines and pyrimidines used in nucleic acid synthesis.
• But abiotic synthesis of ribose - and thus of nucleotides - has been much more difficult. However, success in synthesizing pyrimidine ribonucleotides under conditions that might have existed in the early earth was reported in the 14 May 2009 issue of Nature.
• And in 2015, chemists in Cambridge England led by John Sutherland reported that they had been able to synthesize precursors of 12 of the 20 amino acids and two (of the four) ribonucleotides used by life as well as glycerol-1-phosphate, a precursor of lipids. They created all of these molecules using only hydrogen cyanide (HCN) and hydrogen sulfide (H2S) irradiated with ultraviolet light in the presence of mineral catalysts.
Scenario 2: Molecules from Outer Space
Astronomers, using infrared spectroscopy, have identified a variety of organic molecules in interstellar space, including methane (CH4), methanol (CH3OH), formaldehyde (HCHO), cyanoacetylene (HC3N) (which in spark-discharge experiments is a precursor to the pyrimidine cytosine), polycyclic aromatic hydrocarbonsas well as such inorganic building blocks as carbon dioxide (CO2), carbon monoxide (CO), ammonia (NH3), hydrogen sulfide (H2S), and hydrogen cyanide (HCN).
There have been several reports of producing amino acids and other organic molecules in laboratories by taking a mixture of molecules known to be present in interstellar space such as ammonia (NH3), carbon monoxide (CO), methanol (CH3OH) and water (H2O), hydrogen cyanide (HCN) and exposing it to a temperature close to that of space (near absolute zero) and intense ultraviolet (UV) radiation. Whether or not the molecules that formed terrestrial life arrived here from space, there is little doubt that organic matter continuously rains down on the earth (estimated at 30 tons per day).
Alternatively, organic molecules can be transport to Earth via meteorites as demonstrated with the Murchison Meteorite that that fell near Murchison, Australia on 28 September 1969. This meteorite turned out to contain a variety of organic molecules including: purines and pyrimidines, polyols - compounds with hydroxyl groups on a backbone of 3 to 6 carbons such as glycerol and glyceric acid (sugars are polyols) and the amino acids listed in Table \(1\). The amino acids and their relative proportions were quite similar to the products formed in Miller's experiments.
Murchison meteorite at the The National Museum of Natural History (Washington). (CC SA-BY 3.0; :Basilicofresco).
Table \(1\): Representative amino acids found in the Murchison meteorite. Six of the amino acids (blue) are found in all living things, but the others (yellow) are not normally found in living matter here on earth. The same amino acids are produced in discharge experiments like Miller's.
Glycine Glutamic acid
Alanine Isovaline
Valine Norvaline
Proline N-methylalanine
Aspartic acid N-ethylglycine
Contamination?
The question is if these molecules identified in the Murchison meteorite were simply terrestrial contaminants that got into the meteorite after it fell to earth? Probably not:
• Some of the samples were collected on the same day it fell and subsequently handled with great care to avoid contamination.
• The polyols contained the isotopes carbon-13 and hydrogen-2 (deuterium) in greater amounts than found here on earth.
• The samples lacked certain amino acids that are found in all earthly proteins.
• Only L amino acids occur in earthly proteins, but the amino acids in the meteorite contain both D and L forms (although L forms were slightly more prevalent).
Scenario 3: Deep-Sea Hydrothermal Vents
Some deep-sea hydrothermal vents discharge copious amounts of hydrogen, hydrogen sulfide, and carbon dioxide at temperatures around 100°C. (These are not "black smokers".) These gases bubble up through chambers rich in iron sulfides (FeS, FeS2). These can catalyze the formation of simple organic molecules like acetate. (And life today depends on enzymes that have Fe and S atoms in their active sites.)
Scenario 4: Laboratory Synthesis of Nucleobases Under Conditions Mimicking the Impact of Asteroids or Comets on the Early Earth
Researchers in the Czech Republic reported in 2014 that they had succeeded in the abiotic synthesis of adenine (A), guanine (G), cytosine (C), and uracil (U) — the four bases found in RNA (an RNA beginning?) and three of the four found in DNA. They achieved this by bombarding a mixture of formamide and clay with powerful laser pulses that mimicked the temperature and pressure expected when a large meteorite strikes the earth. Formamide is a simple substance, CH3NO, thought to have been abundant on the early earth and containing the four elements fundamental to all life.
Assembling Polymers
Another problem is how polymers - the basis of life itself - could be assembled.
• In solution, hydrolysis of a growing polymer would soon limit the size it could reach.
• Abiotic synthesis produces a mixture of L and D enantiomers. Each inhibits the polymerization of the other. (So, for example, the presence of D amino acids inhibits the polymerization of L amino acids (the ones that make up proteins here on earth).
This has led to a theory that early polymers were assembled on solid, mineral surfaces that protected them from degradation, and in the laboratory polypeptides and polynucleotides (RNA molecules) containing about ~50 units have been synthesized on mineral (e.g., clay) surfaces.
An RNA Beginning?
All metabolism depends on enzymes and, until recently, every enzyme has turned out to be a protein. But proteins are synthesized from information encoded in DNA and translated into mRNA. So here is a chicken-and-egg dilemma. The synthesis of DNA and RNA requires proteins. So proteins cannot be made without nucleic acids and nucleic acids cannot be made without proteins. The discovery that certain RNA molecules have enzymatic activity provides a possible solution. These RNA molecules — called ribozymes — incorporate both the features required of life: storage of information and the ability to act as catalysts.
While no ribozyme in nature has yet been found that can replicate itself, ribozymes have been synthesized in the laboratory that can catalyze the assembly of short oligonucleotides into exact complements of themselves. The ribozyme serves as both the template on which short lengths of RNA ("oligonucleotides" are assembled following the rules of base pairing and the catalyst for covalently linking these oligonucleotides.
In principal, the minimal functions of life might have begun with RNA and only later did proteins take over the catalytic machinery of metabolism and DNA take over as the repository of the genetic code. Several other bits of evidence support this notion of an original "RNA world":
• Many of the cofactors that play so many roles in life are based on ribose; for example:
• ATP
• NAD
• FAD
• coenzyme A
• cyclic AMP
• GTP
• In the cell, all deoxyribonucleotides are synthesized from ribonucleotide precursors.
• Many bacteria control the transcription and/or translation of certain genes with RNA molecules, not protein molecules.
Reproduction?
Perhaps the earliest form of reproduction was a simple fission of the growing aggregate into two parts - each with identical metabolic and genetic systems intact.
The First Cell?
To function, the machinery of life must be separated from its surroundings - some form of extracellular fluid (ECF). This function is provided by the plasma membrane. Today's plasma membranes are made of a double layer of phospholipids. They are only permeable to small, uncharged molecules like H2O, CO2, and O2. Specialized transmembrane transporters are needed for ions, hydrophilic, and charged organic molecules (e.g., amino acids and nucleotides) to pass into and out of the cell.
However, the same Szostak lab that produced the finding described above reported in the 3 July 2008 issue of Nature that fatty acids, fatty alcohols, and monoglycerides - all molecules that can be synthesized under prebiotic conditions - can also form lipid bilayers and these can spontaneously assemble into enclosed vesicles.
Unlike phospholipid vesicles, these
• admit from the external medium charged molecules like nucleotides
• admit from the external medium hydrophilic molecules like ribose
• grow by self-assembly
• are impermeable to, and thus retain, polymers like oligonucleotides.
These workers loaded their synthetic vesicles with a short single strand of deoxycytidine (dC) structured to provide a template for its replication. When the vesicles were placed in a medium containing (chemically modified) dG, these nucleotides entered the vesicles and assembled into a strand of Gs complementary to the template strand of Cs. Here, then, is a simple system that is a plausible model for the creation of the first cells from the primeval "soup" of organic molecules.
From Unicellular to Multicellular Organisms
This transition is probably the easiest to understand.
Several colonial flagellated green algae provide a clue. These species are called colonial because they are made up simply of clusters of independent cells. If a single cell of Gonium, Pandorina, or Eudorina is isolated from the rest of the colony, it will swim away looking quite like a Chlamydomonas cell. Then, as it undergoes mitosis, it will form a new colony with the characteristic number of cells in that colony.
(The figures are not drawn to scale. Their sizes range from Chlamydomonas which is about 10 µm in diameter - little larger than a human red blood cell - to Volvox whose sphere is some 350 µm in diameter - visible to the naked eye.)
The situation in Pleodorina and Volvox is different. In these organisms, some of the cells of the colony (most in Volvox) are not able to live independently. If a nonreproductive cell is isolated from a Volvox colony, it will fail to reproduce itself by mitosis and eventually will die. What has happened? In some way, as yet unclear, Volvox has crossed the line separating simple colonial organisms from truly multicellular ones. Unlike Gonium, Volvox cannot be considered simply a colony of individual cells. It is a single organism whose cells have lost their ability to live independently. If a sufficient number of them become damaged, the entire sphere of cells will die.
What has Volvox gained? In giving up their independence, the cells of Volvox have become specialists. No longer does every cell carry out all of life's functions (as in colonial forms); instead certain cells specialize to carry out certain functions while leaving other functions to other specialists. In Volvox this process goes no further than having certain cells specialize for reproduction while others, unable to reproduce themselves, fulfill the needs for photosynthesis and locomotion.
In more complex multicellular organisms, the degree of specialization is carried much further. Each cell has one or two precise functions to carry out. It depends on other cells to carry out all the other functions needed to maintain the life of the organism and thus its own.
The specialization and division of labor among cells is the outcome of their history of differentiation. One of the great problems in biology is how differentiation arises among cells, all of which having arisen by mitosis, share the same genes.
The genomes of both Chlamydomonas and Volvox have been sequenced. Although one is unicellular, the other multicellular, they have not only about the same number of protein-encoding genes (14,516 in Chlamydomonas, 14,520 in Volvox) but most of these are homologous. Volvox has only 58 genes that have no relatives in Chlamydomonas and even fewer unique mRNAs.
At one time, many of us would have expected that a multicellular organism like Volvox with its differentiated cells and complex life cycle would have had many more genes than a single-celled organism like Chlamydomonas. But that turns out not to be the case.
How to explain this apparent paradox? My guess is that just as we have seen in the evolution of animals, we are seeing here that the evolution of organismic complexity is not so much a matter of the evolution of new genes but rather the evolution of changes in the control elements (promoters and enhancers) that dictate how and where the basic tool kit of eukaryotic genes will be expressed .
The evidence is compelling that all these organisms are close relatives; that is, belong to the same clade. They illustrate how colonial forms could arise from unicellular ones and multicellular forms from colonial ones.
The Last Universal Common Ancestor (LUCA)?
The 3 kingdoms of contemporary life — archaea, bacteria, and eukaryotes — all share many similarities of their metabolic and genetic systems . Presumably these were present in an organism that was ancestral to these groups: the "LUCA". Although there are not enough data at present to describe LUCA, comparative genomics and proteomics reveal a closer relationship between archaea and eukaryotes than either shares with the bacteria. Except, of course, for the mitochondria and chloroplasts that eukaryotes gained from bacterial endosymbionts. Whether the endosymbionts were acquired before or after a lineage of archaea had acquired a nucleus - and thus started the lineage of eukaryotes - is still uncertain.
Creating Life?
When I headed off to college (in 1949), I wrote an essay speculating on the possibility that some day we would be able to create a living organism from nonliving ingredients. By the time I finished my formal studies in biology — having learned of the incredible complexity of even the simplest organism — I concluded that such a feat could never be accomplished.
Now I'm not so sure.
Several recent advances suggest that we may be getting close to creating life. (But note that these examples represent laboratory manipulations that do not necessarily reflect what may have happened when life first appeared.)
Examples:
• The ability to created membrane-enclosed vesicles that can take in small molecules and assemble them into polymers which remain within the "cell".
• The ability to assemble functional ribosomes — the structures that convert the information encoded in the genome into the proteins that run life — from their components.
• In 2008, scientists at the J. Craig Venter Institute (JCVI) reported (in Science 29 February 2008) that they had succeeded in synthesizing a complete bacterial chromosome — containing 582,970 base pairs — starting from single deoxynucleotides. The entire sequence of the genome of Mycoplasma genitalium was already known. Using this information, they synthesized some 10,000 short oligonucleotides (each about 50 bp long) representing the entire genitalium genome and then - step by step - assembled these into longer and longer fragments until finally they had made the entire circular DNA molecule that is the genome.
Could this be placed in the cytoplasm of a living cell and run it?
The same team showed in the previous year (see Science 3 August 2007) that they could insert an entire chromosome from one species of mycoplasma into the cytoplasm of a related species and, in due course, the recipient lost its own chromosome (perhaps destroyed by restriction enzymes encoded by the donor chromosome) and began expressing the phenotype of the donor. In short, they had changed one species into another. But the donor chromosome was made by the donor bacterium, not synthesized in the laboratory. However, there should be no serious obstacle to achieving the same genome transplantation with a chemically-synthesized chromosome.
They've done it! The same team reported on 20 May 2010 in the online Science Express that they had successfully transplanted a completely synthetic genome — based on that of Mycoplasma mycoides — into the related species Mycoplasma capricolum. The recipient strain grew well and soon acquired the phenotype of the M. mycoides donor.
• In the 4 April 2014 issue of Science (Annaluru, N. et al.), a large group of researchers - including many undergraduates at Johns Hopkins University - reported that they had successfully replaced the natural chromosome 3 in Saccharomyces cerevisiae (which has 16 chromosomes) with a totally-synthetic chromosome.
Their procedure:
1. Chemically synthesize 69- to 79-nt oligonucleotides representing all the stretches of the known chromosome 9 sequence (which contains 316,617 base pairs) except for certain sequences such as transposons, many introns, and transfer RNA genes. In addition new, non-native, sequences such as loxP sites were included to aid future manipulations of the genome.
2. Stitch these together into blocks of ~750 base pairs. This step was done in vitro by undergraduates enrolled in the "Build A Genome" class at Johns Hopkins.
3. Introduce these into yeast cells which ligated them into stretches of DNA containing 2–4 thousand base pairs.
4. Introduce these stepwise into yeast cells so that they replace the equivalent portions of the native chromosome.
5. The result: a strain of yeast that grows just as well with its new artificial chromosome (now containing only 272,871 base pairs) as it did before. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/25%3A_The_Origin_and_Diversity_of_Life/25.02%3A_Origins_of_Life.txt |
Prokaryotic organisms were the first living things on earth and still inhabit every environment, no matter how extreme.
Learning Objectives
• Discuss the origins of prokaryotic organisms in terms of the geologic timeline
Key Points
• All living things can be classified into three main groups called domains; these include the Archaea, the Bacteria, and the Eukarya.
• Prokaryotes arose during the Precambrian Period 3.5 to 3.8 billion years ago.
• Prokaryotic organisms can live in every type of environment on Earth, from very hot, to very cold, to super haline, to very acidic.
• The domains Bacteria and Archaea are the ones containing prokaryotic organisms.
• The Archaea are prokaryotes that inhabit extreme environments, such as inside of volcanoes, while Bacteria are more common organisms, such as E. coli.
Key Terms
• prokaryote: an organism whose cell (or cells) are characterized by the absence of a nucleus or any other membrane-bound organelles
• domain: in the three-domain system, the highest rank in the classification of organisms, above kingdom: Bacteria, Archaea, and Eukarya
• archaea: a taxonomic domain of single-celled organisms lacking nuclei, formerly called archaebacteria, but now known to differ fundamentally from bacteria
Evolution of Prokaryotes
In the recent past, scientists grouped living things into five kingdoms (animals, plants, fungi, protists, and prokaryotes) based on several criteria such as: the absence or presence of a nucleus and other membrane-bound organelles, the absence or presence of cell walls, multicellularity, etc. In the late 20th century, the pioneering work of Carl Woese and others compared sequences of small-subunit ribosomal RNA (SSU rRNA) which resulted in a more fundamental way to group organisms on earth. Based on differences in the structure of cell membranes and in rRNA, Woese and his colleagues proposed that all life on earth evolved along three lineages, called domains. The domain Bacteria comprises all organisms in the kingdom Bacteria, the domain Archaea comprises the rest of the prokaryotes, and the domain Eukarya comprises all eukaryotes, including organisms in the kingdoms Animalia, Plantae, Fungi, and Protista.
The current model of the evolution of the first, living organisms is that these were some form of prokaryotes, which may have evolved out of protobionts. In general, the eukaryotes are thought to have evolved later in the history of life. However, some authors have questioned this conclusion, arguing that the current set of prokaryotic species may have evolved from more complex eukaryotic ancestors through a process of simplification. Others have argued that the three domains of life arose simultaneously, from a set of varied cells that formed a single gene pool.
Two of the three domains, Bacteria and Archaea, are prokaryotic. Based on fossil evidence, prokaryotes were the first inhabitants on Earth, appearing 3.5 to 3.8 billion years ago during the Precambrian Period. These organisms are abundant and ubiquitous; that is, they are present everywhere. In addition to inhabiting moderate environments, they are found in extreme conditions: from boiling springs to permanently frozen environments in Antarctica; from salty environments like the Dead Sea to environments under tremendous pressure, such as the depths of the ocean; and from areas without oxygen, such as a waste management plant, to radioactively-contaminated regions, such as Chernobyl. Prokaryotes reside in the human digestive system and on the skin, are responsible for certain illnesses, and serve an important role in the preparation of many foods. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/25%3A_The_Origin_and_Diversity_of_Life/25.03%3A_Evidence_for_Early_Life/25.3A%3A_Classification_of_Prokaryotes.txt |
Archaea are believed to have evolved from gram-positive bacteria and can occupy more extreme environments.
Learning Objectives
• Distinguish bacteria from archaea in terms of their origins
Key Points
• The first prokaryotes were adapted to the extreme conditions of early earth.
• It has been proposed that archaea evolved from gram-positive bacteria as a response to antibiotic selection pressures.
• Microbial mats and stromatolites represent some of the earliest prokaryotic formations that have been found.
Key Terms
• stromatolite: a laminated, columnar, rock-like structure built over geologic time by microorganisms such as cyanobacteria
• gram-positive: that is stained violet by Gram’s method due to the presence of a peptidoglycan cell wall
• sacculus: a small sac
• indel: either an insertion or deletion mutation in the genetic code
Prokaryotes, the First Inhabitants of Earth
When and where did life begin? What were the conditions on earth when life began? Prokaryotes were the first forms of life on earth, existing for billions of years before plants and animals appeared. The earth and its moon are thought to be about 4.54 billion years old. This estimate is based on evidence from radiometric dating of meteorite material together with other substrate material from earth and the moon. Early earth had a very different atmosphere (contained less molecular oxygen) than it does today and was subjected to strong radiation; thus, the first organisms would have flourished where they were more protected, such as in ocean depths or beneath the surface of the earth. Also at this time, strong volcanic activity was common on Earth. It is probable that these first organisms, the first prokaryotes, were adapted to very high temperatures. Early earth was prone to geological upheaval and volcanic eruption, and was subject to bombardment by mutagenic radiation from the sun. The first organisms were prokaryotes that could withstand these harsh conditions.
Although probable prokaryotic cell fossils date to almost 3.5 billion years ago, most prokaryotes do not have distinctive morphologies; fossil shapes cannot be used to identify them as Archaea. Instead, chemical fossils of unique lipids are more informative because such compounds do not occur in other organisms. Some publications suggest that archaean or eukaryotic lipid remains are present in shales dating from 2.7 billion years ago. Such lipids have also been detected in Precambrian formations. The oldest such traces come from the Isua district of west Greenland, which include earth’s oldest sediments, formed 3.8 billion years ago. The archaeal lineage may be the most ancient that exists on earth.
Within prokaryotes, archaeal cell structure is most similar to that of gram-positive bacteria, largely because both have a single lipid bilayer and usually contain a thick sacculus of varying chemical composition. In phylogenetic trees based upon different gene / protein sequences of prokaryotic homologs, the archaeal homologs are more closely related to those of Gram-positive bacteria. Archaea and gram-positive bacteria also share conserved indels in a number of important proteins, such as Hsp70 and glutamine synthetase.
It has been proposed that the archaea evolved from gram-positive bacteria in response to antibiotic selection pressure. This is suggested by the observation that archaea are resistant to a wide variety of antibiotics that are primarily produced by gram-positive bacteria and that these antibiotics primarily act on the genes that distinguish archaea from bacteria. The evolution of Archaea in response to antibiotic selection, or any other competitive selective pressure, could also explain their adaptation to extreme environments (such as high temperature or acidity) as the result of a search for unoccupied niches to escape from antibiotic-producing organisms.
Microbial Mats
Microbial mats or large biofilms may represent the earliest forms of life on earth; there is fossil evidence of their presence starting about 3.5 billion years ago. A microbial mat is a multi-layered sheet of prokaryotes that includes mostly bacteria, but also archaea. Microbial mats are a few centimeters thick, typically growing where different types of materials interface, mostly on moist surfaces. The various types of prokaryotes that comprise the mats use different metabolic pathways, which is the reason for their various colors. Prokaryotes in a microbial mat are held together by a glue-like sticky substance that they secrete called extracellular matrix.
The first microbial mats likely obtained their energy from chemicals found near hydrothermal vents. A hydrothermal vent is a breakage or fissure in the earth’s surface that releases geothermally-heated water. With the evolution of photosynthesis about 3 billion years ago, some prokaryotes in microbial mats came to use a more widely-available energy source, sunlight, whereas others were still dependent on chemicals from hydrothermal vents for energy and food.
Stromatolites
Fossilized microbial mats represent the earliest record of life on earth. A stromatolite is a sedimentary structure formed when minerals are precipitated out of water by prokaryotes in a microbial mat. Stromatolites form layered rocks made of carbonate or silicate. Although most stromatolites are artifacts from the past, there are places on earth where stromatolites are still forming. For example, growing stromatolites have been found in the Anza-Borrego Desert State Park in San Diego County, California. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/25%3A_The_Origin_and_Diversity_of_Life/25.03%3A_Evidence_for_Early_Life/25.3B%3A_The_Origins_of_Archaea_and_Bacteria.txt |
Prokaryotes are well adapted to living in all types of conditions, including extreme ones, and prefer to live in colonies called biofilms.
Learning Objectives
• Discuss the distinguishing features of extremophiles and the environments that produce biofilms
Key Points
• Prokaryotes live in all environments, no matter how extreme they may be.
• Bacteria that prefer very salty environments are called halophiles, while those that live in very acidic environments are called acidophiles.
• An example of a habitat that halophiles can colonize is the Dead Sea, a body of water that is 10 times saltier than regular ocean water.
• A biofilm is a microbial community held together in a gummy-textured matrix that consists primarily of polysaccharides secreted by the organisms.
• Biofilms can be found clogging pipes, on kitchen counters, or even on the surface of one’s teeth.
Key Terms
• extremophile: an organism that lives under extreme conditions of temperature, salinity, etc; commercially important as a source of enzymes that operate under similar conditions
• halophile: an organism that lives and thrives in an environment of high salinity, often requiring such an environment; a form of extremophile
• alkaliphile: any organism that lives and thrives in an alkaline environment, such as a soda lake; a form of extremophile
Microbes Are Adaptable: Life in Moderate and Extreme Environments
Some organisms have developed strategies that allow them to survive harsh conditions. Prokaryotes thrive in a vast array of environments; some grow in conditions that would seem very normal to us, whereas others are able to thrive and grow under conditions that would kill a plant or animal. Almost all prokaryotes have a cell wall: a protective structure that allows them to survive in both hyper- and hypo-osmotic conditions. Some soil bacteria are able to form endospores that resist heat and drought, thereby allowing the organism to survive until favorable conditions recur. These adaptations, along with others, allow bacteria to be the most abundant life form in all terrestrial and aquatic ecosystems.
Other bacteria and archaea are adapted to grow under extreme conditions and are called extremophiles, meaning “lovers of extremes.” Extremophiles have been found in all kinds of environments: the depth of the oceans, hot springs, the Arctic and the Antarctic, in very dry places, deep inside earth, in harsh chemical environments, and in high radiation environments, just to mention a few. These organisms give us a better understanding of prokaryotic diversity and raise the possibility of finding new prokaryotic species that may lead to the discovery of new therapeutic drugs or have industrial applications. Because they have specialized adaptations that allow them to live in extreme conditions, many extremophiles cannot survive in moderate environments. There are many different groups of extremophiles. They are identified based on the conditions in which they grow best. Several habitats are extreme in multiple ways. For example, a soda lake is both salty and alkaline, so organisms that live in a soda lake must be both alkaliphiles and halophiles. Other extremophiles, like radioresistant organisms, do not prefer an extreme environment (in this case, one with high levels of radiation), but have adapted to survive in it.
Prokaryotes in the Dead Sea
One example of a very harsh environment is the Dead Sea, a hypersaline basin that is located between Jordan and Israel. Hypersaline environments are essentially concentrated seawater. In the Dead Sea, the sodium concentration is 10 times higher than that of seawater. The water also contains high levels of magnesium (about 40 times higher than in seawater) that would be toxic to most living things. Iron, calcium, and magnesium, elements that form divalent ions (Fe2+, Ca2+, and Mg2+), produce what is commonly referred to as “hard” water. Taken together, the high concentration of divalent cations, the acidic pH (6.0), and the intense solar radiation flux make the Dead Sea a unique, and uniquely hostile, ecosystem.
The Ecology of Biofilms
Until a couple of decades ago, microbiologists used to think of prokaryotes as isolated entities living apart. This model, however, does not reflect the true ecology of prokaryotes, most of which prefer to live in communities where they can interact. A biofilm is a microbial community held together in a gummy-textured matrix that consists primarily of polysaccharides secreted by the organisms, together with some proteins and nucleic acids. Biofilms grow attached to surfaces. Some of the best-studied biofilms are composed of prokaryotes, although fungal biofilms have also been described, as well as some composed of a mixture of fungi and bacteria.
Biofilms are present almost everywhere: they can cause the clogging of pipes and readily colonize surfaces in industrial settings. In recent, large-scale outbreaks of bacterial contamination of food, biofilms have played a major role. They also colonize household surfaces, such as kitchen counters, cutting boards, sinks, and toilets, as well as places on the human body, such as the surfaces of our teeth.
Interactions among the organisms that populate a biofilm, together with their protective exopolysaccharidic (EPS) environment, make these communities more robust than free-living, or planktonic, prokaryotes. The sticky substance that holds bacteria together also excludes most antibiotics and disinfectants, making biofilm bacteria hardier than their planktonic counterparts. Overall, biofilms are very difficult to destroy because they are resistant to many common forms of sterilization. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/25%3A_The_Origin_and_Diversity_of_Life/25.03%3A_Evidence_for_Early_Life/25.3C%3A_Extremophiles_and_Biofilms.txt |
Skills to Develop
• Describe how the present-day theory of evolution was developed
• Define adaptation
• Explain convergent and divergent evolution
• Describe homologous and vestigial structures
• Discuss misconceptions about the theory of evolution
Evolution by natural selection describes a mechanism for how species change over time. That species change had been suggested and debated well before Darwin began to explore this idea. The view that species were static and unchanging was grounded in the writings of Plato, yet there were also ancient Greeks who expressed evolutionary ideas. In the eighteenth century, ideas about the evolution of animals were reintroduced by the naturalist Georges-Louis Leclerc Comte de Buffon who observed that various geographic regions have different plant and animal populations, even when the environments are similar. It was also accepted that there were extinct species.
During this time, James Hutton, a Scottish naturalist, proposed that geological change occurred gradually by the accumulation of small changes from processes operating like they are today over long periods of time. This contrasted with the predominant view that the geology of the planet was a consequence of catastrophic events occurring during a relatively brief past. Hutton’s view was popularized in the nineteenth century by the geologist Charles Lyell who became a friend to Darwin. Lyell’s ideas were influential on Darwin’s thinking: Lyell’s notion of the greater age of Earth gave more time for gradual change in species, and the process of change provided an analogy for gradual change in species. In the early nineteenth century, Jean-Baptiste Lamarck published a book that detailed a mechanism for evolutionary change. This mechanism is now referred to as an inheritance of acquired characteristics by which modifications in an individual are caused by its environment, or the use or disuse of a structure during its lifetime, could be inherited by its offspring and thus bring about change in a species. While this mechanism for evolutionary change was discredited, Lamarck’s ideas were an important influence on evolutionary thought.
Charles Darwin and Natural Selection
In the mid-nineteenth century, the actual mechanism for evolution was independently conceived of and described by two naturalists: Charles Darwin and Alfred Russel Wallace. Importantly, each naturalist spent time exploring the natural world on expeditions to the tropics. From 1831 to 1836, Darwin traveled around the world on H.M.S. Beagle, including stops in South America, Australia, and the southern tip of Africa. Wallace traveled to Brazil to collect insects in the Amazon rainforest from 1848 to 1852 and to the Malay Archipelago from 1854 to 1862. Darwin’s journey, like Wallace’s later journeys to the Malay Archipelago, included stops at several island chains, the last being the Galápagos Islands west of Ecuador. On these islands, Darwin observed species of organisms on different islands that were clearly similar, yet had distinct differences. For example, the ground finches inhabiting the Galápagos Islands comprised several species with a unique beak shape (Figure \(1\)). The species on the islands had a graded series of beak sizes and shapes with very small differences between the most similar. He observed that these finches closely resembled another finch species on the mainland of South America. Darwin imagined that the island species might be species modified from one of the original mainland species. Upon further study, he realized that the varied beaks of each finch helped the birds acquire a specific type of food. For example, seed-eating finches had stronger, thicker beaks for breaking seeds, and insect-eating finches had spear-like beaks for stabbing their prey.
Wallace and Darwin both observed similar patterns in other organisms and they independently developed the same explanation for how and why such changes could take place. Darwin called this mechanism natural selection. Natural selection, also known as “survival of the fittest,” is the more prolific reproduction of individuals with favorable traits that survive environmental change because of those traits; this leads to evolutionary change.
For example, a population of giant tortoises found in the Galapagos Archipelago was observed by Darwin to have longer necks than those that lived on other islands with dry lowlands. These tortoises were “selected” because they could reach more leaves and access more food than those with short necks. In times of drought when fewer leaves would be available, those that could reach more leaves had a better chance to eat and survive than those that couldn’t reach the food source. Consequently, long-necked tortoises would be more likely to be reproductively successful and pass the long-necked trait to their offspring. Over time, only long-necked tortoises would be present in the population.
Natural selection, Darwin argued, was an inevitable outcome of three principles that operated in nature. First, most characteristics of organisms are inherited, or passed from parent to offspring. Although no one, including Darwin and Wallace, knew how this happened at the time, it was a common understanding. Second, more offspring are produced than are able to survive, so resources for survival and reproduction are limited. The capacity for reproduction in all organisms outstrips the availability of resources to support their numbers. Thus, there is competition for those resources in each generation. Both Darwin and Wallace’s understanding of this principle came from reading an essay by the economist Thomas Malthus who discussed this principle in relation to human populations. Third, offspring vary among each other in regard to their characteristics and those variations are inherited. Darwin and Wallace reasoned that offspring with inherited characteristics which allow them to best compete for limited resources will survive and have more offspring than those individuals with variations that are less able to compete. Because characteristics are inherited, these traits will be better represented in the next generation. This will lead to change in populations over generations in a process that Darwin called descent with modification. Ultimately, natural selection leads to greater adaptation of the population to its local environment; it is the only mechanism known for adaptive evolution.
Papers by Darwin and Wallace (Figure \(2\)) presenting the idea of natural selection were read together in 1858 before the Linnean Society in London. The following year Darwin’s book, On the Origin of Species, was published. His book outlined in considerable detail his arguments for evolution by natural selection.
Demonstrations of evolution by natural selection are time consuming and difficult to obtain. One of the best examples has been demonstrated in the very birds that helped to inspire Darwin’s theory: the Galápagos finches. Peter and Rosemary Grant and their colleagues have studied Galápagos finch populations every year since 1976 and have provided important demonstrations of natural selection. The Grants found changes from one generation to the next in the distribution of beak shapes with the medium ground finch on the Galápagos island of Daphne Major. The birds have inherited variation in the bill shape with some birds having wide deep bills and others having thinner bills. During a period in which rainfall was higher than normal because of an El Niño, the large hard seeds that large-billed birds ate were reduced in number; however, there was an abundance of the small soft seeds which the small-billed birds ate. Therefore, survival and reproduction were much better in the following years for the small-billed birds. In the years following this El Niño, the Grants measured beak sizes in the population and found that the average bill size was smaller. Since bill size is an inherited trait, parents with smaller bills had more offspring and the size of bills had evolved to be smaller. As conditions improved in 1987 and larger seeds became more available, the trend toward smaller average bill size ceased.
Career Connection: Field Biologist
Many people hike, explore caves, scuba dive, or climb mountains for recreation. People often participate in these activities hoping to see wildlife. Experiencing the outdoors can be incredibly enjoyable and invigorating. What if your job was to be outside in the wilderness? Field biologists by definition work outdoors in the “field.” The term field in this case refers to any location outdoors, even under water. A field biologist typically focuses research on a certain species, group of organisms, or a single habitat (Figure \(3\)).
One objective of many field biologists includes discovering new species that have never been recorded. Not only do such findings expand our understanding of the natural world, but they also lead to important innovations in fields such as medicine and agriculture. Plant and microbial species, in particular, can reveal new medicinal and nutritive knowledge. Other organisms can play key roles in ecosystems or be considered rare and in need of protection. When discovered, these important species can be used as evidence for environmental regulations and laws.
Processes and Patterns of Evolution
Natural selection can only take place if there is variation, or differences, among individuals in a population. Importantly, these differences must have some genetic basis; otherwise, the selection will not lead to change in the next generation. This is critical because variation among individuals can be caused by non-genetic reasons such as an individual being taller because of better nutrition rather than different genes.
Genetic diversity in a population comes from two main mechanisms: mutation and sexual reproduction. Mutation, a change in DNA, is the ultimate source of new alleles, or new genetic variation in any population. The genetic changes caused by mutation can have one of three outcomes on the phenotype. A mutation affects the phenotype of the organism in a way that gives it reduced fitness—lower likelihood of survival or fewer offspring. A mutation may produce a phenotype with a beneficial effect on fitness. And, many mutations will also have no effect on the fitness of the phenotype; these are called neutral mutations. Mutations may also have a whole range of effect sizes on the fitness of the organism that expresses them in their phenotype, from a small effect to a great effect. Sexual reproduction also leads to genetic diversity: when two parents reproduce, unique combinations of alleles assemble to produce the unique genotypes and thus phenotypes in each of the offspring.
A heritable trait that helps the survival and reproduction of an organism in its present environment is called an adaptation. Scientists describe groups of organisms becoming adapted to their environment when a change in the range of genetic variation occurs over time that increases or maintains the “fit” of the population to its environment. The webbed feet of platypuses are an adaptation for swimming. The snow leopards’ thick fur is an adaptation for living in the cold. The cheetahs’ fast speed is an adaptation for catching prey.
Whether or not a trait is favorable depends on the environmental conditions at the time. The same traits are not always selected because environmental conditions can change. For example, consider a species of plant that grew in a moist climate and did not need to conserve water. Large leaves were selected because they allowed the plant to obtain more energy from the sun. Large leaves require more water to maintain than small leaves, and the moist environment provided favorable conditions to support large leaves. After thousands of years, the climate changed, and the area no longer had excess water. The direction of natural selection shifted so that plants with small leaves were selected because those populations were able to conserve water to survive the new environmental conditions.
The evolution of species has resulted in enormous variation in form and function. Sometimes, evolution gives rise to groups of organisms that become tremendously different from each other. When two species evolve in diverse directions from a common point, it is called divergent evolution. Such divergent evolution can be seen in the forms of the reproductive organs of flowering plants which share the same basic anatomies; however, they can look very different as a result of selection in different physical environments and adaptation to different kinds of pollinators (Figure \(4\)).
In other cases, similar phenotypes evolve independently in distantly related species. For example, flight has evolved in both bats and insects, and they both have structures we refer to as wings, which are adaptations to flight. However, the wings of bats and insects have evolved from very different original structures. This phenomenon is called convergent evolution, where similar traits evolve independently in species that do not share a recent common ancestry. The two species came to the same function, flying, but did so separately from each other.
These physical changes occur over enormous spans of time and help explain how evolution occurs. Natural selection acts on individual organisms, which in turn can shape an entire species. Although natural selection may work in a single generation on an individual, it can take thousands or even millions of years for the genotype of an entire species to evolve. It is over these large time spans that life on earth has changed and continues to change.
Evidence of Evolution
The evidence for evolution is compelling and extensive. Looking at every level of organization in living systems, biologists see the signature of past and present evolution. Darwin dedicated a large portion of his book, On the Origin of Species, to identifying patterns in nature that were consistent with evolution, and since Darwin, our understanding has become clearer and broader.
Fossils
Fossils provide solid evidence that organisms from the past are not the same as those found today, and fossils show a progression of evolution. Scientists determine the age of fossils and categorize them from all over the world to determine when the organisms lived relative to each other. The resulting fossil record tells the story of the past and shows the evolution of form over millions of years (Figure \(5\)). For example, scientists have recovered highly detailed records showing the evolution of humans and horses (Figure \(5\)). The whale flipper shares a similar morphology to appendages of birds and mammals (Figure \(6\)) indicating that these species share a common ancestor.
Anatomy and Embryology
Another type of evidence for evolution is the presence of structures in organisms that share the same basic form. For example, the bones in the appendages of a human, dog, bird, and whale all share the same overall construction (Figure \(6\)) resulting from their origin in the appendages of a common ancestor. Over time, evolution led to changes in the shapes and sizes of these bones in different species, but they have maintained the same overall layout. Scientists call these synonymous parts homologous structures.
Some structures exist in organisms that have no apparent function at all, and appear to be residual parts from a past common ancestor. These unused structures without function are called vestigial structures. Other examples of vestigial structures are wings on flightless birds, leaves on some cacti, and hind leg bones in whales.
Link to Learning
Visit this interactive site to guess which bones structures are homologous and which are analogous, and see examples of evolutionary adaptations to illustrate these concepts.
Another evidence of evolution is the convergence of form in organisms that share similar environments. For example, species of unrelated animals, such as the arctic fox and ptarmigan, living in the arctic region have been selected for seasonal white phenotypes during winter to blend with the snow and ice (Figure \(7\)). These similarities occur not because of common ancestry, but because of similar selection pressures—the benefits of not being seen by predators.
Embryology, the study of the development of the anatomy of an organism to its adult form, also provides evidence of relatedness between now widely divergent groups of organisms. Mutational tweaking in the embryo can have such magnified consequences in the adult that embryo formation tends to be conserved. As a result, structures that are absent in some groups often appear in their embryonic forms and disappear by the time the adult or juvenile form is reached. For example, all vertebrate embryos, including humans, exhibit gill slits and tails at some point in their early development. These disappear in the adults of terrestrial groups but are maintained in adult forms of aquatic groups such as fish and some amphibians. Great ape embryos, including humans, have a tail structure during their development that is lost by the time of birth.
Biogeography
The geographic distribution of organisms on the planet follows patterns that are best explained by evolution in conjunction with the movement of tectonic plates over geological time. Broad groups that evolved before the breakup of the supercontinent Pangaea (about 200 million years ago) are distributed worldwide. Groups that evolved since the breakup appear uniquely in regions of the planet, such as the unique flora and fauna of northern continents that formed from the supercontinent Laurasia and of the southern continents that formed from the supercontinent Gondwana. The presence of members of the plant family Proteaceae in Australia, southern Africa, and South America is best explained by their presence prior to the southern supercontinent Gondwana breaking up.
The great diversification of marsupials in Australia and the absence of other mammals reflect Australia’s long isolation. Australia has an abundance of endemic species—species found nowhere else—which is typical of islands whose isolation by expanses of water prevents species from migrating. Over time, these species diverge evolutionarily into new species that look very different from their ancestors that may exist on the mainland. The marsupials of Australia, the finches on the Galápagos, and many species on the Hawaiian Islands are all unique to their one point of origin, yet they display distant relationships to ancestral species on mainlands.
Molecular Biology
Like anatomical structures, the structures of the molecules of life reflect descent with modification. Evidence of a common ancestor for all of life is reflected in the universality of DNA as the genetic material and in the near universality of the genetic code and the machinery of DNA replication and expression. Fundamental divisions in life between the three domains are reflected in major structural differences in otherwise conservative structures such as the components of ribosomes and the structures of membranes. In general, the relatedness of groups of organisms is reflected in the similarity of their DNA sequences—exactly the pattern that would be expected from descent and diversification from a common ancestor.
DNA sequences have also shed light on some of the mechanisms of evolution. For example, it is clear that the evolution of new functions for proteins commonly occurs after gene duplication events that allow the free modification of one copy by mutation, selection, or drift (changes in a population’s gene pool resulting from chance), while the second copy continues to produce a functional protein.
Misconceptions of Evolution
Although the theory of evolution generated some controversy when it was first proposed, it was almost universally accepted by biologists, particularly younger biologists, within 20 years after publication of On the Origin of Species. Nevertheless, the theory of evolution is a difficult concept and misconceptions about how it works abound
Link to Learning
This site addresses some of the main misconceptions associated with the theory of evolution.
Evolution Is Just a Theory
Critics of the theory of evolution dismiss its importance by purposefully confounding the everyday usage of the word “theory” with the way scientists use the word. In science, a “theory” is understood to be a body of thoroughly tested and verified explanations for a set of observations of the natural world. Scientists have a theory of the atom, a theory of gravity, and the theory of relativity, each of which describes understood facts about the world. In the same way, the theory of evolution describes facts about the living world. As such, a theory in science has survived significant efforts to discredit it by scientists. In contrast, a “theory” in common vernacular is a word meaning a guess or suggested explanation; this meaning is more akin to the scientific concept of “hypothesis.” When critics of evolution say evolution is “just a theory,” they are implying that there is little evidence supporting it and that it is still in the process of being rigorously tested. This is a mischaracterization.
Individuals Evolve
Evolution is the change in genetic composition of a population over time, specifically over generations, resulting from differential reproduction of individuals with certain alleles. Individuals do change over their lifetime, obviously, but this is called development and involves changes programmed by the set of genes the individual acquired at birth in coordination with the individual’s environment. When thinking about the evolution of a characteristic, it is probably best to think about the change of the average value of the characteristic in the population over time. For example, when natural selection leads to bill-size change in medium-ground finches in the Galápagos, this does not mean that individual bills on the finches are changing. If one measures the average bill size among all individuals in the population at one time and then measures the average bill size in the population several years later, this average value will be different as a result of evolution. Although some individuals may survive from the first time to the second, they will still have the same bill size; however, there will be many new individuals that contribute to the shift in average bill size.
Evolution Explains the Origin of Life
It is a common misunderstanding that evolution includes an explanation of life’s origins. Conversely, some of the theory’s critics believe that it cannot explain the origin of life. The theory does not try to explain the origin of life. The theory of evolution explains how populations change over time and how life diversifies the origin of species. It does not shed light on the beginnings of life including the origins of the first cells, which is how life is defined. The mechanisms of the origin of life on Earth are a particularly difficult problem because it occurred a very long time ago, and presumably it just occurred once. Importantly, biologists believe that the presence of life on Earth precludes the possibility that the events that led to life on Earth can be repeated because the intermediate stages would immediately become food for existing living things.
However, once a mechanism of inheritance was in place in the form of a molecule like DNA either within a cell or pre-cell, these entities would be subject to the principle of natural selection. More effective reproducers would increase in frequency at the expense of inefficient reproducers. So while evolution does not explain the origin of life, it may have something to say about some of the processes operating once pre-living entities acquired certain properties.
Organisms Evolve on Purpose
Statements such as “organisms evolve in response to a change in an environment” are quite common, but such statements can lead to two types of misunderstandings. First, the statement must not be understood to mean that individual organisms evolve. The statement is shorthand for “a population evolves in response to a changing environment.” However, a second misunderstanding may arise by interpreting the statement to mean that the evolution is somehow intentional. A changed environment results in some individuals in the population, those with particular phenotypes, benefiting and therefore producing proportionately more offspring than other phenotypes. This results in change in the population if the characteristics are genetically determined.
It is also important to understand that the variation that natural selection works on is already in a population and does not arise in response to an environmental change. For example, applying antibiotics to a population of bacteria will, over time, select a population of bacteria that are resistant to antibiotics. The resistance, which is caused by a gene, did not arise by mutation because of the application of the antibiotic. The gene for resistance was already present in the gene pool of the bacteria, likely at a low frequency. The antibiotic, which kills the bacterial cells without the resistance gene, strongly selects individuals that are resistant, since these would be the only ones that survived and divided. Experiments have demonstrated that mutations for antibiotic resistance do not arise as a result of antibiotic.
In a larger sense, evolution is not goal directed. Species do not become “better” over time; they simply track their changing environment with adaptations that maximize their reproduction in a particular environment at a particular time. Evolution has no goal of making faster, bigger, more complex, or even smarter species, despite the commonness of this kind of language in popular discourse. What characteristics evolve in a species are a function of the variation present and the environment, both of which are constantly changing in a non-directional way. What trait is fit in one environment at one time may well be fatal at some point in the future. This holds equally well for a species of insect as it does the human species.
Summary
Evolution is the process of adaptation through mutation which allows more desirable characteristics to be passed to the next generation. Over time, organisms evolve more characteristics that are beneficial to their survival. For living organisms to adapt and change to environmental pressures, genetic variation must be present. With genetic variation, individuals have differences in form and function that allow some to survive certain conditions better than others. These organisms pass their favorable traits to their offspring. Eventually, environments change, and what was once a desirable, advantageous trait may become an undesirable trait and organisms may further evolve. Evolution may be convergent with similar traits evolving in multiple species or divergent with diverse traits evolving in multiple species that came from a common ancestor. Evidence of evolution can be observed by means of DNA code and the fossil record, and also by the existence of homologous and vestigial structures.
Glossary
adaptation
heritable trait or behavior in an organism that aids in its survival and reproduction in its present environment
convergent evolution
process by which groups of organisms independently evolve to similar forms
divergent evolution
process by which groups of organisms evolve in diverse directions from a common point
homologous structures
parallel structures in diverse organisms that have a common ancestor
natural selection
reproduction of individuals with favorable genetic traits that survive environmental change because of those traits, leading to evolutionary change
variation
genetic differences among individuals in a population
vestigial structure
physical structure present in an organism but that has no apparent function and appears to be from a functional structure in a distant ancestor
25.04: Earth's Changing System
Skills to Develop
• List the unifying characteristics of eukaryotes
• Describe what scientists know about the origins of eukaryotes based on the last common ancestor
• Explain endosymbiotic theory
Living things fall into three large groups: Archaea, Bacteria, and Eukarya. The first two have prokaryotic cells, and the third contains all eukaryotes. A relatively sparse fossil record is available to help discern what the first members of each of these lineages looked like, so it is possible that all the events that led to the last common ancestor of extant eukaryotes will remain unknown. However, comparative biology of extant organisms and the limited fossil record provide some insight into the history of Eukarya.
The earliest fossils found appear to be Bacteria, most likely cyanobacteria. They are about 3.5 billion years old and are recognizable because of their relatively complex structure and, for prokaryotes, relatively large cells. Most other prokaryotes have small cells, 1 or 2 µm in size, and would be difficult to pick out as fossils. Most living eukaryotes have cells measuring 10 µm or greater. Structures this size, which might be fossils, appear in the geological record about 2.1 billion years ago.
Characteristics of Eukaryotes
Data from these fossils have led comparative biologists to the conclusion that living eukaryotes are all descendants of a single common ancestor. Mapping the characteristics found in all major groups of eukaryotes reveals that the following characteristics must have been present in the last common ancestor, because these characteristics are present in at least some of the members of each major lineage.
1. Cells with nuclei surrounded by a nuclear envelope with nuclear pores. This is the single characteristic that is both necessary and sufficient to define an organism as a eukaryote. All extant eukaryotes have cells with nuclei.
2. Mitochondria. Some extant eukaryotes have very reduced remnants of mitochondria in their cells, whereas other members of their lineages have “typical” mitochondria.
3. A cytoskeleton containing the structural and motility components called actin microfilaments and microtubules. All extant eukaryotes have these cytoskeletal elements.
4. Flagella and cilia, organelles associated with cell motility. Some extant eukaryotes lack flagella and/or cilia, but they are descended from ancestors that possessed them.
5. Chromosomes, each consisting of a linear DNA molecule coiled around basic (alkaline) proteins called histones. The few eukaryotes with chromosomes lacking histones clearly evolved from ancestors that had them.
6. Mitosis, a process of nuclear division wherein replicated chromosomes are divided and separated using elements of the cytoskeleton. Mitosis is universally present in eukaryotes.
7. Sex, a process of genetic recombination unique to eukaryotes in which diploid nuclei at one stage of the life cycle undergo meiosis to yield haploid nuclei and subsequent karyogamy, a stage where two haploid nuclei fuse together to create a diploid zygote nucleus.
8. Members of all major lineages have cell walls, and it might be reasonable to conclude that the last common ancestor could make cell walls during some stage of its life cycle. However, not enough is known about eukaryotes’ cell walls and their development to know how much homology exists among them. If the last common ancestor could make cell walls, it is clear that this ability must have been lost in many groups.
Endosymbiosis and the Evolution of Eukaryotes
In order to understand eukaryotic organisms fully, it is necessary to understand that all extant eukaryotes are descendants of a chimeric organism that was a composite of a host cell and the cell(s) of an alpha-proteobacterium that “took up residence” inside it. This major theme in the origin of eukaryotes is known as endosymbiosis, one cell engulfing another such that the engulfed cell survives and both cells benefit. Over many generations, a symbiotic relationship can result in two organisms that depend on each other so completely that neither could survive on its own. Endosymbiotic events likely contributed to the origin of the last common ancestor of today’s eukaryotes and to later diversification in certain lineages of eukaryotes (Figure \(4\)). Before explaining this further, it is necessary to consider metabolism in prokaryotes.
Prokaryotic Metabolism
Many important metabolic processes arose in prokaryotes, and some of these, such as nitrogen fixation, are never found in eukaryotes. The process of aerobic respiration is found in all major lineages of eukaryotes, and it is localized in the mitochondria. Aerobic respiration is also found in many lineages of prokaryotes, but it is not present in all of them, and many forms of evidence suggest that such anaerobic prokaryotes never carried out aerobic respiration nor did their ancestors.
While today’s atmosphere is about one-fifth molecular oxygen (O2), geological evidence shows that it originally lacked O2. Without oxygen, aerobic respiration would not be expected, and living things would have relied on fermentation instead. At some point before, about 3.5 billion years ago, some prokaryotes began using energy from sunlight to power anabolic processes that reduce carbon dioxide to form organic compounds. That is, they evolved the ability to photosynthesize. Hydrogen, derived from various sources, was captured using light-powered reactions to reduce fixed carbon dioxide in the Calvin cycle. The group of Gram-negative bacteria that gave rise to cyanobacteria used water as the hydrogen source and released O2 as a waste product.
Eventually, the amount of photosynthetic oxygen built up in some environments to levels that posed a risk to living organisms, since it can damage many organic compounds. Various metabolic processes evolved that protected organisms from oxygen, one of which, aerobic respiration, also generated high levels of ATP. It became widely present among prokaryotes, including in a group we now call alpha-proteobacteria. Organisms that did not acquire aerobic respiration had to remain in oxygen-free environments. Originally, oxygen-rich environments were likely localized around places where cyanobacteria were active, but by about 2 billion years ago, geological evidence shows that oxygen was building up to higher concentrations in the atmosphere. Oxygen levels similar to today’s levels only arose within the last 700 million years.
Recall that the first fossils that we believe to be eukaryotes date to about 2 billion years old, so they appeared as oxygen levels were increasing. Also, recall that all extant eukaryotes descended from an ancestor with mitochondria. These organelles were first observed by light microscopists in the late 1800s, where they appeared to be somewhat worm-shaped structures that seemed to be moving around in the cell. Some early observers suggested that they might be bacteria living inside host cells, but these hypotheses remained unknown or rejected in most scientific communities.
Endosymbiotic Theory
As cell biology developed in the twentieth century, it became clear that mitochondria were the organelles responsible for producing ATP using aerobic respiration. In the 1960s, American biologist Lynn Margulis developed endosymbiotic theory, which states that eukaryotes may have been a product of one cell engulfing another, one living within another, and evolving over time until the separate cells were no longer recognizable as such. In 1967, Margulis introduced new work on the theory and substantiated her findings through microbiological evidence. Although Margulis’ work initially was met with resistance, this once-revolutionary hypothesis is now widely (but not completely) accepted, with work progressing on uncovering the steps involved in this evolutionary process and the key players involved. Much still remains to be discovered about the origins of the cells that now make up the cells in all living eukaryotes.
Broadly, it has become clear that many of our nuclear genes and the molecular machinery responsible for replication and expression appear closely related to those in Archaea. On the other hand, the metabolic organelles and genes responsible for many energy-harvesting processes had their origins in bacteria. Much remains to be clarified about how this relationship occurred; this continues to be an exciting field of discovery in biology. For instance, it is not known whether the endosymbiotic event that led to mitochondria occurred before or after the host cell had a nucleus. Such organisms would be among the extinct precursors of the last common ancestor of eukaryotes.
Mitochondria
One of the major features distinguishing prokaryotes from eukaryotes is the presence of mitochondria. Eukaryotic cells may contain anywhere from one to several thousand mitochondria, depending on the cell’s level of energy consumption. Each mitochondrion measures 1 to 10 or greater micrometers in length and exists in the cell as an organelle that can be ovoid to worm-shaped to intricately branched (Figure \(1\)). Mitochondria arise from the division of existing mitochondria; they may fuse together; and they may be moved around inside the cell by interactions with the cytoskeleton. However, mitochondria cannot survive outside the cell. As the atmosphere was oxygenated by photosynthesis, and as successful aerobic prokaryotes evolved, evidence suggests that an ancestral cell with some membrane compartmentalization engulfed a free-living aerobic prokaryote, specifically an alpha-proteobacterium, thereby giving the host cell the ability to use oxygen to release energy stored in nutrients. Alpha-proteobacteria are a large group of bacteria that includes species symbiotic with plants, disease organisms that can infect humans via ticks, and many free-living species that use light for energy. Several lines of evidence support that mitochondria are derived from this endosymbiotic event. Most mitochondria are shaped like alpha-proteobacteria and are surrounded by two membranes, which would result when one membrane-bound organism was engulfed into a vacuole by another membrane-bound organism. The mitochondrial inner membrane is extensive and involves substantial infoldings called cristae that resemble the textured, outer surface of alpha-proteobacteria. The matrix and inner membrane are rich with the enzymes necessary for aerobic respiration.
Mitochondria divide independently by a process that resembles binary fission in prokaryotes. Specifically, mitochondria are not formed from scratch (de novo) by the eukaryotic cell; they reproduce within it and are distributed with the cytoplasm when a cell divides or two cells fuse. Therefore, although these organelles are highly integrated into the eukaryotic cell, they still reproduce as if they are independent organisms within the cell. However, their reproduction is synchronized with the activity and division of the cell. Mitochondria have their own (usually) circular DNA chromosome that is stabilized by attachments to the inner membrane and carries genes similar to genes expressed by alpha-proteobacteria. Mitochondria also have special ribosomes and transfer RNAs that resemble these components in prokaryotes. These features all support that mitochondria were once free-living prokaryotes.
Mitochondria that carry out aerobic respiration have their own genomes, with genes similar to those in alpha-proteobacteria. However, many of the genes for respiratory proteins are located in the nucleus. When these genes are compared to those of other organisms, they appear to be of alpha-proteobacterial origin. Additionally, in some eukaryotic groups, such genes are found in the mitochondria, whereas in other groups, they are found in the nucleus. This has been interpreted as evidence that genes have been transferred from the endosymbiont chromosome to the host genome. This loss of genes by the endosymbiont is probably one explanation why mitochondria cannot live without a host.
Some living eukaryotes are anaerobic and cannot survive in the presence of too much oxygen. Some appear to lack organelles that could be recognized as mitochondria. In the 1970s to the early 1990s, many biologists suggested that some of these eukaryotes were descended from ancestors whose lineages had diverged from the lineage of mitochondrion-containing eukaryotes before endosymbiosis occurred. However, later findings suggest that reduced organelles are found in most, if not all, anaerobic eukaryotes, and that all eukaryotes appear to carry some genes in their nuclei that are of mitochondrial origin. In addition to the aerobic generation of ATP, mitochondria have several other metabolic functions. One of these functions is to generate clusters of iron and sulfur that are important cofactors of many enzymes. Such functions are often associated with the reduced mitochondrion-derived organelles of anaerobic eukaryotes. Therefore, most biologists accept that the last common ancestor of eukaryotes had mitochondria.
Plastids
Some groups of eukaryotes are photosynthetic. Their cells contain, in addition to the standard eukaryotic organelles, another kind of organelle called a plastid. When such cells are carrying out photosynthesis, their plastids are rich in the pigment chlorophyll a and a range of other pigments, called accessory pigments, which are involved in harvesting energy from light. Photosynthetic plastids are called chloroplasts (Figure \(2\)).
Like mitochondria, plastids appear to have an endosymbiotic origin. This hypothesis was also championed by Lynn Margulis. Plastids are derived from cyanobacteria that lived inside the cells of an ancestral, aerobic, heterotrophic eukaryote. This is called primary endosymbiosis, and plastids of primary origin are surrounded by two membranes. The best evidence is that this has happened twice in the history of eukaryotes. In one case, the common ancestor of the major lineage/supergroup Archaeplastida took on a cyanobacterial endosymbiont; in the other, the ancestor of the small amoeboid rhizarian taxon, Paulinella, took on a different cyanobacterial endosymbiont. Almost all photosynthetic eukaryotes are descended from the first event, and only a couple of species are derived from the other.
Cyanobacteria are a group of Gram-negative bacteria with all the conventional structures of the group. However, unlike most prokaryotes, they have extensive, internal membrane-bound sacs called thylakoids. Chlorophyll is a component of these membranes, as are many of the proteins of the light reactions of photosynthesis. Cyanobacteria also have the peptidoglycan wall and lipopolysaccharide layer associated with Gram-negative bacteria.
Chloroplasts of primary origin have thylakoids, a circular DNA chromosome, and ribosomes similar to those of cyanobacteria. Each chloroplast is surrounded by two membranes. In the group of Archaeplastida called the glaucophytes and in Paulinella, a thin peptidoglycan layer is present between the outer and inner plastid membranes. All other plastids lack this relictual cyanobacterial wall. The outer membrane surrounding the plastid is thought to be derived from the vacuole in the host, and the inner membrane is thought to be derived from the plasma membrane of the symbiont.
There is also, as with the case of mitochondria, strong evidence that many of the genes of the endosymbiont were transferred to the nucleus. Plastids, like mitochondria, cannot live independently outside the host. In addition, like mitochondria, plastids are derived from the division of other plastids and never built from scratch. Researchers have suggested that the endosymbiotic event that led to Archaeplastida occurred 1 to 1.5 billion years ago, at least 5 hundred million years after the fossil record suggests that eukaryotes were present.
Not all plastids in eukaryotes are derived directly from primary endosymbiosis. Some of the major groups of algae became photosynthetic by secondary endosymbiosis, that is, by taking in either green algae or red algae (both from Archaeplastida) as endosymbionts (Figure \(3\)). Numerous microscopic and genetic studies have supported this conclusion. Secondary plastids are surrounded by three or more membranes, and some secondary plastids even have clear remnants of the nucleus of endosymbiotic alga. Others have not “kept” any remnants. There are cases where tertiary or higher-order endosymbiotic events are the best explanations for plastids in some eukaryotes.
Art Connection
What evidence is there that mitochondria were incorporated into the ancestral eukaryotic cell before chloroplasts?
Evolution Connection: Secondary Endosymbiosis in Chlorarachniophytes
Endosymbiosis involves one cell engulfing another to produce, over time, a coevolved relationship in which neither cell could survive alone. The chloroplasts of red and green algae, for instance, are derived from the engulfment of a photosynthetic cyanobacterium by an early prokaryote.
This leads to the question of the possibility of a cell containing an endosymbiont to itself become engulfed, resulting in a secondary endosymbiosis. Molecular and morphological evidence suggest that the chlorarachniophyte protists are derived from a secondary endosymbiotic event. Chlorarachniophytes are rare algae indigenous to tropical seas and sand that can be classified into the rhizarian supergroup. Chlorarachniophytes extend thin cytoplasmic strands, interconnecting themselves with other chlorarachniophytes, in a cytoplasmic network. These protists are thought to have originated when a eukaryote engulfed a green alga, the latter of which had already established an endosymbiotic relationship with a photosynthetic cyanobacterium (Figure \(5\)).
Several lines of evidence support that chlorarachniophytes evolved from secondary endosymbiosis. The chloroplasts contained within the green algal endosymbionts still are capable of photosynthesis, making chlorarachniophytes photosynthetic. The green algal endosymbiont also exhibits a stunted vestigial nucleus. In fact, it appears that chlorarachniophytes are the products of an evolutionarily recent secondary endosymbiotic event. The plastids of chlorarachniophytes are surrounded by four membranes: The first two correspond to the inner and outer membranes of the photosynthetic cyanobacterium, the third corresponds to the green alga, and the fourth corresponds to the vacuole that surrounded the green alga when it was engulfed by the chlorarachniophyte ancestor. In other lineages that involved secondary endosymbiosis, only three membranes can be identified around plastids. This is currently rectified as a sequential loss of a membrane during the course of evolution.
The process of secondary endosymbiosis is not unique to chlorarachniophytes. In fact, secondary endosymbiosis of green algae also led to euglenid protists, whereas secondary endosymbiosis of red algae led to the evolution of dinoflagellates, apicomplexans, and stramenopiles.
Summary
The oldest fossil evidence of eukaryotes is about 2 billion years old. Fossils older than this all appear to be prokaryotes. It is probable that today’s eukaryotes are descended from an ancestor that had a prokaryotic organization. The last common ancestor of today’s Eukarya had several characteristics, including cells with nuclei that divided mitotically and contained linear chromosomes where the DNA was associated with histones, a cytoskeleton and endomembrane system, and the ability to make cilia/flagella during at least part of its life cycle. It was aerobic because it had mitochondria that were the result of an aerobic alpha-proteobacterium that lived inside a host cell. Whether this host had a nucleus at the time of the initial symbiosis remains unknown. The last common ancestor may have had a cell wall for at least part of its life cycle, but more data are needed to confirm this hypothesis. Today’s eukaryotes are very diverse in their shapes, organization, life cycles, and number of cells per individual.
Art Connections
Figure \(4\): What evidence is there that mitochondria were incorporated into the ancestral eukaryotic cell before chloroplasts?
Answer
All eukaryotic cells have mitochondria, but not all eukaryotic cells have chloroplasts.
Glossary
endosymbiosis
engulfment of one cell within another such that the engulfed cell survives, and both cells benefit; the process responsible for the evolution of mitochondria and chloroplasts in eukaryotes
endosymbiotic theory
theory that states that eukaryotes may have been a product of one cell engulfing another, one living within another, and evolving over time until the separate cells were no longer recognizable as such
plastid
one of a group of related organelles in plant cells that are involved in the storage of starches, fats, proteins, and pigments | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/25%3A_The_Origin_and_Diversity_of_Life/25.04%3A_Earth%27s_Changing_System/25.4.01%3A_Eukaryotic_Origins.txt |
Skills to Develop
• Define global climate change
• Summarize the effects of the Industrial Revolution on global atmospheric carbon dioxide concentration
• Describe three natural factors affecting long-term global climate
• List two or more greenhouse gases and describe their role in the greenhouse effect
All biomes are universally affected by global conditions, such as climate, that ultimately shape each biome’s environment. Scientists who study climate have noted a series of marked changes that have gradually become increasingly evident during the last sixty years. Global climate change is the term used to describe altered global weather patterns, including a worldwide increase in temperature, due largely to rising levels of atmospheric carbon dioxide.
Climate and Weather
A common misconception about global climate change is that a specific weather event occurring in a particular region (for example, a very cool week in June in central Indiana) is evidence of global climate change. However, a cold week in June is a weather-related event and not a climate-related one. These misconceptions often arise because of confusion over the terms climate and weather.
Climate refers to the long-term, predictable atmospheric conditions of a specific area. The climate of a biome is characterized by having consistent temperature and annual rainfall ranges. Climate does not address the amount of rain that fell on one particular day in a biome or the colder-than-average temperatures that occurred on one day. In contrast, weather refers to the conditions of the atmosphere during a short period of time. Weather forecasts are usually made for 48-hour cycles. Long-range weather forecasts are available but can be unreliable.
To better understand the difference between climate and weather, imagine that you are planning an outdoor event in northern Wisconsin. You would be thinking about climate when you plan the event in the summer rather than the winter because you have long-term knowledge that any given Saturday in the months of May to August would be a better choice for an outdoor event in Wisconsin than any given Saturday in January. However, you cannot determine the specific day that the event should be held on because it is difficult to accurately predict the weather on a specific day. Climate can be considered “average” weather.
Global Climate Change
Climate change can be understood by approaching three areas of study:
• current and past global climate change
• causes of past and present-day global climate change
• ancient and current results of climate change
It is helpful to keep these three different aspects of climate change clearly separated when consuming media reports about global climate change. It is common for reports and discussions about global climate change to confuse the data showing that Earth’s climate is changing with the factors that drive this climate change.
Evidence for Global Climate Change
Since scientists cannot go back in time to directly measure climatic variables, such as average temperature and precipitation, they must instead indirectly measure temperature. To do this, scientists rely on historical evidence of Earth’s past climate.
Antarctic ice cores are a key example of such evidence. These ice cores are samples of polar ice obtained by means of drills that reach thousands of meters into ice sheets or high mountain glaciers. Viewing the ice cores is like traveling backwards through time; the deeper the sample, the earlier the time period. Trapped within the ice are bubbles of air and other biological evidence that can reveal temperature and carbon dioxide data. Antarctic ice cores have been collected and analyzed to indirectly estimate the temperature of the Earth over the past 400,000 years (Figure \(1\)a). The 0 °C on this graph refers to the long-term average. Temperatures that are greater than 0 °C exceed Earth’s long-term average temperature. Conversely, temperatures that are less than 0 °C are less than Earth’s average temperature. This figure shows that there have been periodic cycles of increasing and decreasing temperature.
Before the late 1800s, the Earth has been as much as 9 °C cooler and about 3 °C warmer. Note that the graph in Figure \(1\)b shows that the atmospheric concentration of carbon dioxide has also risen and fallen in periodic cycles; note the relationship between carbon dioxide concentration and temperature. Figure \(1\)b shows that carbon dioxide levels in the atmosphere have historically cycled between 180 and 300 parts per million (ppm) by volume.
Figure \(1\)a does not show the last 2,000 years with enough detail to compare the changes of Earth’s temperature during the last 400,000 years with the temperature change that has occurred in the more recent past. Two significant temperature anomalies, or irregularities, have occurred in the last 2000 years. These are the Medieval Climate Anomaly (or the Medieval Warm Period) and the Little Ice Age. A third temperature anomaly aligns with the Industrial Era. The Medieval Climate Anomaly occurred between 900 and 1300 AD. During this time period, many climate scientists think that slightly warmer weather conditions prevailed in many parts of the world; the higher-than-average temperature changes varied between 0.10 °C and 0.20 °C above the norm. Although 0.10 °C does not seem large enough to produce any noticeable change, it did free seas of ice. Because of this warming, the Vikings were able to colonize Greenland.
The Little Ice Age was a cold period that occurred between 1550 AD and 1850 AD. During this time, a slight cooling of a little less than 1 °C was observed in North America, Europe, and possibly other areas of the Earth. This 1 °C change in global temperature is a seemingly small deviation in temperature (as was observed during the Medieval Climate Anomaly); however, it also resulted in noticeable changes. Historical accounts reveal a time of exceptionally harsh winters with much snow and frost.
The Industrial Revolution, which began around 1750, was characterized by changes in much of human society. Advances in agriculture increased the food supply, which improved the standard of living for people in Europe and the United States. New technologies were invented and provided jobs and cheaper goods. These new technologies were powered using fossil fuels, especially coal. The Industrial Revolution starting in the early nineteenth century ushered in the beginning of the Industrial Era. When a fossil fuel is burned, carbon dioxide is released. With the beginning of the Industrial Era, atmospheric carbon dioxide began to rise (Figure \(2\)).
Current and Past Drivers of Global Climate Change
Since it is not possible to go back in time to directly observe and measure climate, scientists use indirect evidence to determine the drivers, or factors, that may be responsible for climate change. The indirect evidence includes data collected using ice cores, boreholes (a narrow shaft bored into the ground), tree rings, glacier lengths, pollen remains, and ocean sediments. The data shows a correlation between the timing of temperature changes and drivers of climate change: before the Industrial Era (pre-1780), there were three drivers of climate change that were not related to human activity or atmospheric gases. The first of these is the Milankovitch cycles. The Milankovitch cycles describe the effects of slight changes in the Earth’s orbit on Earth’s climate. The length of the Milankovitch cycles ranges between 19,000 and 100,000 years. In other words, one could expect to see some predictable changes in the Earth’s climate associated with changes in the Earth’s orbit at a minimum of every 19,000 years.
The variation in the sun’s intensity is the second natural factor responsible for climate change. Solar intensity is the amount of solar power or energy the sun emits in a given amount of time. There is a direct relationship between solar intensity and temperature. As solar intensity increases (or decreases), the Earth’s temperature correspondingly increases (or decreases). Changes in solar intensity have been proposed as one of several possible explanations for the Little Ice Age.
Finally, volcanic eruptions are a third natural driver of climate change. Volcanic eruptions can last a few days, but the solids and gases released during an eruption can influence the climate over a period of a few years, causing short-term climate changes. The gases and solids released by volcanic eruptions can include carbon dioxide, water vapor, sulfur dioxide, hydrogen sulfide, hydrogen, and carbon monoxide. Generally, volcanic eruptions cool the climate. This occurred in 1783 when volcanos in Iceland erupted and caused the release of large volumes of sulfuric oxide. This led to haze-effect cooling, a global phenomenon that occurs when dust, ash, or other suspended particles block out sunlight and trigger lower global temperatures as a result; haze-effect cooling usually extends for one or more years. In Europe and North America, haze-effect cooling produced some of the lowest average winter temperatures on record in 1783 and 1784.
Greenhouse gases are probably the most significant drivers of the climate. When heat energy from the sun strikes the Earth, gases known as greenhouse gases trap the heat in the atmosphere, as do the glass panes of a greenhouse keep heat from escaping. The greenhouse gases that affect Earth include carbon dioxide, methane, water vapor, nitrous oxide, and ozone. Approximately half of the radiation from the sun passes through these gases in the atmosphere and strikes the Earth. This radiation is converted into thermal radiation on the Earth’s surface, and then a portion of that energy is re-radiated back into the atmosphere. Greenhouse gases, however, reflect much of the thermal energy back to the Earth’s surface. The more greenhouse gases there are in the atmosphere, the more thermal energy is reflected back to the Earth’s surface. Greenhouse gases absorb and emit radiation and are an important factor in the greenhouse effect: the warming of Earth due to carbon dioxide and other greenhouse gases in the atmosphere.
Evidence supports the relationship between atmospheric concentrations of carbon dioxide and temperature: as carbon dioxide rises, global temperature rises. Since 1950, the concentration of atmospheric carbon dioxide has increased from about 280 ppm to 382 ppm in 2006. In 2011, the atmospheric carbon dioxide concentration was 392 ppm. However, the planet would not be inhabitable by current life forms if water vapor did not produce its drastic greenhouse warming effect.
Scientists look at patterns in data and try to explain differences or deviations from these patterns. The atmospheric carbon dioxide data reveal a historical pattern of carbon dioxide increasing and decreasing, cycling between a low of 180 ppm and a high of 300 ppm. Scientists have concluded that it took around 50,000 years for the atmospheric carbon dioxide level to increase from its low minimum concentration to its higher maximum concentration. However, starting recently, atmospheric carbon dioxide concentrations have increased beyond the historical maximum of 300 ppm. The current increases in atmospheric carbon dioxide have happened very quickly—in a matter of hundreds of years rather than thousands of years. What is the reason for this difference in the rate of change and the amount of increase in carbon dioxide? A key factor that must be recognized when comparing the historical data and the current data is the presence of modern human society; no other driver of climate change has yielded changes in atmospheric carbon dioxide levels at this rate or to this magnitude.
Human activity releases carbon dioxide and methane, two of the most important greenhouse gases, into the atmosphere in several ways. The primary mechanism that releases carbon dioxide is the burning of fossil fuels, such as gasoline, coal, and natural gas (Figure \(3\)). Deforestation, cement manufacture, animal agriculture, the clearing of land, and the burning of forests are other human activities that release carbon dioxide. Methane (CH4) is produced when bacteria break down organic matter under anaerobic conditions. Anaerobic conditions can happen when organic matter is trapped underwater (such as in rice paddies) or in the intestines of herbivores. Methane can also be released from natural gas fields and the decomposition that occurs in landfills. Another source of methane is the melting of clathrates. Clathrates are frozen chunks of ice and methane found at the bottom of the ocean. When water warms, these chunks of ice melt and methane is released. As the ocean’s water temperature increases, the rate at which clathrates melt is increasing, releasing even more methane. This leads to increased levels of methane in the atmosphere, which further accelerates the rate of global warming. This is an example of the positive feedback loop that is leading to the rapid rate of increase of global temperatures.
Documented Results of Climate Change: Past and Present
Scientists have geological evidence of the consequences of long-ago climate change. Modern-day phenomena such as retreating glaciers and melting polar ice cause a continual rise in sea level. Meanwhile, changes in climate can negatively affect organisms.
Geological Climate Change
Global warming has been associated with at least one planet-wide extinction event during the geological past. The Permian extinction event occurred about 251 million years ago toward the end of the roughly 50-million-year-long geological time span known as the Permian period. This geologic time period was one of the three warmest periods in Earth’s geologic history. Scientists estimate that approximately 70 percent of the terrestrial plant and animal species and 84 percent of marine species became extinct, vanishing forever near the end of the Permian period. Organisms that had adapted to wet and warm climatic conditions, such as annual rainfall of 300–400 cm (118–157 in) and 20 °C–30 °C (68 °F–86 °F) in the tropical wet forest, may not have been able to survive the Permian climate change.
Link to Learning
Watch this NASA video to discover the mixed effects of global warming on plant growth. While scientists found that warmer temperatures in the 1980s and 1990s caused an increase in plant productivity, this advantage has since been counteracted by more frequent droughts.
Present Climate Change
A number of global events have occurred that may be attributed to climate change during our lifetimes. Glacier National Park in Montana is undergoing the retreat of many of its glaciers, a phenomenon known as glacier recession. In 1850, the area contained approximately 150 glaciers. By 2010, however, the park contained only about 24 glaciers greater than 25 acres in size. One of these glaciers is the Grinnell Glacier (Figure \(4\)) at Mount Gould. Between 1966 and 2005, the size of Grinnell Glacier shrank by 40 percent. Similarly, the mass of the ice sheets in Greenland and the Antarctic is decreasing: Greenland lost 150–250 km3 of ice per year between 2002 and 2006. In addition, the size and thickness of the Arctic sea ice is decreasing.
This loss of ice is leading to increases in the global sea level. On average, the sea is rising at a rate of 1.8 mm per year. However, between 1993 and 2010 the rate of sea level increase ranged between 2.9 and 3.4 mm per year. A variety of factors affect the volume of water in the ocean, including the temperature of the water (the density of water is related to its temperature) and the amount of water found in rivers, lakes, glaciers, polar ice caps, and sea ice. As glaciers and polar ice caps melt, there is a significant contribution of liquid water that was previously frozen.
In addition to some abiotic conditions changing in response to climate change, many organisms are also being affected by the changes in temperature. Temperature and precipitation play key roles in determining the geographic distribution and phenology of plants and animals. (Phenology is the study of the effects of climatic conditions on the timing of periodic lifecycle events, such as flowering in plants or migration in birds.) Researchers have shown that 385 plant species in Great Britain are flowering 4.5 days sooner than was recorded earlier during the previous 40 years. In addition, insect-pollinated species were more likely to flower earlier than wind-pollinated species. The impact of changes in flowering date would be mitigated if the insect pollinators emerged earlier. This mismatched timing of plants and pollinators could result in injurious ecosystem effects because, for continued survival, insect-pollinated plants must flower when their pollinators are present.
Summary
The Earth has gone through periodic cycles of increases and decreases in temperature. During the past 2000 years, the Medieval Climate Anomaly was a warmer period, while the Little Ice Age was unusually cool. Both of these irregularities can be explained by natural causes of changes in climate, and, although the temperature changes were small, they had significant effects. Natural drivers of climate change include Milankovitch cycles, changes in solar activity, and volcanic eruptions. None of these factors, however, leads to rapid increases in global temperature or sustained increases in carbon dioxide. The burning of fossil fuels is an important source of greenhouse gases, which plays a major role in the greenhouse effect. Long ago, global warming resulted in the Permian extinction: a large-scale extinction event that is documented in the fossil record. Currently, modern-day climate change is associated with the increased melting of glaciers and polar ice sheets, resulting in a gradual increase in sea level. Plants and animals can also be affected by global climate change when the timing of seasonal events, such as flowering or pollination, is affected by global warming.
Glossary
clathrates
frozen chunks of ice and methane found at the bottom of the ocean
climate
long-term, predictable atmospheric conditions present in a specific area
global climate change
altered global weather patterns, including a worldwide increase in temperature, due largely to rising levels of atmospheric carbon dioxide
greenhouse effect
warming of Earth due to carbon dioxide and other greenhouse gases in the atmosphere
greenhouse gases
atmospheric gases such as carbon dioxide and methane that absorb and emit radiation, thus trapping heat in Earth’s atmosphere
haze-effect cooling
effect of the gases and solids from a volcanic eruption on global climate
Milankovitch cycles
cyclic changes in the Earth's orbit that may affect climate
solar intensity
amount of solar power energy the sun emits in a given amount of time
weather
conditions of the atmosphere during a short period of time | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/25%3A_The_Origin_and_Diversity_of_Life/25.04%3A_Earth%27s_Changing_System/25.4.02%3A_Climate_and_the_Effects_of_Global_Climate_Change.txt |
Skills to Develop
• Describe how the present-day theory of evolution was developed
• Define adaptation
• Explain convergent and divergent evolution
• Describe homologous and vestigial structures
• Discuss misconceptions about the theory of evolution
Evolution by natural selection describes a mechanism for how species change over time. That species change had been suggested and debated well before Darwin began to explore this idea. The view that species were static and unchanging was grounded in the writings of Plato, yet there were also ancient Greeks who expressed evolutionary ideas. In the eighteenth century, ideas about the evolution of animals were reintroduced by the naturalist Georges-Louis Leclerc Comte de Buffon who observed that various geographic regions have different plant and animal populations, even when the environments are similar. It was also accepted that there were extinct species.
During this time, James Hutton, a Scottish naturalist, proposed that geological change occurred gradually by the accumulation of small changes from processes operating like they are today over long periods of time. This contrasted with the predominant view that the geology of the planet was a consequence of catastrophic events occurring during a relatively brief past. Hutton’s view was popularized in the nineteenth century by the geologist Charles Lyell who became a friend to Darwin. Lyell’s ideas were influential on Darwin’s thinking: Lyell’s notion of the greater age of Earth gave more time for gradual change in species, and the process of change provided an analogy for gradual change in species. In the early nineteenth century, Jean-Baptiste Lamarck published a book that detailed a mechanism for evolutionary change. This mechanism is now referred to as an inheritance of acquired characteristics by which modifications in an individual are caused by its environment, or the use or disuse of a structure during its lifetime, could be inherited by its offspring and thus bring about change in a species. While this mechanism for evolutionary change was discredited, Lamarck’s ideas were an important influence on evolutionary thought.
Charles Darwin and Natural Selection
In the mid-nineteenth century, the actual mechanism for evolution was independently conceived of and described by two naturalists: Charles Darwin and Alfred Russel Wallace. Importantly, each naturalist spent time exploring the natural world on expeditions to the tropics. From 1831 to 1836, Darwin traveled around the world on H.M.S. Beagle, including stops in South America, Australia, and the southern tip of Africa. Wallace traveled to Brazil to collect insects in the Amazon rainforest from 1848 to 1852 and to the Malay Archipelago from 1854 to 1862. Darwin’s journey, like Wallace’s later journeys to the Malay Archipelago, included stops at several island chains, the last being the Galápagos Islands west of Ecuador. On these islands, Darwin observed species of organisms on different islands that were clearly similar, yet had distinct differences. For example, the ground finches inhabiting the Galápagos Islands comprised several species with a unique beak shape (Figure \(1\)). The species on the islands had a graded series of beak sizes and shapes with very small differences between the most similar. He observed that these finches closely resembled another finch species on the mainland of South America. Darwin imagined that the island species might be species modified from one of the original mainland species. Upon further study, he realized that the varied beaks of each finch helped the birds acquire a specific type of food. For example, seed-eating finches had stronger, thicker beaks for breaking seeds, and insect-eating finches had spear-like beaks for stabbing their prey.
Wallace and Darwin both observed similar patterns in other organisms and they independently developed the same explanation for how and why such changes could take place. Darwin called this mechanism natural selection. Natural selection, also known as “survival of the fittest,” is the more prolific reproduction of individuals with favorable traits that survive environmental change because of those traits; this leads to evolutionary change.
For example, a population of giant tortoises found in the Galapagos Archipelago was observed by Darwin to have longer necks than those that lived on other islands with dry lowlands. These tortoises were “selected” because they could reach more leaves and access more food than those with short necks. In times of drought when fewer leaves would be available, those that could reach more leaves had a better chance to eat and survive than those that couldn’t reach the food source. Consequently, long-necked tortoises would be more likely to be reproductively successful and pass the long-necked trait to their offspring. Over time, only long-necked tortoises would be present in the population.
Natural selection, Darwin argued, was an inevitable outcome of three principles that operated in nature. First, most characteristics of organisms are inherited, or passed from parent to offspring. Although no one, including Darwin and Wallace, knew how this happened at the time, it was a common understanding. Second, more offspring are produced than are able to survive, so resources for survival and reproduction are limited. The capacity for reproduction in all organisms outstrips the availability of resources to support their numbers. Thus, there is competition for those resources in each generation. Both Darwin and Wallace’s understanding of this principle came from reading an essay by the economist Thomas Malthus who discussed this principle in relation to human populations. Third, offspring vary among each other in regard to their characteristics and those variations are inherited. Darwin and Wallace reasoned that offspring with inherited characteristics which allow them to best compete for limited resources will survive and have more offspring than those individuals with variations that are less able to compete. Because characteristics are inherited, these traits will be better represented in the next generation. This will lead to change in populations over generations in a process that Darwin called descent with modification. Ultimately, natural selection leads to greater adaptation of the population to its local environment; it is the only mechanism known for adaptive evolution.
Papers by Darwin and Wallace (Figure \(2\)) presenting the idea of natural selection were read together in 1858 before the Linnean Society in London. The following year Darwin’s book, On the Origin of Species, was published. His book outlined in considerable detail his arguments for evolution by natural selection.
Demonstrations of evolution by natural selection are time consuming and difficult to obtain. One of the best examples has been demonstrated in the very birds that helped to inspire Darwin’s theory: the Galápagos finches. Peter and Rosemary Grant and their colleagues have studied Galápagos finch populations every year since 1976 and have provided important demonstrations of natural selection. The Grants found changes from one generation to the next in the distribution of beak shapes with the medium ground finch on the Galápagos island of Daphne Major. The birds have inherited variation in the bill shape with some birds having wide deep bills and others having thinner bills. During a period in which rainfall was higher than normal because of an El Niño, the large hard seeds that large-billed birds ate were reduced in number; however, there was an abundance of the small soft seeds which the small-billed birds ate. Therefore, survival and reproduction were much better in the following years for the small-billed birds. In the years following this El Niño, the Grants measured beak sizes in the population and found that the average bill size was smaller. Since bill size is an inherited trait, parents with smaller bills had more offspring and the size of bills had evolved to be smaller. As conditions improved in 1987 and larger seeds became more available, the trend toward smaller average bill size ceased.
Career Connection: Field Biologist
Many people hike, explore caves, scuba dive, or climb mountains for recreation. People often participate in these activities hoping to see wildlife. Experiencing the outdoors can be incredibly enjoyable and invigorating. What if your job was to be outside in the wilderness? Field biologists by definition work outdoors in the “field.” The term field in this case refers to any location outdoors, even under water. A field biologist typically focuses research on a certain species, group of organisms, or a single habitat (Figure \(3\)).
One objective of many field biologists includes discovering new species that have never been recorded. Not only do such findings expand our understanding of the natural world, but they also lead to important innovations in fields such as medicine and agriculture. Plant and microbial species, in particular, can reveal new medicinal and nutritive knowledge. Other organisms can play key roles in ecosystems or be considered rare and in need of protection. When discovered, these important species can be used as evidence for environmental regulations and laws.
Processes and Patterns of Evolution
Natural selection can only take place if there is variation, or differences, among individuals in a population. Importantly, these differences must have some genetic basis; otherwise, the selection will not lead to change in the next generation. This is critical because variation among individuals can be caused by non-genetic reasons such as an individual being taller because of better nutrition rather than different genes.
Genetic diversity in a population comes from two main mechanisms: mutation and sexual reproduction. Mutation, a change in DNA, is the ultimate source of new alleles, or new genetic variation in any population. The genetic changes caused by mutation can have one of three outcomes on the phenotype. A mutation affects the phenotype of the organism in a way that gives it reduced fitness—lower likelihood of survival or fewer offspring. A mutation may produce a phenotype with a beneficial effect on fitness. And, many mutations will also have no effect on the fitness of the phenotype; these are called neutral mutations. Mutations may also have a whole range of effect sizes on the fitness of the organism that expresses them in their phenotype, from a small effect to a great effect. Sexual reproduction also leads to genetic diversity: when two parents reproduce, unique combinations of alleles assemble to produce the unique genotypes and thus phenotypes in each of the offspring.
A heritable trait that helps the survival and reproduction of an organism in its present environment is called an adaptation. Scientists describe groups of organisms becoming adapted to their environment when a change in the range of genetic variation occurs over time that increases or maintains the “fit” of the population to its environment. The webbed feet of platypuses are an adaptation for swimming. The snow leopards’ thick fur is an adaptation for living in the cold. The cheetahs’ fast speed is an adaptation for catching prey.
Whether or not a trait is favorable depends on the environmental conditions at the time. The same traits are not always selected because environmental conditions can change. For example, consider a species of plant that grew in a moist climate and did not need to conserve water. Large leaves were selected because they allowed the plant to obtain more energy from the sun. Large leaves require more water to maintain than small leaves, and the moist environment provided favorable conditions to support large leaves. After thousands of years, the climate changed, and the area no longer had excess water. The direction of natural selection shifted so that plants with small leaves were selected because those populations were able to conserve water to survive the new environmental conditions.
The evolution of species has resulted in enormous variation in form and function. Sometimes, evolution gives rise to groups of organisms that become tremendously different from each other. When two species evolve in diverse directions from a common point, it is called divergent evolution. Such divergent evolution can be seen in the forms of the reproductive organs of flowering plants which share the same basic anatomies; however, they can look very different as a result of selection in different physical environments and adaptation to different kinds of pollinators (Figure \(4\)).
In other cases, similar phenotypes evolve independently in distantly related species. For example, flight has evolved in both bats and insects, and they both have structures we refer to as wings, which are adaptations to flight. However, the wings of bats and insects have evolved from very different original structures. This phenomenon is called convergent evolution, where similar traits evolve independently in species that do not share a recent common ancestry. The two species came to the same function, flying, but did so separately from each other.
These physical changes occur over enormous spans of time and help explain how evolution occurs. Natural selection acts on individual organisms, which in turn can shape an entire species. Although natural selection may work in a single generation on an individual, it can take thousands or even millions of years for the genotype of an entire species to evolve. It is over these large time spans that life on earth has changed and continues to change.
Evidence of Evolution
The evidence for evolution is compelling and extensive. Looking at every level of organization in living systems, biologists see the signature of past and present evolution. Darwin dedicated a large portion of his book, On the Origin of Species, to identifying patterns in nature that were consistent with evolution, and since Darwin, our understanding has become clearer and broader.
Fossils
Fossils provide solid evidence that organisms from the past are not the same as those found today, and fossils show a progression of evolution. Scientists determine the age of fossils and categorize them from all over the world to determine when the organisms lived relative to each other. The resulting fossil record tells the story of the past and shows the evolution of form over millions of years (Figure \(5\)). For example, scientists have recovered highly detailed records showing the evolution of humans and horses (Figure \(5\)). The whale flipper shares a similar morphology to appendages of birds and mammals (Figure \(6\)) indicating that these species share a common ancestor.
Anatomy and Embryology
Another type of evidence for evolution is the presence of structures in organisms that share the same basic form. For example, the bones in the appendages of a human, dog, bird, and whale all share the same overall construction (Figure \(6\)) resulting from their origin in the appendages of a common ancestor. Over time, evolution led to changes in the shapes and sizes of these bones in different species, but they have maintained the same overall layout. Scientists call these synonymous parts homologous structures.
Some structures exist in organisms that have no apparent function at all, and appear to be residual parts from a past common ancestor. These unused structures without function are called vestigial structures. Other examples of vestigial structures are wings on flightless birds, leaves on some cacti, and hind leg bones in whales.
Link to Learning
Visit this interactive site to guess which bones structures are homologous and which are analogous, and see examples of evolutionary adaptations to illustrate these concepts.
Another evidence of evolution is the convergence of form in organisms that share similar environments. For example, species of unrelated animals, such as the arctic fox and ptarmigan, living in the arctic region have been selected for seasonal white phenotypes during winter to blend with the snow and ice (Figure \(7\)). These similarities occur not because of common ancestry, but because of similar selection pressures—the benefits of not being seen by predators.
Embryology, the study of the development of the anatomy of an organism to its adult form, also provides evidence of relatedness between now widely divergent groups of organisms. Mutational tweaking in the embryo can have such magnified consequences in the adult that embryo formation tends to be conserved. As a result, structures that are absent in some groups often appear in their embryonic forms and disappear by the time the adult or juvenile form is reached. For example, all vertebrate embryos, including humans, exhibit gill slits and tails at some point in their early development. These disappear in the adults of terrestrial groups but are maintained in adult forms of aquatic groups such as fish and some amphibians. Great ape embryos, including humans, have a tail structure during their development that is lost by the time of birth.
Biogeography
The geographic distribution of organisms on the planet follows patterns that are best explained by evolution in conjunction with the movement of tectonic plates over geological time. Broad groups that evolved before the breakup of the supercontinent Pangaea (about 200 million years ago) are distributed worldwide. Groups that evolved since the breakup appear uniquely in regions of the planet, such as the unique flora and fauna of northern continents that formed from the supercontinent Laurasia and of the southern continents that formed from the supercontinent Gondwana. The presence of members of the plant family Proteaceae in Australia, southern Africa, and South America is best explained by their presence prior to the southern supercontinent Gondwana breaking up.
The great diversification of marsupials in Australia and the absence of other mammals reflect Australia’s long isolation. Australia has an abundance of endemic species—species found nowhere else—which is typical of islands whose isolation by expanses of water prevents species from migrating. Over time, these species diverge evolutionarily into new species that look very different from their ancestors that may exist on the mainland. The marsupials of Australia, the finches on the Galápagos, and many species on the Hawaiian Islands are all unique to their one point of origin, yet they display distant relationships to ancestral species on mainlands.
Molecular Biology
Like anatomical structures, the structures of the molecules of life reflect descent with modification. Evidence of a common ancestor for all of life is reflected in the universality of DNA as the genetic material and in the near universality of the genetic code and the machinery of DNA replication and expression. Fundamental divisions in life between the three domains are reflected in major structural differences in otherwise conservative structures such as the components of ribosomes and the structures of membranes. In general, the relatedness of groups of organisms is reflected in the similarity of their DNA sequences—exactly the pattern that would be expected from descent and diversification from a common ancestor.
DNA sequences have also shed light on some of the mechanisms of evolution. For example, it is clear that the evolution of new functions for proteins commonly occurs after gene duplication events that allow the free modification of one copy by mutation, selection, or drift (changes in a population’s gene pool resulting from chance), while the second copy continues to produce a functional protein.
Misconceptions of Evolution
Although the theory of evolution generated some controversy when it was first proposed, it was almost universally accepted by biologists, particularly younger biologists, within 20 years after publication of On the Origin of Species. Nevertheless, the theory of evolution is a difficult concept and misconceptions about how it works abound
Link to Learning
This site addresses some of the main misconceptions associated with the theory of evolution.
Evolution Is Just a Theory
Critics of the theory of evolution dismiss its importance by purposefully confounding the everyday usage of the word “theory” with the way scientists use the word. In science, a “theory” is understood to be a body of thoroughly tested and verified explanations for a set of observations of the natural world. Scientists have a theory of the atom, a theory of gravity, and the theory of relativity, each of which describes understood facts about the world. In the same way, the theory of evolution describes facts about the living world. As such, a theory in science has survived significant efforts to discredit it by scientists. In contrast, a “theory” in common vernacular is a word meaning a guess or suggested explanation; this meaning is more akin to the scientific concept of “hypothesis.” When critics of evolution say evolution is “just a theory,” they are implying that there is little evidence supporting it and that it is still in the process of being rigorously tested. This is a mischaracterization.
Individuals Evolve
Evolution is the change in genetic composition of a population over time, specifically over generations, resulting from differential reproduction of individuals with certain alleles. Individuals do change over their lifetime, obviously, but this is called development and involves changes programmed by the set of genes the individual acquired at birth in coordination with the individual’s environment. When thinking about the evolution of a characteristic, it is probably best to think about the change of the average value of the characteristic in the population over time. For example, when natural selection leads to bill-size change in medium-ground finches in the Galápagos, this does not mean that individual bills on the finches are changing. If one measures the average bill size among all individuals in the population at one time and then measures the average bill size in the population several years later, this average value will be different as a result of evolution. Although some individuals may survive from the first time to the second, they will still have the same bill size; however, there will be many new individuals that contribute to the shift in average bill size.
Evolution Explains the Origin of Life
It is a common misunderstanding that evolution includes an explanation of life’s origins. Conversely, some of the theory’s critics believe that it cannot explain the origin of life. The theory does not try to explain the origin of life. The theory of evolution explains how populations change over time and how life diversifies the origin of species. It does not shed light on the beginnings of life including the origins of the first cells, which is how life is defined. The mechanisms of the origin of life on Earth are a particularly difficult problem because it occurred a very long time ago, and presumably it just occurred once. Importantly, biologists believe that the presence of life on Earth precludes the possibility that the events that led to life on Earth can be repeated because the intermediate stages would immediately become food for existing living things.
However, once a mechanism of inheritance was in place in the form of a molecule like DNA either within a cell or pre-cell, these entities would be subject to the principle of natural selection. More effective reproducers would increase in frequency at the expense of inefficient reproducers. So while evolution does not explain the origin of life, it may have something to say about some of the processes operating once pre-living entities acquired certain properties.
Organisms Evolve on Purpose
Statements such as “organisms evolve in response to a change in an environment” are quite common, but such statements can lead to two types of misunderstandings. First, the statement must not be understood to mean that individual organisms evolve. The statement is shorthand for “a population evolves in response to a changing environment.” However, a second misunderstanding may arise by interpreting the statement to mean that the evolution is somehow intentional. A changed environment results in some individuals in the population, those with particular phenotypes, benefiting and therefore producing proportionately more offspring than other phenotypes. This results in change in the population if the characteristics are genetically determined.
It is also important to understand that the variation that natural selection works on is already in a population and does not arise in response to an environmental change. For example, applying antibiotics to a population of bacteria will, over time, select a population of bacteria that are resistant to antibiotics. The resistance, which is caused by a gene, did not arise by mutation because of the application of the antibiotic. The gene for resistance was already present in the gene pool of the bacteria, likely at a low frequency. The antibiotic, which kills the bacterial cells without the resistance gene, strongly selects individuals that are resistant, since these would be the only ones that survived and divided. Experiments have demonstrated that mutations for antibiotic resistance do not arise as a result of antibiotic.
In a larger sense, evolution is not goal directed. Species do not become “better” over time; they simply track their changing environment with adaptations that maximize their reproduction in a particular environment at a particular time. Evolution has no goal of making faster, bigger, more complex, or even smarter species, despite the commonness of this kind of language in popular discourse. What characteristics evolve in a species are a function of the variation present and the environment, both of which are constantly changing in a non-directional way. What trait is fit in one environment at one time may well be fatal at some point in the future. This holds equally well for a species of insect as it does the human species.
Summary
Evolution is the process of adaptation through mutation which allows more desirable characteristics to be passed to the next generation. Over time, organisms evolve more characteristics that are beneficial to their survival. For living organisms to adapt and change to environmental pressures, genetic variation must be present. With genetic variation, individuals have differences in form and function that allow some to survive certain conditions better than others. These organisms pass their favorable traits to their offspring. Eventually, environments change, and what was once a desirable, advantageous trait may become an undesirable trait and organisms may further evolve. Evolution may be convergent with similar traits evolving in multiple species or divergent with diverse traits evolving in multiple species that came from a common ancestor. Evidence of evolution can be observed by means of DNA code and the fossil record, and also by the existence of homologous and vestigial structures.
Glossary
adaptation
heritable trait or behavior in an organism that aids in its survival and reproduction in its present environment
convergent evolution
process by which groups of organisms independently evolve to similar forms
divergent evolution
process by which groups of organisms evolve in diverse directions from a common point
homologous structures
parallel structures in diverse organisms that have a common ancestor
natural selection
reproduction of individuals with favorable genetic traits that survive environmental change because of those traits, leading to evolutionary change
variation
genetic differences among individuals in a population
vestigial structure
physical structure present in an organism but that has no apparent function and appears to be from a functional structure in a distant ancestor
25.05: Ever-Changing Life on Earth
Skills to Develop
• List the unifying characteristics of eukaryotes
• Describe what scientists know about the origins of eukaryotes based on the last common ancestor
• Explain endosymbiotic theory
Living things fall into three large groups: Archaea, Bacteria, and Eukarya. The first two have prokaryotic cells, and the third contains all eukaryotes. A relatively sparse fossil record is available to help discern what the first members of each of these lineages looked like, so it is possible that all the events that led to the last common ancestor of extant eukaryotes will remain unknown. However, comparative biology of extant organisms and the limited fossil record provide some insight into the history of Eukarya.
The earliest fossils found appear to be Bacteria, most likely cyanobacteria. They are about 3.5 billion years old and are recognizable because of their relatively complex structure and, for prokaryotes, relatively large cells. Most other prokaryotes have small cells, 1 or 2 µm in size, and would be difficult to pick out as fossils. Most living eukaryotes have cells measuring 10 µm or greater. Structures this size, which might be fossils, appear in the geological record about 2.1 billion years ago.
Characteristics of Eukaryotes
Data from these fossils have led comparative biologists to the conclusion that living eukaryotes are all descendants of a single common ancestor. Mapping the characteristics found in all major groups of eukaryotes reveals that the following characteristics must have been present in the last common ancestor, because these characteristics are present in at least some of the members of each major lineage.
1. Cells with nuclei surrounded by a nuclear envelope with nuclear pores. This is the single characteristic that is both necessary and sufficient to define an organism as a eukaryote. All extant eukaryotes have cells with nuclei.
2. Mitochondria. Some extant eukaryotes have very reduced remnants of mitochondria in their cells, whereas other members of their lineages have “typical” mitochondria.
3. A cytoskeleton containing the structural and motility components called actin microfilaments and microtubules. All extant eukaryotes have these cytoskeletal elements.
4. Flagella and cilia, organelles associated with cell motility. Some extant eukaryotes lack flagella and/or cilia, but they are descended from ancestors that possessed them.
5. Chromosomes, each consisting of a linear DNA molecule coiled around basic (alkaline) proteins called histones. The few eukaryotes with chromosomes lacking histones clearly evolved from ancestors that had them.
6. Mitosis, a process of nuclear division wherein replicated chromosomes are divided and separated using elements of the cytoskeleton. Mitosis is universally present in eukaryotes.
7. Sex, a process of genetic recombination unique to eukaryotes in which diploid nuclei at one stage of the life cycle undergo meiosis to yield haploid nuclei and subsequent karyogamy, a stage where two haploid nuclei fuse together to create a diploid zygote nucleus.
8. Members of all major lineages have cell walls, and it might be reasonable to conclude that the last common ancestor could make cell walls during some stage of its life cycle. However, not enough is known about eukaryotes’ cell walls and their development to know how much homology exists among them. If the last common ancestor could make cell walls, it is clear that this ability must have been lost in many groups.
Endosymbiosis and the Evolution of Eukaryotes
In order to understand eukaryotic organisms fully, it is necessary to understand that all extant eukaryotes are descendants of a chimeric organism that was a composite of a host cell and the cell(s) of an alpha-proteobacterium that “took up residence” inside it. This major theme in the origin of eukaryotes is known as endosymbiosis, one cell engulfing another such that the engulfed cell survives and both cells benefit. Over many generations, a symbiotic relationship can result in two organisms that depend on each other so completely that neither could survive on its own. Endosymbiotic events likely contributed to the origin of the last common ancestor of today’s eukaryotes and to later diversification in certain lineages of eukaryotes (Figure \(4\)). Before explaining this further, it is necessary to consider metabolism in prokaryotes.
Prokaryotic Metabolism
Many important metabolic processes arose in prokaryotes, and some of these, such as nitrogen fixation, are never found in eukaryotes. The process of aerobic respiration is found in all major lineages of eukaryotes, and it is localized in the mitochondria. Aerobic respiration is also found in many lineages of prokaryotes, but it is not present in all of them, and many forms of evidence suggest that such anaerobic prokaryotes never carried out aerobic respiration nor did their ancestors.
While today’s atmosphere is about one-fifth molecular oxygen (O2), geological evidence shows that it originally lacked O2. Without oxygen, aerobic respiration would not be expected, and living things would have relied on fermentation instead. At some point before, about 3.5 billion years ago, some prokaryotes began using energy from sunlight to power anabolic processes that reduce carbon dioxide to form organic compounds. That is, they evolved the ability to photosynthesize. Hydrogen, derived from various sources, was captured using light-powered reactions to reduce fixed carbon dioxide in the Calvin cycle. The group of Gram-negative bacteria that gave rise to cyanobacteria used water as the hydrogen source and released O2 as a waste product.
Eventually, the amount of photosynthetic oxygen built up in some environments to levels that posed a risk to living organisms, since it can damage many organic compounds. Various metabolic processes evolved that protected organisms from oxygen, one of which, aerobic respiration, also generated high levels of ATP. It became widely present among prokaryotes, including in a group we now call alpha-proteobacteria. Organisms that did not acquire aerobic respiration had to remain in oxygen-free environments. Originally, oxygen-rich environments were likely localized around places where cyanobacteria were active, but by about 2 billion years ago, geological evidence shows that oxygen was building up to higher concentrations in the atmosphere. Oxygen levels similar to today’s levels only arose within the last 700 million years.
Recall that the first fossils that we believe to be eukaryotes date to about 2 billion years old, so they appeared as oxygen levels were increasing. Also, recall that all extant eukaryotes descended from an ancestor with mitochondria. These organelles were first observed by light microscopists in the late 1800s, where they appeared to be somewhat worm-shaped structures that seemed to be moving around in the cell. Some early observers suggested that they might be bacteria living inside host cells, but these hypotheses remained unknown or rejected in most scientific communities.
Endosymbiotic Theory
As cell biology developed in the twentieth century, it became clear that mitochondria were the organelles responsible for producing ATP using aerobic respiration. In the 1960s, American biologist Lynn Margulis developed endosymbiotic theory, which states that eukaryotes may have been a product of one cell engulfing another, one living within another, and evolving over time until the separate cells were no longer recognizable as such. In 1967, Margulis introduced new work on the theory and substantiated her findings through microbiological evidence. Although Margulis’ work initially was met with resistance, this once-revolutionary hypothesis is now widely (but not completely) accepted, with work progressing on uncovering the steps involved in this evolutionary process and the key players involved. Much still remains to be discovered about the origins of the cells that now make up the cells in all living eukaryotes.
Broadly, it has become clear that many of our nuclear genes and the molecular machinery responsible for replication and expression appear closely related to those in Archaea. On the other hand, the metabolic organelles and genes responsible for many energy-harvesting processes had their origins in bacteria. Much remains to be clarified about how this relationship occurred; this continues to be an exciting field of discovery in biology. For instance, it is not known whether the endosymbiotic event that led to mitochondria occurred before or after the host cell had a nucleus. Such organisms would be among the extinct precursors of the last common ancestor of eukaryotes.
Mitochondria
One of the major features distinguishing prokaryotes from eukaryotes is the presence of mitochondria. Eukaryotic cells may contain anywhere from one to several thousand mitochondria, depending on the cell’s level of energy consumption. Each mitochondrion measures 1 to 10 or greater micrometers in length and exists in the cell as an organelle that can be ovoid to worm-shaped to intricately branched (Figure \(1\)). Mitochondria arise from the division of existing mitochondria; they may fuse together; and they may be moved around inside the cell by interactions with the cytoskeleton. However, mitochondria cannot survive outside the cell. As the atmosphere was oxygenated by photosynthesis, and as successful aerobic prokaryotes evolved, evidence suggests that an ancestral cell with some membrane compartmentalization engulfed a free-living aerobic prokaryote, specifically an alpha-proteobacterium, thereby giving the host cell the ability to use oxygen to release energy stored in nutrients. Alpha-proteobacteria are a large group of bacteria that includes species symbiotic with plants, disease organisms that can infect humans via ticks, and many free-living species that use light for energy. Several lines of evidence support that mitochondria are derived from this endosymbiotic event. Most mitochondria are shaped like alpha-proteobacteria and are surrounded by two membranes, which would result when one membrane-bound organism was engulfed into a vacuole by another membrane-bound organism. The mitochondrial inner membrane is extensive and involves substantial infoldings called cristae that resemble the textured, outer surface of alpha-proteobacteria. The matrix and inner membrane are rich with the enzymes necessary for aerobic respiration.
Mitochondria divide independently by a process that resembles binary fission in prokaryotes. Specifically, mitochondria are not formed from scratch (de novo) by the eukaryotic cell; they reproduce within it and are distributed with the cytoplasm when a cell divides or two cells fuse. Therefore, although these organelles are highly integrated into the eukaryotic cell, they still reproduce as if they are independent organisms within the cell. However, their reproduction is synchronized with the activity and division of the cell. Mitochondria have their own (usually) circular DNA chromosome that is stabilized by attachments to the inner membrane and carries genes similar to genes expressed by alpha-proteobacteria. Mitochondria also have special ribosomes and transfer RNAs that resemble these components in prokaryotes. These features all support that mitochondria were once free-living prokaryotes.
Mitochondria that carry out aerobic respiration have their own genomes, with genes similar to those in alpha-proteobacteria. However, many of the genes for respiratory proteins are located in the nucleus. When these genes are compared to those of other organisms, they appear to be of alpha-proteobacterial origin. Additionally, in some eukaryotic groups, such genes are found in the mitochondria, whereas in other groups, they are found in the nucleus. This has been interpreted as evidence that genes have been transferred from the endosymbiont chromosome to the host genome. This loss of genes by the endosymbiont is probably one explanation why mitochondria cannot live without a host.
Some living eukaryotes are anaerobic and cannot survive in the presence of too much oxygen. Some appear to lack organelles that could be recognized as mitochondria. In the 1970s to the early 1990s, many biologists suggested that some of these eukaryotes were descended from ancestors whose lineages had diverged from the lineage of mitochondrion-containing eukaryotes before endosymbiosis occurred. However, later findings suggest that reduced organelles are found in most, if not all, anaerobic eukaryotes, and that all eukaryotes appear to carry some genes in their nuclei that are of mitochondrial origin. In addition to the aerobic generation of ATP, mitochondria have several other metabolic functions. One of these functions is to generate clusters of iron and sulfur that are important cofactors of many enzymes. Such functions are often associated with the reduced mitochondrion-derived organelles of anaerobic eukaryotes. Therefore, most biologists accept that the last common ancestor of eukaryotes had mitochondria.
Plastids
Some groups of eukaryotes are photosynthetic. Their cells contain, in addition to the standard eukaryotic organelles, another kind of organelle called a plastid. When such cells are carrying out photosynthesis, their plastids are rich in the pigment chlorophyll a and a range of other pigments, called accessory pigments, which are involved in harvesting energy from light. Photosynthetic plastids are called chloroplasts (Figure \(2\)).
Like mitochondria, plastids appear to have an endosymbiotic origin. This hypothesis was also championed by Lynn Margulis. Plastids are derived from cyanobacteria that lived inside the cells of an ancestral, aerobic, heterotrophic eukaryote. This is called primary endosymbiosis, and plastids of primary origin are surrounded by two membranes. The best evidence is that this has happened twice in the history of eukaryotes. In one case, the common ancestor of the major lineage/supergroup Archaeplastida took on a cyanobacterial endosymbiont; in the other, the ancestor of the small amoeboid rhizarian taxon, Paulinella, took on a different cyanobacterial endosymbiont. Almost all photosynthetic eukaryotes are descended from the first event, and only a couple of species are derived from the other.
Cyanobacteria are a group of Gram-negative bacteria with all the conventional structures of the group. However, unlike most prokaryotes, they have extensive, internal membrane-bound sacs called thylakoids. Chlorophyll is a component of these membranes, as are many of the proteins of the light reactions of photosynthesis. Cyanobacteria also have the peptidoglycan wall and lipopolysaccharide layer associated with Gram-negative bacteria.
Chloroplasts of primary origin have thylakoids, a circular DNA chromosome, and ribosomes similar to those of cyanobacteria. Each chloroplast is surrounded by two membranes. In the group of Archaeplastida called the glaucophytes and in Paulinella, a thin peptidoglycan layer is present between the outer and inner plastid membranes. All other plastids lack this relictual cyanobacterial wall. The outer membrane surrounding the plastid is thought to be derived from the vacuole in the host, and the inner membrane is thought to be derived from the plasma membrane of the symbiont.
There is also, as with the case of mitochondria, strong evidence that many of the genes of the endosymbiont were transferred to the nucleus. Plastids, like mitochondria, cannot live independently outside the host. In addition, like mitochondria, plastids are derived from the division of other plastids and never built from scratch. Researchers have suggested that the endosymbiotic event that led to Archaeplastida occurred 1 to 1.5 billion years ago, at least 5 hundred million years after the fossil record suggests that eukaryotes were present.
Not all plastids in eukaryotes are derived directly from primary endosymbiosis. Some of the major groups of algae became photosynthetic by secondary endosymbiosis, that is, by taking in either green algae or red algae (both from Archaeplastida) as endosymbionts (Figure \(3\)). Numerous microscopic and genetic studies have supported this conclusion. Secondary plastids are surrounded by three or more membranes, and some secondary plastids even have clear remnants of the nucleus of endosymbiotic alga. Others have not “kept” any remnants. There are cases where tertiary or higher-order endosymbiotic events are the best explanations for plastids in some eukaryotes.
Art Connection
What evidence is there that mitochondria were incorporated into the ancestral eukaryotic cell before chloroplasts?
Evolution Connection: Secondary Endosymbiosis in Chlorarachniophytes
Endosymbiosis involves one cell engulfing another to produce, over time, a coevolved relationship in which neither cell could survive alone. The chloroplasts of red and green algae, for instance, are derived from the engulfment of a photosynthetic cyanobacterium by an early prokaryote.
This leads to the question of the possibility of a cell containing an endosymbiont to itself become engulfed, resulting in a secondary endosymbiosis. Molecular and morphological evidence suggest that the chlorarachniophyte protists are derived from a secondary endosymbiotic event. Chlorarachniophytes are rare algae indigenous to tropical seas and sand that can be classified into the rhizarian supergroup. Chlorarachniophytes extend thin cytoplasmic strands, interconnecting themselves with other chlorarachniophytes, in a cytoplasmic network. These protists are thought to have originated when a eukaryote engulfed a green alga, the latter of which had already established an endosymbiotic relationship with a photosynthetic cyanobacterium (Figure \(5\)).
Several lines of evidence support that chlorarachniophytes evolved from secondary endosymbiosis. The chloroplasts contained within the green algal endosymbionts still are capable of photosynthesis, making chlorarachniophytes photosynthetic. The green algal endosymbiont also exhibits a stunted vestigial nucleus. In fact, it appears that chlorarachniophytes are the products of an evolutionarily recent secondary endosymbiotic event. The plastids of chlorarachniophytes are surrounded by four membranes: The first two correspond to the inner and outer membranes of the photosynthetic cyanobacterium, the third corresponds to the green alga, and the fourth corresponds to the vacuole that surrounded the green alga when it was engulfed by the chlorarachniophyte ancestor. In other lineages that involved secondary endosymbiosis, only three membranes can be identified around plastids. This is currently rectified as a sequential loss of a membrane during the course of evolution.
The process of secondary endosymbiosis is not unique to chlorarachniophytes. In fact, secondary endosymbiosis of green algae also led to euglenid protists, whereas secondary endosymbiosis of red algae led to the evolution of dinoflagellates, apicomplexans, and stramenopiles.
Summary
The oldest fossil evidence of eukaryotes is about 2 billion years old. Fossils older than this all appear to be prokaryotes. It is probable that today’s eukaryotes are descended from an ancestor that had a prokaryotic organization. The last common ancestor of today’s Eukarya had several characteristics, including cells with nuclei that divided mitotically and contained linear chromosomes where the DNA was associated with histones, a cytoskeleton and endomembrane system, and the ability to make cilia/flagella during at least part of its life cycle. It was aerobic because it had mitochondria that were the result of an aerobic alpha-proteobacterium that lived inside a host cell. Whether this host had a nucleus at the time of the initial symbiosis remains unknown. The last common ancestor may have had a cell wall for at least part of its life cycle, but more data are needed to confirm this hypothesis. Today’s eukaryotes are very diverse in their shapes, organization, life cycles, and number of cells per individual.
Art Connections
Figure \(4\): What evidence is there that mitochondria were incorporated into the ancestral eukaryotic cell before chloroplasts?
Answer
All eukaryotic cells have mitochondria, but not all eukaryotic cells have chloroplasts.
Glossary
endosymbiosis
engulfment of one cell within another such that the engulfed cell survives, and both cells benefit; the process responsible for the evolution of mitochondria and chloroplasts in eukaryotes
endosymbiotic theory
theory that states that eukaryotes may have been a product of one cell engulfing another, one living within another, and evolving over time until the separate cells were no longer recognizable as such
plastid
one of a group of related organelles in plant cells that are involved in the storage of starches, fats, proteins, and pigments | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/25%3A_The_Origin_and_Diversity_of_Life/25.05%3A_Ever-Changing_Life_on_Earth/25.5.01%3A_Eukaryotic_Origins.txt |
Skills to Develop
• Describe the features that characterized the earliest animals and when they appeared on earth
• Explain the significance of the Cambrian period for animal evolution and the changes in animal diversity that took place during that time
• Describe some of the unresolved questions surrounding the Cambrian explosion
• Discuss the implications of mass animal extinctions that have occurred in evolutionary history
Many questions regarding the origins and evolutionary history of the animal kingdom continue to be researched and debated, as new fossil and molecular evidence change prevailing theories. Some of these questions include the following: How long have animals existed on Earth? What were the earliest members of the animal kingdom, and what organism was their common ancestor? While animal diversity increased during the Cambrian period of the Paleozoic era, 530 million years ago, modern fossil evidence suggests that primitive animal species existed much earlier.
Pre-Cambrian Animal Life
The time before the Cambrian period is known as the Ediacaran period (from about 635 million years ago to 543 million years ago), the final period of the late Proterozoic Neoproterozoic Era (Figure \(1\)). It is believed that early animal life, termed Ediacaran biota, evolved from protists at this time. Some protest species called choanoflagellates closely resemble the choanocyte cells in the simplest animals, sponges. In addition to their morphological similarity, molecular analyses have revealed similar sequence homologies in their DNA.
The earliest life comprising Ediacaran biota was long believed to include only tiny, sessile, soft-bodied sea creatures. However, recently there has been increasing scientific evidence suggesting that more varied and complex animal species lived during this time, and possibly even before the Ediacaran period.
Fossils believed to represent the oldest animals with hard body parts were recently discovered in South Australia. These sponge-like fossils, named Coronacollina acula, date back as far as 560 million years, and are believed to show the existence of hard body parts and spicules that extended 20–40 cm from the main body (estimated about 5 cm long). Other fossils from the Ediacaran period are shown in Figure \(2\).
Another recent fossil discovery may represent the earliest animal species ever found. While the validity of this claim is still under investigation, these primitive fossils appear to be small, one-centimeter long, sponge-like creatures. These fossils from South Australia date back 650 million years, actually placing the putative animal before the great ice age extinction event that marked the transition between the Cryogenian period and the Ediacaran period. Until this discovery, most scientists believed that there was no animal life prior to the Ediacaran period. Many scientists now believe that animals may in fact have evolved during the Cryogenian period.
The Cambrian Explosion of Animal Life
The Cambrian period, occurring between approximately 542–488 million years ago, marks the most rapid evolution of new animal phyla and animal diversity in Earth’s history. It is believed that most of the animal phyla in existence today had their origins during this time, often referred to as the Cambrian explosion (Figure 27.4.3). Echinoderms, mollusks, worms, arthropods, and chordates arose during this period. One of the most dominant species during the Cambrian period was the trilobite, an arthropod that was among the first animals to exhibit a sense of vision (Figure \(4\)).
The cause of the Cambrian explosion is still debated. There are many theories that attempt to answer this question. Environmental changes may have created a more suitable environment for animal life. Examples of these changes include rising atmospheric oxygen levels and large increases in oceanic calcium concentrations that preceded the Cambrian period (Figure \(5\)). Some scientists believe that an expansive, continental shelf with numerous shallow lagoons or pools provided the necessary living space for larger numbers of different types of animals to co-exist. There is also support for theories that argue that ecological relationships between species, such as changes in the food web, competition for food and space, and predator-prey relationships, were primed to promote a sudden massive coevolution of species. Yet other theories claim genetic and developmental reasons for the Cambrian explosion. The morphological flexibility and complexity of animal development afforded by the evolution of Hox control genes may have provided the necessary opportunities for increases in possible animal morphologies at the time of the Cambrian period. Theories that attempt to explain why the Cambrian explosion happened must be able to provide valid reasons for the massive animal diversification, as well as explain why it happened when it did. There is evidence that both supports and refutes each of the theories described above, and the answer may very well be a combination of these and other theories.
However, unresolved questions about the animal diversification that took place during the Cambrian period remain. For example, we do not understand how the evolution of so many species occurred in such a short period of time. Was there really an “explosion” of life at this particular time? Some scientists question the validity of the this idea, because there is increasing evidence to suggest that more animal life existed prior to the Cambrian period and that other similar species’ so-called explosions (or radiations) occurred later in history as well. Furthermore, the vast diversification of animal species that appears to have begun during the Cambrian period continued well into the following Ordovician period. Despite some of these arguments, most scientists agree that the Cambrian period marked a time of impressively rapid animal evolution and diversification that is unmatched elsewhere during history.
Link to Learning
View an animation of what ocean life may have been like during the Cambrian explosion.
Post-Cambrian Evolution and Mass Extinctions
The periods that followed the Cambrian during the Paleozoic Era are marked by further animal evolution and the emergence of many new orders, families, and species. As animal phyla continued to diversify, new species adapted to new ecological niches. During the Ordovician period, which followed the Cambrian period, plant life first appeared on land. This change allowed formerly aquatic animal species to invade land, feeding directly on plants or decaying vegetation. Continual changes in temperature and moisture throughout the remainder of the Paleozoic Era due to continental plate movements encouraged the development of new adaptations to terrestrial existence in animals, such as limbed appendages in amphibians and epidermal scales in reptiles.
Changes in the environment often create new niches (living spaces) that contribute to rapid speciation and increased diversity. On the other hand, cataclysmic events, such as volcanic eruptions and meteor strikes that obliterate life, can result in devastating losses of diversity. Such periods of mass extinction (Figure \(6\)) have occurred repeatedly in the evolutionary record of life, erasing some genetic lines while creating room for others to evolve into the empty niches left behind. The end of the Permian period (and the Paleozoic Era) was marked by the largest mass extinction event in Earth’s history, a loss of roughly 95 percent of the extant species at that time. Some of the dominant phyla in the world’s oceans, such as the trilobites, disappeared completely. On land, the disappearance of some dominant species of Permian reptiles made it possible for a new line of reptiles to emerge, the dinosaurs. The warm and stable climatic conditions of the ensuing Mesozoic Era promoted an explosive diversification of dinosaurs into every conceivable niche in land, air, and water. Plants, too, radiated into new landscapes and empty niches, creating complex communities of producers and consumers, some of which became very large on the abundant food available.
Another mass extinction event occurred at the end of the Cretaceous period, bringing the Mesozoic Era to an end. Skies darkened and temperatures fell as a large meteor impact and tons of volcanic ash blocked incoming sunlight. Plants died, herbivores and carnivores starved, and the mostly cold-blooded dinosaurs ceded their dominance of the landscape to more warm-blooded mammals. In the following Cenozoic Era, mammals radiated into terrestrial and aquatic niches once occupied by dinosaurs, and birds, the warm-blooded offshoots of one line of the ruling reptiles, became aerial specialists. The appearance and dominance of flowering plants in the Cenozoic Era created new niches for insects, as well as for birds and mammals. Changes in animal species diversity during the late Cretaceous and early Cenozoic were also promoted by a dramatic shift in Earth’s geography, as continental plates slid over the crust into their current positions, leaving some animal groups isolated on islands and continents, or separated by mountain ranges or inland seas from other competitors. Early in the Cenozoic, new ecosystems appeared, with the evolution of grasses and coral reefs. Late in the Cenozoic, further extinctions followed by speciation occurred during ice ages that covered high latitudes with ice and then retreated, leaving new open spaces for colonization.
Link to Learning
Watch the following video to learn more about the mass extinctions.
Career Connection: Paleontologist
Natural history museums contain the fossil casts of extinct animals and information about how these animals evolved, lived, and died. Paleontogists are scientists who study prehistoric life. They use fossils to observe and explain how life evolved on Earth and how species interacted with each other and with the environment. A paleontologist needs to be knowledgeable in biology, ecology, chemistry, geology, and many other scientific disciplines. A paleontologist’s work may involve field studies: searching for and studying fossils. In addition to digging for and finding fossils, paleontologists also prepare fossils for further study and analysis. Although dinosaurs are probably the first animals that come to mind when thinking about paleontology, paleontologists study everything from plant life, fungi, and fish to sea animals and birds.
An undergraduate degree in earth science or biology is a good place to start toward the career path of becoming a paleontologist. Most often, a graduate degree is necessary. Additionally, work experience in a museum or in a paleontology lab is useful.
Summary
The most rapid diversification and evolution of animal species in all of history occurred during the Cambrian period of the Paleozoic Era, a phenomenon known as the Cambrian explosion. Until recently, scientists believed that there were only very few tiny and simplistic animal species in existence before this period. However, recent fossil discoveries have revealed that additional, larger, and more complex animals existed during the Ediacaran period, and even possibly earlier, during the Cryogenian period. Still, the Cambrian period undoubtedly witnessed the emergence of the majority of animal phyla that we know today, although many questions remain unresolved about this historical phenomenon.
The remainder of the Paleozoic Era is marked by the growing appearance of new classes, families, and species, and the early colonization of land by certain marine animals. The evolutionary history of animals is also marked by numerous major extinction events, each of which wiped out a majority of extant species. Some species of most animal phyla survived these extinctions, allowing the phyla to persist and continue to evolve into species that we see today.
Glossary
Cambrian explosion
time during the Cambrian period (542–488 million years ago) when most of the animal phyla in existence today evolved
Cryogenian period
geologic period (850–630 million years ago) characterized by a very cold global climate
Ediacaran period
geological period (630–542 million years ago) when the oldest definite multicellular organisms with tissues evolved
mass extinction
event that wipes out the majority of species within a relatively short geological time period | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/25%3A_The_Origin_and_Diversity_of_Life/25.05%3A_Ever-Changing_Life_on_Earth/25.5.02%3A_The_Evolutionary_History_of_the_Animal_Kingdom.txt |
Skills to Develop
• Describe how viruses were first discovered and how they are detected
• Discuss three hypotheses about how viruses evolved
• Recognize the basic shapes of viruses
• Understand past and emerging classification systems for viruses
Viruses are diverse entities. They vary in their structure, their replication methods, and in their target hosts. Nearly all forms of life—from bacteria and archaea to eukaryotes such as plants, animals, and fungi—have viruses that infect them. While most biological diversity can be understood through evolutionary history, such as how species have adapted to conditions and environments, much about virus origins and evolution remains unknown.
Discovery and Detection
Viruses were first discovered after the development of a porcelain filter, called the Chamberland-Pasteur filter, which could remove all bacteria visible in the microscope from any liquid sample. In 1886, Adolph Meyer demonstrated that a disease of tobacco plants, tobacco mosaic disease, could be transferred from a diseased plant to a healthy one via liquid plant extracts. In 1892, Dmitri Ivanowski showed that this disease could be transmitted in this way even after the Chamberland-Pasteur filter had removed all viable bacteria from the extract. Still, it was many years before it was proven that these “filterable” infectious agents were not simply very small bacteria but were a new type of very small, disease-causing particle.
Virions, single virus particles, are very small, about 20–250 nanometers in diameter. These individual virus particles are the infectious form of a virus outside the host cell. Unlike bacteria (which are about 100-times larger), we cannot see viruses with a light microscope, with the exception of some large virions of the poxvirus family. It was not until the development of the electron microscope in the late 1930s that scientists got their first good view of the structure of the tobacco mosaic virus (TMV) (Figure \(1\)) and other viruses (Figure \(1\)). The surface structure of virions can be observed by both scanning and transmission electron microscopy, whereas the internal structures of the virus can only be observed in images from a transmission electron microscope. The use of these technologies has allowed for the discovery of many viruses of all types of living organisms. They were initially grouped by shared morphology. Later, groups of viruses were classified by the type of nucleic acid they contained, DNA or RNA, and whether their nucleic acid was single- or double-stranded. More recently, molecular analysis of viral replicative cycles has further refined their classification.
Evolution of Viruses
Although biologists have accumulated a significant amount of knowledge about how present-day viruses evolve, much less is known about how viruses originated in the first place. When exploring the evolutionary history of most organisms, scientists can look at fossil records and similar historic evidence. However, viruses do not fossilize, so researchers must conjecture by investigating how today’s viruses evolve and by using biochemical and genetic information to create speculative virus histories.
While most findings agree that viruses don’t have a single common ancestor, scholars have yet to find a single hypothesis about virus origins that is fully accepted in the field. One such hypothesis, called devolution or the regressive hypothesis, proposes to explain the origin of viruses by suggesting that viruses evolved from free-living cells. However, many components of how this process might have occurred are a mystery. A second hypothesis (called escapist or the progressive hypothesis) accounts for viruses having either an RNA or a DNA genome and suggests that viruses originated from RNA and DNA molecules that escaped from a host cell. A third hypothesis posits a system of self-replication similar to that of other self-replicating molecules, likely evolving alongside the cells they rely on as hosts; studies of some plant pathogens support this hypothesis.
As technology advances, scientists may develop and refine further hypotheses to explain the origin of viruses. The emerging field called virus molecular systematics attempts to do just that through comparisons of sequenced genetic material. These researchers hope to one day better understand the origin of viruses, a discovery that could lead to advances in the treatments for the ailments they produce.
Viral Morphology
Viruses are acellular, meaning they are biological entities that do not have a cellular structure. They therefore lack most of the components of cells, such as organelles, ribosomes, and the plasma membrane. A virion consists of a nucleic acid core, an outer protein coating or capsid, and sometimes an outer envelope made of protein and phospholipid membranes derived from the host cell. Viruses may also contain additional proteins, such as enzymes. The most obvious difference between members of viral families is their morphology, which is quite diverse. An interesting feature of viral complexity is that the complexity of the host does not correlate with the complexity of the virion. Some of the most complex virion structures are observed in bacteriophages, viruses that infect the simplest living organisms, bacteria.
Morphology
Viruses come in many shapes and sizes, but these are consistent and distinct for each viral family. All virions have a nucleic acid genome covered by a protective layer of proteins, called a capsid. The capsid is made up of protein subunits called capsomeres. Some viral capsids are simple polyhedral “spheres,” whereas others are quite complex in structure.
In general, the shapes of viruses are classified into four groups: filamentous, isometric (or icosahedral), enveloped, and head and tail. Filamentous viruses are long and cylindrical. Many plant viruses are filamentous, including TMV. Isometric viruses have shapes that are roughly spherical, such as poliovirus or herpesviruses. Enveloped viruses have membranes surrounding capsids. Animal viruses, such as HIV, are frequently enveloped. Head and tail viruses infect bacteria and have a head that is similar to icosahedral viruses and a tail shape like filamentous viruses.
Many viruses use some sort of glycoprotein to attach to their host cells via molecules on the cell called viral receptors (Figure \(2\)). For these viruses, attachment is a requirement for later penetration of the cell membrane, so they can complete their replication inside the cell. The receptors that viruses use are molecules that are normally found on cell surfaces and have their own physiological functions. Viruses have simply evolved to make use of these molecules for their own replication. For example, HIV uses the CD4 molecule on T lymphocytes as one of its receptors. CD4 is a type of molecule called a cell adhesion molecule, which functions to keep different types of immune cells in close proximity to each other during the generation of a T lymphocyte immune response.
Among the most complex virions known, the T4 bacteriophage, which infects the Escherichia coli bacterium, has a tail structure that the virus uses to attach to host cells and a head structure that houses its DNA.
Adenovirus, a non-enveloped animal virus that causes respiratory illnesses in humans, uses glycoprotein spikes protruding from its capsomeres to attach to host cells. Non-enveloped viruses also include those that cause polio (poliovirus), plantar warts (papillomavirus), and hepatitis A (hepatitis A virus).
Enveloped virions like HIV, the causative agent in AIDS, consist of nucleic acid (RNA in the case of HIV) and capsid proteins surrounded by a phospholipid bilayer envelope and its associated proteins. Glycoproteins embedded in the viral envelope are used to attach to host cells. Other envelope proteins are the matrix proteins that stabilize the envelope and often play a role in the assembly of progeny virions. Chicken pox, influenza, and mumps are examples of diseases caused by viruses with envelopes. Because of the fragility of the envelope, non-enveloped viruses are more resistant to changes in temperature, pH, and some disinfectants than enveloped viruses.
Overall, the shape of the virion and the presence or absence of an envelope tell us little about what disease the virus may cause or what species it might infect, but they are still useful means to begin viral classification (Figure \(3\)).
Exercise \(1\)
Which of the following statements about virus structure is true?
1. All viruses are encased in a viral membrane.
2. The capsomere is made up of small protein subunits called capsids.
3. DNA is the genetic material in all viruses.
4. Glycoproteins help the virus attach to the host cell.
Answer
D
Types of Nucleic Acid
Unlike nearly all living organisms that use DNA as their genetic material, viruses may use either DNA or RNA as theirs. The virus core contains the genome or total genetic content of the virus. Viral genomes tend to be small, containing only those genes that encode proteins that the virus cannot get from the host cell. This genetic material may be single- or double-stranded. It may also be linear or circular. While most viruses contain a single nucleic acid, others have genomes that have several, which are called segments.
In DNA viruses, the viral DNA directs the host cell’s replication proteins to synthesize new copies of the viral genome and to transcribe and translate that genome into viral proteins. DNA viruses cause human diseases, such as chickenpox, hepatitis B, and some venereal diseases, like herpes and genital warts.
RNA viruses contain only RNA as their genetic material. To replicate their genomes in the host cell, the RNA viruses encode enzymes that can replicate RNA into DNA, which cannot be done by the host cell. These RNA polymerase enzymes are more likely to make copying errors than DNA polymerases, and therefore often make mistakes during transcription. For this reason, mutations in RNA viruses occur more frequently than in DNA viruses. This causes them to change and adapt more rapidly to their host. Human diseases caused by RNA viruses include hepatitis C, measles, and rabies.
Virus Classification
To understand the features shared among different groups of viruses, a classification scheme is necessary. As most viruses are not thought to have evolved from a common ancestor, however, the methods that scientists use to classify living things are not very useful. Biologists have used several classification systems in the past, based on the morphology and genetics of the different viruses. However, these earlier classification methods grouped viruses differently, based on which features of the virus they were using to classify them. The most commonly used classification method today is called the Baltimore classification scheme and is based on how messenger RNA (mRNA) is generated in each particular type of virus.
Past Systems of Classification
Viruses are classified in several ways: by factors such as their core content (Table \(1\) and Figure \(2\)), the structure of their capsids, and whether they have an outer envelope. The type of genetic material (DNA or RNA) and its structure (single- or double-stranded, linear or circular, and segmented or non-segmented) are used to classify the virus core structures.
Table \(1\): Virus Classification by Genome Structure and Core
Core Classifications Examples
• RNA
• DNA
• Rabies virus, retroviruses
• Herpesviruses, smallpox virus
• Single-stranded
• Double-stranded
• Rabies virus, retroviruses
• Herpesviruses, smallpox virus
• Linear
• Circular
• Rabies virus, retroviruses, herpesviruses, smallpox virus
• Papillomaviruses, many bacteriophages
• Non-segmented: genome consists of a single segment of genetic material
• Segmented: genome is divided into multiple segments
• Parainfluenza viruses
• Influenza viruses
Viruses can also be classified by the design of their capsids (Figure \(3\) and Figure \(4\)). Capsids are classified as naked icosahedral, enveloped icosahedral, enveloped helical, naked helical, and complex (Figure \(5\) and Figure \(6\)). The type of genetic material (DNA or RNA) and its structure (single- or double-stranded, linear or circular, and segmented or non-segmented) are used to classify the virus core structures (Table \(2\)).
Table \(2\): Virus Classification by Capsid Structure
Capsid Classification Examples
Naked icosahedral Hepatitis A virus, polioviruses
Enveloped icosahedral Epstein-Barr virus, herpes simplex virus, rubella virus, yellow fever virus, HIV-1
Enveloped helical Influenza viruses, mumps virus, measles virus, rabies virus
Naked helical Tobacco mosaic virus
Complex with many proteins; some have combinations of icosahedral and helical capsid structures Herpesviruses, smallpox virus, hepatitis B virus, T4 bacteriophage
Baltimore Classification
The most commonly used system of virus classification was developed by Nobel Prize-winning biologist David Baltimore in the early 1970s. In addition to the differences in morphology and genetics mentioned above, the Baltimore classification scheme groups viruses according to how the mRNA is produced during the replicative cycle of the virus.
Group I viruses contain double-stranded DNA (dsDNA) as their genome. Their mRNA is produced by transcription in much the same way as with cellular DNA. Group II viruses have single-stranded DNA (ssDNA) as their genome. They convert their single-stranded genomes into a dsDNA intermediate before transcription to mRNA can occur. Group III viruses use dsRNA as their genome. The strands separate, and one of them is used as a template for the generation of mRNA using the RNA-dependent RNA polymerase encoded by the virus. Group IV viruses have ssRNA as their genome with a positive polarity. Positive polarity means that the genomic RNA can serve directly as mRNA. Intermediates of dsRNA, called replicative intermediates, are made in the process of copying the genomic RNA. Multiple, full-length RNA strands of negative polarity (complimentary to the positive-stranded genomic RNA) are formed from these intermediates, which may then serve as templates for the production of RNA with positive polarity, including both full-length genomic RNA and shorter viral mRNAs. Group V viruses contain ssRNA genomes with a negative polarity, meaning that their sequence is complementary to the mRNA. As with Group IV viruses, dsRNA intermediates are used to make copies of the genome and produce mRNA. In this case, the negative-stranded genome can be converted directly to mRNA. Additionally, full-length positive RNA strands are made to serve as templates for the production of the negative-stranded genome. Group VI viruses have diploid (two copies) ssRNA genomes that must be converted, using the enzyme reverse transcriptase, to dsDNA; the dsDNA is then transported to the nucleus of the host cell and inserted into the host genome. Then, mRNA can be produced by transcription of the viral DNA that was integrated into the host genome. Group VII viruses have partial dsDNA genomes and make ssRNA intermediates that act as mRNA, but are also converted back into dsDNA genomes by reverse transcriptase, necessary for genome replication. The characteristics of each group in the Baltimore classification are summarized in the Table \(3\) with examples of each group.
Table \(3\): Baltimore Classification
Group Characteristics Mode of mRNA Production Example
I Double-stranded DNA mRNA is transcribed directly from the DNA template Herpes simplex (herpesvirus)
II Single-stranded DNA DNA is converted to double-stranded form before RNA is transcribed Canine parvovirus (parvovirus)
III Double-stranded RNA mRNA is transcribed from the RNA genome Childhood gastroenteritis (rotavirus)
IV Single stranded RNA (+) Genome functions as mRNA Common cold (pircornavirus)
V Single stranded RNA (-) mRNA is transcribed from the RNA genome Rabies (rhabdovirus)
VI Single stranded RNA viruses with reverse transcriptase Reverse transcriptase makes DNA from the RNA genome; DNA is then incorporated in the host genome; mRNA is transcribed from the incorporated DNA Human immunodeficiency virus (HIV)
VII Double stranded DNA viruses with reverse transcriptase The viral genome is double-stranded DNA, but viral DNA is replicated through an RNA intermediate; the RNA may serve directly as mRNA or as a template to make mRNA Hepatitis B virus (hepadnavirus)
Summary
Viruses are tiny, acellular entities that can usually only be seen with an electron microscope. Their genomes contain either DNA or RNA—never both—and they replicate using the replication proteins of a host cell. Viruses are diverse, infecting archaea, bacteria, fungi, plants, and animals. Viruses consist of a nucleic acid core surrounded by a protein capsid with or without an outer lipid envelope. The capsid shape, presence of an envelope, and core composition dictate some elements of the classification of viruses. The most commonly used classification method, the Baltimore classification, categorizes viruses based on how they produce their mRNA.
Glossary
acellular
lacking cells
capsid
protein coating of the viral core
capsomere
protein subunit that makes up the capsid
envelope
lipid bilayer that envelopes some viruses
group I virus
virus with a dsDNA genome
group II virus
virus with a ssDNA genome
group III virus
virus with a dsRNA genome
group IV virus
virus with a ssRNA genome with positive polarity
group V virus
virus with a ssRNA genome with negative polarity
group VI virus
virus with a ssRNA genomes converted into dsDNA by reverse transcriptase
group VII virus
virus with a single-stranded mRNA converted into dsDNA for genome replication
matrix protein
envelope protein that stabilizes the envelope and often plays a role in the assembly of progeny virions
negative polarity
ssRNA viruses with genomes complimentary to their mRNA
positive polarity
ssRNA virus with a genome that contains the same base sequences and codons found in their mRNA
replicative intermediate
dsRNA intermediate made in the process of copying genomic RNA
reverse transcriptase
enzyme found in Baltimore groups VI and VII that converts single-stranded RNA into double-stranded DNA
viral receptor
glycoprotein used to attach a virus to host cells via molecules on the cell
virion
individual virus particle outside a host cell
virus core
contains the virus genome
26.01: The Nature of Viruses
Skills to Develop
• List the steps of replication and explain what occurs at each step
• Describe the lytic and lysogenic cycles of virus replication
• Explain the transmission and diseases of animal and plant viruses
• Discuss the economic impact of animal and plant viruses
Viruses can be seen as obligate, intracellular parasites. A virus must attach to a living cell, be taken inside, manufacture its proteins and copy its genome, and find a way to escape the cell so that the virus can infect other cells. Viruses can infect only certain species of hosts and only certain cells within that host. Cells that a virus may use to replicate are called permissive. For most viruses, the molecular basis for this specificity is that a particular surface molecule known as the viral receptor must be found on the host cell surface for the virus to attach. Also, metabolic and host cell immune response differences seen in different cell types based on differential gene expression are a likely factor in which cells a virus may target for replication. The permissive cell must make the substances that the virus needs or the virus will not be able to replicate there.
Steps of Virus Infections
A virus must use cell processes to replicate. The viral replication cycle can produce dramatic biochemical and structural changes in the host cell, which may cause cell damage. These changes, called cytopathic (causing cell damage) effects, can change cell functions or even destroy the cell. Some infected cells, such as those infected by the common cold virus known as rhinovirus, die through lysis (bursting) or apoptosis (programmed cell death or “cell suicide”), releasing all progeny virions at once. The symptoms of viral diseases result from the immune response to the virus, which attempts to control and eliminate the virus from the body, and from cell damage caused by the virus. Many animal viruses, such as HIV (human immunodeficiency virus), leave the infected cells of the immune system by a process known as budding, where virions leave the cell individually. During the budding process, the cell does not undergo lysis and is not immediately killed. However, the damage to the cells that the virus infects may make it impossible for the cells to function normally, even though the cells remain alive for a period of time. Most productive viral infections follow similar steps in the virus replication cycle: attachment, penetration, uncoating, replication, assembly, and release (Figure \(1\)).
Attachment
A virus attaches to a specific receptor site on the host cell membrane through attachment proteins in the capsid or via glycoproteins embedded in the viral envelope. The specificity of this interaction determines the host—and the cells within the host—that can be infected by a particular virus. This can be illustrated by thinking of several keys and several locks, where each key will fit only one specific lock.
Entry
The nucleic acid of bacteriophages enters the host cell naked, leaving the capsid outside the cell. Plant and animal viruses can enter through endocytosis, in which the cell membrane surrounds and engulfs the entire virus. Some enveloped viruses enter the cell when the viral envelope fuses directly with the cell membrane. Once inside the cell, the viral capsid is degraded, and the viral nucleic acid is released, which then becomes available for replication and transcription.
Replication and Assembly
The replication mechanism depends on the viral genome. DNA viruses usually use host cell proteins and enzymes to make additional DNA that is transcribed to messenger RNA (mRNA), which is then used to direct protein synthesis. RNA viruses usually use the RNA core as a template for synthesis of viral genomic RNA and mRNA. The viral mRNA directs the host cell to synthesize viral enzymes and capsid proteins, and assemble new virions. Of course, there are exceptions to this pattern. If a host cell does not provide the enzymes necessary for viral replication, viral genes supply the information to direct synthesis of the missing proteins. Retroviruses, such as HIV, have an RNA genome that must be reverse transcribed into DNA, which then is incorporated into the host cell genome. They are within group VI of the Baltimore classification scheme. To convert RNA into DNA, retroviruses must contain genes that encode the virus-specific enzyme reverse transcriptase that transcribes an RNA template to DNA. Reverse transcription never occurs in uninfected host cells—the needed enzyme reverse transcriptase is only derived from the expression of viral genes within the infected host cells. The fact that HIV produces some of its own enzymes not found in the host has allowed researchers to develop drugs that inhibit these enzymes. These drugs, including the reverse transcriptase inhibitor AZT, inhibit HIV replication by reducing the activity of the enzyme without affecting the host’s metabolism. This approach has led to the development of a variety of drugs used to treat HIV and has been effective at reducing the number of infectious virions (copies of viral RNA) in the blood to non-detectable levels in many HIV-infected individuals.
Egress
The last stage of viral replication is the release of the new virions produced in the host organism, where they are able to infect adjacent cells and repeat the replication cycle. As you’ve learned, some viruses are released when the host cell dies, and other viruses can leave infected cells by budding through the membrane without directly killing the cell.
Exercise \(1\)
Influenza virus is packaged in a viral envelope that fuses with the plasma membrane. This way, the virus can exit the host cell without killing it. What advantage does the virus gain by keeping the host cell alive?
Answer
The host cell can continue to make new virus particles.
Link to Learning
Watch a video on viruses, identifying structures, modes of transmission, replication, and more.
Different Hosts and Their Viruses
As you’ve learned, viruses are often very specific as to which hosts and which cells within the host they will infect. This feature of a virus makes it specific to one or a few species of life on Earth. On the other hand, so many different types of viruses exist on Earth that nearly every living organism has its own set of viruses that tries to infect its cells. Even the smallest and simplest of cells, prokaryotic bacteria, may be attacked by specific types of viruses.
Bacteriophages
Bacteriophages are viruses that infect bacteria (Figure \(2\)). When infection of a cell by a bacteriophage results in the production of new virions, the infection is said to be productive. If the virions are released by bursting the cell, the virus replicates by means of a lytic cycle (Figure \(3\)).
An example of a lytic bacteriophage is T4, which infects Escherichia coli found in the human intestinal tract. Sometimes, however, a virus can remain within the cell without being released. For example, when a temperate bacteriophage infects a bacterial cell, it replicates by means of a lysogenic cycle (Figure \(3\)), and the viral genome is incorporated into the genome of the host cell. When the phage DNA is incorporated into the host cell genome, it is called a prophage. An example of a lysogenic bacteriophage is the λ (lambda) virus, which also infects the E. coli bacterium. Viruses that infect plant or animal cells may also undergo infections where they are not producing virions for long periods. An example is the animal herpesviruses, including herpes simplex viruses, the cause of oral and genital herpes in humans. In a process called latency, these viruses can exist in nervous tissue for long periods of time without producing new virions, only to leave latency periodically and cause lesions in the skin where the virus replicates. Even though there are similarities between lysogeny and latency, the term lysogenic cycle is usually reserved to describe bacteriophages. Latency will be described in more detail below.
Exercise \(2\)
Which of the following statements is false?
1. In the lytic cycle, new phage are produced and released into the environment.
2. In the lysogenic cycle, phage DNA is incorporated into the host genome.
3. An environmental stressor can cause the phage to initiate the lysogenic cycle.
4. Cell lysis only occurs in the lytic cycle.
Answer
C
Animal Viruses
Animal viruses, unlike the viruses of plants and bacteria, do not have to penetrate a cell wall to gain access to the host cell. Non-enveloped or “naked” animal viruses may enter cells in two different ways. As a protein in the viral capsid binds to its receptor on the host cell, the virus may be taken inside the cell via a vesicle during the normal cell process of receptor-mediated endocytosis. An alternative method of cell penetration used by non-enveloped viruses is for capsid proteins to undergo shape changes after binding to the receptor, creating channels in the host cell membrane. The viral genome is then “injected” into the host cell through these channels in a manner analogous to that used by many bacteriophages. Enveloped viruses also have two ways of entering cells after binding to their receptors: receptor-mediated endocytosis, or fusion. Many enveloped viruses enter the cell by receptor-mediated endocytosis in a fashion similar to some non-enveloped viruses. On the other hand, fusion only occurs with enveloped virions. These viruses, which include HIV among others, use special fusion proteins in their envelopes to cause the envelope to fuse with the plasma membrane of the cell, thus releasing the genome and capsid of the virus into the cell cytoplasm.
After making their proteins and copying their genomes, animal viruses complete the assembly of new virions and exit the cell. As we have already discussed using the example of HIV, enveloped animal viruses may bud from the cell membrane as they assemble themselves, taking a piece of the cell’s plasma membrane in the process. On the other hand, non-enveloped viral progeny, such as rhinoviruses, accumulate in infected cells until there is a signal for lysis or apoptosis, and all virions are released together.
As you will learn in the next module, animal viruses are associated with a variety of human diseases. Some of them follow the classic pattern of acute disease, where symptoms get increasingly worse for a short period followed by the elimination of the virus from the body by the immune system and eventual recovery from the infection. Examples of acute viral diseases are the common cold and influenza. Other viruses cause long-term chronic infections, such as the virus causing hepatitis C, whereas others, like herpes simplex virus, only cause intermittent symptoms. Still other viruses, such as human herpesviruses 6 and 7, which in some cases can cause the minor childhood disease roseola, often successfully cause productive infections without causing any symptoms at all in the host, and thus we say these patients have an asymptomatic infection.
In hepatitis C infections, the virus grows and reproduces in liver cells, causing low levels of liver damage. The damage is so low that infected individuals are often unaware that they are infected, and many infections are detected only by routine blood work on patients with risk factors such as intravenous drug use. On the other hand, since many of the symptoms of viral diseases are caused by immune responses, a lack of symptoms is an indication of a weak immune response to the virus. This allows for the virus to escape elimination by the immune system and persist in individuals for years, all the while producing low levels of progeny virions in what is known as a chronic viral disease. Chronic infection of the liver by this virus leads to a much greater chance of developing liver cancer, sometimes as much as 30 years after the initial infection.
As already discussed, herpes simplex virus can remain in a state of latency in nervous tissue for months, even years. As the virus “hides” in the tissue and makes few if any viral proteins, there is nothing for the immune response to act against, and immunity to the virus slowly declines. Under certain conditions, including various types of physical and psychological stress, the latent herpes simplex virus may be reactivated and undergo a lytic replication cycle in the skin, causing the lesions associated with the disease. Once virions are produced in the skin and viral proteins are synthesized, the immune response is again stimulated and resolves the skin lesions in a few days by destroying viruses in the skin. As a result of this type of replicative cycle, appearances of cold sores and genital herpes outbreaks only occur intermittently, even though the viruses remain in the nervous tissue for life. Latent infections are common with other herpesviruses as well, including the varicella-zoster virus that causes chickenpox. After having a chickenpox infection in childhood, the varicella-zoster virus can remain latent for many years and reactivate in adults to cause the painful condition known as “shingles” (Figure \(4\)).
Some animal-infecting viruses, including the hepatitis C virus discussed above, are known as oncogenic viruses: They have the ability to cause cancer. These viruses interfere with the normal regulation of the host cell cycle either by either introducing genes that stimulate unregulated cell growth (oncogenes) or by interfering with the expression of genes that inhibit cell growth. Oncogenic viruses can be either DNA or RNA viruses. Cancers known to be associated with viral infections include cervical cancer caused by human papillomavirus (HPV) (Figure \(5\)), liver cancer caused by hepatitis B virus, T-cell leukemia, and several types of lymphoma.
Link to Learning
Visit the interactive animations showing the various stages of the replicative cycles of animal viruses and click on the flash animation links.
Plant Viruses
Plant viruses, like other viruses, contain a core of either DNA or RNA. You have already learned about one of these, the tobacco mosaic virus. As plant viruses have a cell wall to protect their cells, these viruses do not use receptor-mediated endocytosis to enter host cells as is seen with animal viruses. For many plant viruses to be transferred from plant to plant, damage to some of the plants’ cells must occur to allow the virus to enter a new host. This damage is often caused by weather, insects, animals, fire, or human activities like farming or landscaping. Additionally, plant offspring may inherit viral diseases from parent plants. Plant viruses can be transmitted by a variety of vectors, through contact with an infected plant’s sap, by living organisms such as insects and nematodes, and through pollen. When plants viruses are transferred between different plants, this is known as horizontal transmission, and when they are inherited from a parent, this is called vertical transmission.
Symptoms of viral diseases vary according to the virus and its host (Table \(1\)). One common symptom is hyperplasia, the abnormal proliferation of cells that causes the appearance of plant tumors known as galls. Other viruses induce hypoplasia, or decreased cell growth, in the leaves of plants, causing thin, yellow areas to appear. Still other viruses affect the plant by directly killing plant cells, a process known as cell necrosis. Other symptoms of plant viruses include malformed leaves, black streaks on the stems of the plants, altered growth of stems, leaves, or fruits, and ring spots, which are circular or linear areas of discoloration found in a leaf.
Table \(1\): Some Common Symptoms of Plant Viral Diseases
Symptom Appears as
Hyperplasia Galls (tumors)
Hypoplasia Thinned, yellow splotches on leaves
Cell necrosis Dead, blackened stems, leaves, or fruit
Abnormal growth patterns Malformed stems, leaves, or fruit
Discoloration Yellow, red, or black lines, or rings in stems, leaves, or fruit
Plant viruses can seriously disrupt crop growth and development, significantly affecting our food supply. They are responsible for poor crop quality and quantity globally, and can bring about huge economic losses annually. Others viruses may damage plants used in landscaping. Some viruses that infect agricultural food plants include the name of the plant they infect, such as tomato spotted wilt virus, bean common mosaic virus, and cucumber mosaic virus. In plants used for landscaping, two of the most common viruses are peony ring spot and rose mosaic virus. There are far too many plant viruses to discuss each in detail, but symptoms of bean common mosaic virus result in lowered bean production and stunted, unproductive plants. In the ornamental rose, the rose mosaic disease causes wavy yellow lines and colored splotches on the leaves of the plant.
Summary
Viral replication within a living cell always produces changes in the cell, sometimes resulting in cell death and sometimes slowly killing the infected cells. There are six basic stages in the virus replication cycle: attachment, penetration, uncoating, replication, assembly, and release. A viral infection may be productive, resulting in new virions, or nonproductive, which means that the virus remains inside the cell without producing new virions. Bacteriophages are viruses that infect bacteria. They have two different modes of replication: the lytic cycle, where the virus replicates and bursts out of the bacteria, and the lysogenic cycle, which involves the incorporation of the viral genome into the bacterial host genome. Animal viruses cause a variety of infections, with some causing chronic symptoms (hepatitis C), some intermittent symptoms (latent viruses such a herpes simplex virus 1), and others that cause very few symptoms, if any (human herpesviruses 6 and 7). Oncogenic viruses in animals have the ability to cause cancer by interfering with the regulation of the host cell cycle. Viruses of plants are responsible for significant economic damage in both agriculture and plants used for ornamentation.
Glossary
acute disease
disease where the symptoms rise and fall within a short period of time
asymptomatic disease
disease where there are no symptoms and the individual is unaware of being infected unless lab tests are performed
AZT
anti-HIV drug that inhibits the viral enzyme reverse transcriptase
bacteriophage
virus that infects bacteria
budding
method of exit from the cell used in certain animal viruses, where virions leave the cell individually by capturing a piece of the host plasma membrane
cell necrosis
cell death
chronic infection
describes when the virus persists in the body for a long period of time
cytopathic
causing cell damage
fusion
method of entry by some enveloped viruses, where the viral envelope fuses with the plasma membrane of the host cell
gall
appearance of a plant tumor
horizontal transmission
transmission of a disease from parent to offspring
hyperplasia
abnormally high cell growth and division
hypoplasia
abnormally low cell growth and division
intermittent symptom
symptom that occurs periodically
latency
virus that remains in the body for a long period of time but only causes intermittent symptoms
lysis
bursting of a cell
lytic cycle
type of virus replication in which virions are released through lysis, or bursting, of the cell
lysogenic cycle
type of virus replication in which the viral genome is incorporated into the genome of the host cell
oncogenic virus
virus that has the ability to cause cancer
permissive
cell type that is able to support productive replication of a virus
productive
viral infection that leads to the production of new virions
prophage
phage DNA that is incorporated into the host cell genome
vertical transmission
transmission of disease between unrelated individuals | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/26%3A_Viruses/26.01%3A_The_Nature_of_Viruses/26.1.01%3A_Virus_Infections_and_Hosts.txt |
Learning Objectives
• Describe how viruses are classified
To understand the features shared among different groups of viruses, a classification scheme is necessary. However, most viruses are not thought to have evolved from a common ancestor, so the methods that scientists use to classify living things are not very useful. Biologists have used several classification systems in the past, based on the morphology and genetics of the different viruses. However, these earlier classification methods grouped viruses based on which features of the virus they were using to classify them. The most commonly-used classification method today is called the Baltimore classification scheme which is based on how messenger RNA (mRNA) is generated in each particular type of virus. The surface structure of virions can be observed by both scanning and transmission electron microscopy, whereas the internal structures of the virus can only be observed in images from a transmission electron microscope.
Past Systems of Classification
Viruses are classified in several ways: by factors such as their core content, the structure of their capsids, and whether they have an outer envelope. Viruses may use either DNA or RNA as their genetic material. The virus core contains the genome or total genetic content of the virus. Viral genomes tend to be small, containing only those genes that encode proteins that the virus cannot obtain from the host cell. This genetic material may be single- or double-stranded. It may also be linear or circular. While most viruses contain a single nucleic acid, others have genomes that have several, which are called segments. The type of genetic material (DNA or RNA) and its structure (single- or double-stranded, linear or circular, and segmented or non-segmented) are used to classify the virus core structures.
Viruses can also be classified by the design of their capsids. Isometric viruses have shapes that are roughly spherical, such as poliovirus or herpesviruses. Enveloped viruses have membranes surrounding capsids. Animal viruses, such as HIV, are frequently enveloped. Head and tail viruses infect bacteria and have a head that is similar to icosahedral viruses and a tail shape like filamentous viruses. Capsids are classified as naked icosahedral, enveloped icosahedral, enveloped helical, naked helical, and complex. For example, the tobacco mosaic virus has a naked helical capsid. The adenovirus has an icosahedral capsid.
Baltimore Classification
The most commonly-used system of virus classification was developed by Nobel Prize-winning biologist David Baltimore in the early 1970s. In addition to the differences in morphology and genetics mentioned above, the Baltimore classification scheme groups viruses according to how the mRNA is produced during the replicative cycle of the virus. Viruses can contain double-stranded DNA (dsDNA), single-stranded DNA (ssDNA), double-stranded RNA (dsRNA), single-stranded RNA with a positive polarity (ssRNA), ssRNA with a negative polarity, diploid (two copies) ssRNA, and partial dsDNA genomes. Positive polarity means that the genomic RNA can serve directly as mRNA and a negative polarity means that their sequence is complementary to the mRNA.
Key Points
• The type of genetic material, either DNA or RNA, and whether its structure is single- or double-stranded, linear or circular, and segmented or non-segmented are factors for classification.
• Virus capsids can be classified as naked icosahedral, enveloped icosahedral, enveloped helical, naked helical, and complex.
• Virus can either have an envelope or not.
• A more recent system, the Baltimore classification scheme, groups viruses into seven classes according to how the mRNA is produced during the replicative cycle of the virus.
Key Terms
• Baltimore classification: a classification scheme that groups viruses into seven classes according to how the mRNA is produced during the replicative cycle of the virus
• messenger RNA: Messenger RNA (mRNA) is a molecule of RNA that encodes a chemical “blueprint” for a protein product. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/26%3A_Viruses/26.02%3A_Viral_Diversity.txt |
Bacteriophages, viruses that infect bacteria, may undergo a lytic or lysogenic cycle.
Learning Objectives
• Describe the lytic and lysogenic cycles of bacteriophages
Key Points
• Viruses are species specific, but almost every species on Earth can be affected by some form of virus.
• The lytic cycle involves the reproduction of viruses using a host cell to manufacture more viruses; the viruses then burst out of the cell.
• The lysogenic cycle involves the incorporation of the viral genome into the host cell genome, infecting it from within.
Key Terms
• latency: The ability of a pathogenic virus to lie dormant within a cell.
• bacteriophage: A virus that specifically infects bacteria.
• lytic cycle: The normal process of viral reproduction involving penetration of the cell membrane, nucleic acid synthesis, and lysis of the host cell.
• lysogenic cycle: A form of viral reproduction involving the fusion of the nucleic acid of a bacteriophage with that of a host, followed by proliferation of the resulting prophage.
Different Hosts and Their Viruses
Viruses are often very specific as to which hosts and which cells within the host they will infect. This feature of a virus makes it specific to one or a few species of life on earth. So many different types of viruses exist that nearly every living organism has its own set of viruses that try to infect its cells. Even the smallest and simplest of cells, prokaryotic bacteria, may be attacked by specific types of viruses.
Bacteriophages
Bacteriophages are viruses that infect bacteria. Bacteriophages may have a lytic cycle or a lysogenic cycle, and a few viruses are capable of carrying out both. When infection of a cell by a bacteriophage results in the production of new virions, the infection is said to be productive.
Lytic Cycle
With lytic phages, bacterial cells are broken open (lysed) and destroyed after immediate replication of the virion. As soon as the cell is destroyed, the phage progeny can find new hosts to infect. An example of a lytic bacteriophage is T4, which infects E. coli found in the human intestinal tract. Lytic phages are more suitable for phage therapy.
Some lytic phages undergo a phenomenon known as lysis inhibition, where completed phage progeny will not immediately lyse out of the cell if extracellular phage concentrations are high.
Lysogenic Cycle
In contrast, the lysogenic cycle does not result in immediate lysing of the host cell. Those phages able to undergo lysogeny are known as temperate phages. Their viral genome will integrate with host DNA and replicate along with it fairly harmlessly, or may even become established as a plasmid. The virus remains dormant until host conditions deteriorate, perhaps due to depletion of nutrients; then, the endogenous phages (known as prophages) become active. At this point they initiate the reproductive cycle, resulting in lysis of the host cell. As the lysogenic cycle allows the host cell to continue to survive and reproduce, the virus is reproduced in all of the cell’s offspring. An example of a bacteriophage known to follow the lysogenic cycle and the lytic cycle is the phage lambda of E. coli.
Latency Period
Viruses that infect plant or animal cells may also undergo infections where they are not producing virions for long periods. An example is the animal herpes viruses, including herpes simplex viruses, which cause oral and genital herpes in humans. In a process called latency, these viruses can exist in nervous tissue for long periods of time without producing new virions, only to leave latency periodically and cause lesions in the skin where the virus replicates. Even though there are similarities between lysogeny and latency, the term lysogenic cycle is usually reserved to describe bacteriophages. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/26%3A_Viruses/26.03%3A_Bacteriophage-_Bacterial_Viruses.txt |
Animal viruses have their genetic material copied by a host cell after which they are released into the environment to cause disease.
Learning Objectives
• Describe various animal viruses and the diseases they cause
Key Points
• Animal viruses may enter a host cell by either receptor -mediated endocytosis or by changing shape and entering the cell through the cell membrane.
• Viruses cause diseases in humans and other animals; they often have to run their course before symptoms disappear.
• Examples of viral animal diseases include hepatitis C, chicken pox, and shingles.
Key Terms
• receptor-mediated endocytosis: a process by which cells internalize molecules (endocytosis) by the inward budding of plasma membrane vesicles containing proteins with receptor sites specific to the molecules being internalized
Animal Viruses
Animal viruses, unlike the viruses of plants and bacteria, do not have to penetrate a cell wall to gain access to the host cell. Non-enveloped or “naked” animal viruses may enter cells in two different ways. When a protein in the viral capsid binds to its receptor on the host cell, the virus may be taken inside the cell via a vesicle during the normal cell process of receptor-mediated endocytosis. An alternative method of cell penetration used by non-enveloped viruses is for capsid proteins to undergo shape changes after binding to the receptor, creating channels in the host cell membrane. The viral genome is then “injected” into the host cell through these channels in a manner analogous to that used by many bacteriophages. Enveloped viruses also have two ways of entering cells after binding to their receptors: receptor-mediated endocytosis and fusion. Many enveloped viruses enter the cell by receptor-mediated endocytosis in a fashion similar to some non-enveloped viruses. On the other hand, fusion only occurs with enveloped virions. These viruses, which include HIV among others, use special fusion proteins in their envelopes to cause the envelope to fuse with the plasma membrane of the cell, thus releasing the genome and capsid of the virus into the cell cytoplasm.
After making their proteins and copying their genomes, animal viruses complete the assembly of new virions and exit the cell. Using the example of HIV, enveloped animal viruses may bud from the cell membrane as they assemble themselves, taking a piece of the cell’s plasma membrane in the process. On the other hand, non-enveloped viral progeny, such as rhinoviruses, accumulate in infected cells until there is a signal for lysis or apoptosis, and all virions are released together.
Animal viruses are associated with a variety of human diseases. Some of them follow the classic pattern of acute disease, where symptoms worsen for a short period followed by the elimination of the virus from the body by the immune system with eventual recovery from the infection. Examples of acute viral diseases are the common cold and influenza. Other viruses cause long-term chronic infections, such as the virus causing hepatitis C, whereas others, like herpes simplex virus, cause only intermittent symptoms. Still other viruses, such as human herpes viruses 6 and 7, which in some cases can cause the minor childhood disease roseola, often successfully cause productive infections without causing any symptoms at all in the host; these patients have an asymptomatic infection.
In hepatitis C infections, the virus grows and reproduces in liver cells, causing low levels of liver damage. The damage is so low that infected individuals are often unaware that they are infected, with many infections only detected by routine blood work on patients with risk factors such as intravenous drug use. Since many of the symptoms of viral diseases are caused by immune responses, a lack of symptoms is an indication of a weak immune response to the virus. This allows the virus to escape elimination by the immune system and persist in individuals for years, while continuing to produce low levels of progeny virions in what is known as a chronic viral disease. Chronic infection of the liver by this virus leads to a much greater chance of developing liver cancer, sometimes as much as 30 years after the initial infection.
As mentioned, herpes simplex virus can remain in a state of latency in nervous tissue for months, even years. As the virus “hides” in the tissue and makes few if any viral proteins, there is nothing for the immune response to act against; immunity to the virus slowly declines. Under certain conditions, including various types of physical and psychological stress, the latent herpes simplex virus may be reactivated and undergo a lytic replication cycle in the skin, causing the lesions associated with the disease. Once virions are produced in the skin and viral proteins are synthesized, the immune response is again stimulated and resolves the skin lesions in a few days by destroying viruses in the skin. As a result of this type of replicative cycle, appearances of cold sores and genital herpes outbreaks only occur intermittently, even though the viruses remain in the nervous tissue for life. Latent infections are common with other herpes viruses as well, including the varicella-zoster virus that causes chickenpox. After having a chickenpox infection in childhood, the varicella-zoster virus can remain latent for many years and reactivate in adults to cause the painful condition known as “shingles”. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/26%3A_Viruses/26.04%3A_Viral_Diseases_of_Humans.txt |
Prions are infectious particles that contain no nucleic acids, and viroids are small plant pathogens that do not encode proteins.
Learning Objectives
• Describe prions and viroids and their basic properties
Key Points
• The prion appears to be the first infectious agent found whose transmission is not reliant upon genes made of DNA or RNA.
• An infectious structural variant of a normal cellular protein called PrP (prion protein) is known to cause spongiform encephalopathies.
• Prions have been implicated in fatal neurodegenerative diseases, such as kuru in humans and bovine spongiform encephalopathy (BSE) in cattle.
• Loss of motor control and unusual behaviors are common symptoms of individuals with kuru and BSE; symptoms are usually followed by death.
• Viroids do not have a capsid or outer envelope and can reproduce only within a host cell.
• Viroids are not known to cause any human diseases, but they are responsible for crop failures and the loss of millions of dollars in agricultural revenue each year.
Key Terms
• prion: a self-propagating misfolded conformer of a protein that is responsible for a number of diseases that affect the brain and other neural tissue
• proteinaceous: of, pertaining to, or consisting of protein
• viroid: plant pathogens that consist of just a short section of RNA, but without the protein coat typical of viruses
Prions
Prions, so-called because they are proteinaceous, are infectious particles, smaller than viruses, that contain no nucleic acids (neither DNA nor RNA). Historically, the idea of an infectious agent that did not use nucleic acids was considered impossible, but pioneering work by Nobel Prize-winning biologist Stanley Prusiner has convinced the majority of biologists that such agents do indeed exist.
Fatal neurodegenerative diseases, such as kuru in humans and bovine spongiform encephalopathy (BSE) in cattle (commonly known as “mad cow disease”), were shown to be transmitted by prions. The disease was spread by the consumption of meat, nervous tissue, or internal organs between members of the same species. Kuru, native to humans in Papua New Guinea, was spread from human to human via ritualistic cannibalism. BSE, originally detected in the United Kingdom, spread between cattle by the practice of including cattle nervous tissue in feed for other cattle. Individuals with kuru and BSE show symptoms of loss of motor control and unusual behaviors, such as uncontrolled bursts of laughter with kuru, followed by death. Kuru was controlled by inducing the population to abandon its ritualistic cannibalism.
On the other hand, BSE was initially thought to affect only cattle. Cattle that died of BSE had developed lesions or “holes” in the brain, causing the brain tissue to resemble a sponge. Later on in the outbreak, however, it was shown that a similar encephalopathy in humans known as variant Creutzfeldt-Jakob disease (CJD) could be acquired from eating beef from animals with BSE, sparking bans by various countries on the importation of British beef and causing considerable economic damage to the British beef industry. BSE still exists in various areas. Although a rare disease, individuals that acquire CJD are difficult to treat. The disease spreads from human to human by blood, so many countries have banned blood donation from regions associated with BSE.
The cause of spongiform encephalopathies, such as kuru and BSE, is an infectious structural variant of a normal cellular protein called PrP (prion protein). It is this variant that constitutes the prion particle. PrP exists in two forms: PrPc, the normal form of the protein, and PrPsc, the infectious form. Once introduced into the body, the PrPsc contained within the prion binds to PrPc and converts it to PrPsc. This leads to an exponential increase of the PrPsc protein, which aggregates. PrPsc is folded abnormally; the resulting conformation (shape) is directly responsible for the lesions seen in the brains of infected cattle. Thus, although not without some detractors among scientists, the prion appears to be an entirely new form of infectious agent; the first one found whose transmission is not reliant upon genes made of DNA or RNA.
Viroids
Viroids are plant pathogens: small, single-stranded, circular RNA particles that are much simpler than a virus. They do not have a capsid or outer envelope, but, as with viruses, can reproduce only within a host cell. Viroids do not, however, manufacture any proteins. They produce only a single, specific RNA molecule. Human diseases caused by viroids have yet to be identified.
Viroid-infected plants are responsible for crop failures and the loss of millions of dollars in agricultural revenue each year. Some of the plants they infect include potatoes, cucumbers, tomatoes, chrysanthemums, avocados, and coconut palms. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/26%3A_Viruses/26.05%3A_Prions_and_Viroids-_Infectious_Subviral_Particles.txt |
• 27.1: Prokaryotic Diversity
• 27.2: Prokaryotic Cell Structure
There are many differences between prokaryotic and eukaryotic cells. However, all cells have four common structures: the plasma membrane, which functions as a barrier for the cell and separates the cell from its environment; the cytoplasm, a jelly-like substance inside the cell; nucleic acids, the genetic material of the cell; and ribosomes, where protein synthesis takes place.
• 27.3: Prokaryotic Genetics
There are many differences between prokaryotic and eukaryotic cells. However, all cells have four common structures: the plasma membrane, which functions as a barrier for the cell and separates the cell from its environment; the cytoplasm, a jelly-like substance inside the cell; nucleic acids, the genetic material of the cell; and ribosomes, where protein synthesis takes place.
• 27.4: The Metabolic Diversity of Prokaryotes
Prokaryotes are metabolically diverse organisms. There are many different environments on Earth with various energy and carbon sources, and variable conditions. Prokaryotes have been able to live in every environment by using whatever energy and carbon sources are available. Prokaryotes fill many niches on Earth, including being involved in nutrient cycles such as nitrogen and carbon cycles, decomposing dead organisms, and thriving inside living organisms, including humans.
• 27.5: Microbial Ecology
• 27.6: Bacterial Diseases of Humans
Devastating pathogen-borne diseases and plagues, both viral and bacterial in nature, have affected humans since the beginning of human history. The true cause of these diseases was not understood at the time, and some people thought that diseases were a spiritual punishment. Over time, people came to realize that staying apart from afflicted persons, and disposing of the corpses and personal belongings of victims of illness, reduced their own chances of getting sick.
27: Prokaryotes
Prokaryotic organisms were the first living things on earth and still inhabit every environment, no matter how extreme.
Learning Objectives
• Discuss the origins of prokaryotic organisms in terms of the geologic timeline
Key Points
• All living things can be classified into three main groups called domains; these include the Archaea, the Bacteria, and the Eukarya.
• Prokaryotes arose during the Precambrian Period 3.5 to 3.8 billion years ago.
• Prokaryotic organisms can live in every type of environment on Earth, from very hot, to very cold, to super haline, to very acidic.
• The domains Bacteria and Archaea are the ones containing prokaryotic organisms.
• The Archaea are prokaryotes that inhabit extreme environments, such as inside of volcanoes, while Bacteria are more common organisms, such as E. coli.
Key Terms
• prokaryote: an organism whose cell (or cells) are characterized by the absence of a nucleus or any other membrane-bound organelles
• domain: in the three-domain system, the highest rank in the classification of organisms, above kingdom: Bacteria, Archaea, and Eukarya
• archaea: a taxonomic domain of single-celled organisms lacking nuclei, formerly called archaebacteria, but now known to differ fundamentally from bacteria
Evolution of Prokaryotes
In the recent past, scientists grouped living things into five kingdoms (animals, plants, fungi, protists, and prokaryotes) based on several criteria such as: the absence or presence of a nucleus and other membrane-bound organelles, the absence or presence of cell walls, multicellularity, etc. In the late 20th century, the pioneering work of Carl Woese and others compared sequences of small-subunit ribosomal RNA (SSU rRNA) which resulted in a more fundamental way to group organisms on earth. Based on differences in the structure of cell membranes and in rRNA, Woese and his colleagues proposed that all life on earth evolved along three lineages, called domains. The domain Bacteria comprises all organisms in the kingdom Bacteria, the domain Archaea comprises the rest of the prokaryotes, and the domain Eukarya comprises all eukaryotes, including organisms in the kingdoms Animalia, Plantae, Fungi, and Protista.
The current model of the evolution of the first, living organisms is that these were some form of prokaryotes, which may have evolved out of protobionts. In general, the eukaryotes are thought to have evolved later in the history of life. However, some authors have questioned this conclusion, arguing that the current set of prokaryotic species may have evolved from more complex eukaryotic ancestors through a process of simplification. Others have argued that the three domains of life arose simultaneously, from a set of varied cells that formed a single gene pool.
Two of the three domains, Bacteria and Archaea, are prokaryotic. Based on fossil evidence, prokaryotes were the first inhabitants on Earth, appearing 3.5 to 3.8 billion years ago during the Precambrian Period. These organisms are abundant and ubiquitous; that is, they are present everywhere. In addition to inhabiting moderate environments, they are found in extreme conditions: from boiling springs to permanently frozen environments in Antarctica; from salty environments like the Dead Sea to environments under tremendous pressure, such as the depths of the ocean; and from areas without oxygen, such as a waste management plant, to radioactively-contaminated regions, such as Chernobyl. Prokaryotes reside in the human digestive system and on the skin, are responsible for certain illnesses, and serve an important role in the preparation of many foods. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/27%3A_Prokaryotes/27.01%3A_Prokaryotic_Diversity.txt |
Skills to Develop
• Describe the basic structure of a typical prokaryote
• Describe important differences in structure between Archaea and Bacteria
There are many differences between prokaryotic and eukaryotic cells. However, all cells have four common structures: the plasma membrane, which functions as a barrier for the cell and separates the cell from its environment; the cytoplasm, a jelly-like substance inside the cell; nucleic acids, the genetic material of the cell; and ribosomes, where protein synthesis takes place. Prokaryotes come in various shapes, but many fall into three categories: cocci (spherical), bacilli (rod-shaped), and spirilli (spiral-shaped) (Figure \(1\)).
The Prokaryotic Cell
Recall that prokaryotes (Figure \(2\)) are unicellular organisms that lack organelles or other internal membrane-bound structures. Therefore, they do not have a nucleus but instead generally have a single chromosome—a piece of circular, double-stranded DNA located in an area of the cell called the nucleoid. Most prokaryotes have a cell wall outside the plasma membrane.
Recall that prokaryotes are divided into two different domains, Bacteria and Archaea, which together with Eukarya, comprise the three domains of life (Figure \(3\)).
The composition of the cell wall differs significantly between the domains Bacteria and Archaea. The composition of their cell walls also differs from the eukaryotic cell walls found in plants (cellulose) or fungi and insects (chitin). The cell wall functions as a protective layer, and it is responsible for the organism’s shape. Some bacteria have an outer capsule outside the cell wall. Other structures are present in some prokaryotic species, but not in others (Table \(1\)). For example, the capsule found in some species enables the organism to attach to surfaces, protects it from dehydration and attack by phagocytic cells, and makes pathogens more resistant to our immune responses. Some species also have flagella (singular, flagellum) used for locomotion, and pili (singular, pilus) used for attachment to surfaces. Plasmids, which consist of extra-chromosomal DNA, are also present in many species of bacteria and archaea.
Characteristics of phyla of Bacteria are described in Figure \(4\) and Figure \(5\); Archaea are described in Figure \(6\).
The Plasma Membrane
The plasma membrane is a thin lipid bilayer (6 to 8 nanometers) that completely surrounds the cell and separates the inside from the outside. Its selectively permeable nature keeps ions, proteins, and other molecules within the cell and prevents them from diffusing into the extracellular environment, while other molecules may move through the membrane. Recall that the general structure of a cell membrane is a phospholipid bilayer composed of two layers of lipid molecules. In archaeal cell membranes, isoprene (phytanyl) chains linked to glycerol replace the fatty acids linked to glycerol in bacterial membranes. Some archaeal membranes are lipid monolayers instead of bilayers (Figure \(7\)).
The Cell Wall
The cytoplasm of prokaryotic cells has a high concentration of dissolved solutes. Therefore, the osmotic pressure within the cell is relatively high. The cell wall is a protective layer that surrounds some cells and gives them shape and rigidity. It is located outside the cell membrane and prevents osmotic lysis (bursting due to increasing volume). The chemical composition of the cell walls varies between archaea and bacteria, and also varies between bacterial species.
Bacterial cell walls contain peptidoglycan, composed of polysaccharide chains that are cross-linked by unusual peptides containing both L- and D-amino acids including D-glutamic acid and D-alanine. Proteins normally have only L-amino acids; as a consequence, many of our antibiotics work by mimicking D-amino acids and therefore have specific effects on bacterial cell wall development. There are more than 100 different forms of peptidoglycan. S-layer (surface layer) proteins are also present on the outside of cell walls of both archaea and bacteria.
Bacteria are divided into two major groups: Gram positive and Gram negative, based on their reaction to Gram staining. Note that all Gram-positive bacteria belong to one phylum; bacteria in the other phyla (Proteobacteria, Chlamydias, Spirochetes, Cyanobacteria, and others) are Gram-negative. The Gram staining method is named after its inventor, Danish scientist Hans Christian Gram (1853–1938). The different bacterial responses to the staining procedure are ultimately due to cell wall structure. Gram-positive organisms typically lack the outer membrane found in Gram-negative organisms (Figure \(8\)). Up to 90 percent of the cell wall in Gram-positive bacteria is composed of peptidoglycan, and most of the rest is composed of acidic substances called teichoic acids. Teichoic acids may be covalently linked to lipids in the plasma membrane to form lipoteichoic acids. Lipoteichoic acids anchor the cell wall to the cell membrane. Gram-negative bacteria have a relatively thin cell wall composed of a few layers of peptidoglycan (only 10 percent of the total cell wall), surrounded by an outer envelope containing lipopolysaccharides (LPS) and lipoproteins. This outer envelope is sometimes referred to as a second lipid bilayer. The chemistry of this outer envelope is very different, however, from that of the typical lipid bilayer that forms plasma membranes.
Art Connection
Which of the following statements is true?
1. Gram-positive bacteria have a single cell wall anchored to the cell membrane by lipoteichoic acid.
2. Porins allow entry of substances into both Gram-positive and Gram-negative bacteria.
3. The cell wall of Gram-negative bacteria is thick, and the cell wall of Gram-positive bacteria is thin.
4. Gram-negative bacteria have a cell wall made of peptidoglycan, whereas Gram-positive bacteria have a cell wall made of lipoteichoic acid.
Archaean cell walls do not have peptidoglycan. There are four different types of Archaean cell walls. One type is composed of pseudopeptidoglycan, which is similar to peptidoglycan in morphology but contains different sugars in the polysaccharide chain. The other three types of cell walls are composed of polysaccharides, glycoproteins, or pure protein.
Table \(1\): Structural Differences and Similarities between Bacteria and Archaea
Structural Characteristic Bacteria Archaea
Cell type Prokaryotic Prokaryotic
Cell morphology Variable Variable
Cell wall Contains peptidoglycan Does not contain peptidoglycan
Cell membrane type Lipid bilayer Lipid bilayer or lipid monolayer
Plasma membrane lipids Fatty acids Phytanyl groups
Reproduction
Reproduction in prokaryotes is asexual and usually takes place by binary fission. Recall that the DNA of a prokaryote exists as a single, circular chromosome. Prokaryotes do not undergo mitosis. Rather the chromosome is replicated and the two resulting copies separate from one another, due to the growth of the cell. The prokaryote, now enlarged, is pinched inward at its equator and the two resulting cells, which are clones, separate. Binary fission does not provide an opportunity for genetic recombination or genetic diversity, but prokaryotes can share genes by three other mechanisms.
In transformation, the prokaryote takes in DNA found in its environment that is shed by other prokaryotes. If a nonpathogenic bacterium takes up DNA for a toxin gene from a pathogen and incorporates the new DNA into its own chromosome, it too may become pathogenic. In transduction, bacteriophages, the viruses that infect bacteria, sometimes also move short pieces of chromosomal DNA from one bacterium to another. Transduction results in a recombinant organism. Archaea are not affected by bacteriophages but instead have their own viruses that translocate genetic material from one individual to another. In conjugation, DNA is transferred from one prokaryote to another by means of a pilus, which brings the organisms into contact with one another. The DNA transferred can be in the form of a plasmid or as a hybrid, containing both plasmid and chromosomal DNA. These three processes of DNA exchange are shown in Figure \(9\).
Reproduction can be very rapid: a few minutes for some species. This short generation time coupled with mechanisms of genetic recombination and high rates of mutation result in the rapid evolution of prokaryotes, allowing them to respond to environmental changes (such as the introduction of an antibiotic) very quickly.
Evolution Connection: The Evolution of Prokaryotes
How do scientists answer questions about the evolution of prokaryotes? Unlike with animals, artifacts in the fossil record of prokaryotes offer very little information. Fossils of ancient prokaryotes look like tiny bubbles in rock. Some scientists turn to genetics and to the principle of the molecular clock, which holds that the more recently two species have diverged, the more similar their genes (and thus proteins) will be. Conversely, species that diverged long ago will have more genes that are dissimilar.
Scientists at the NASA Astrobiology Institute and at the European Molecular Biology Laboratory collaborated to analyze the molecular evolution of 32 specific proteins common to 72 species of prokaryotes.1 The model they derived from their data indicates that three important groups of bacteria—Actinobacteria, Deinococcus, and Cyanobacteria (which the authors call Terrabacteria)—were the first to colonize land. (Recall that Deinococcus is a genus of prokaryote—a bacterium—that is highly resistant to ionizing radiation.) Cyanobacteria are photosynthesizers, while Actinobacteria are a group of very common bacteria that include species important in decomposition of organic wastes.
The timelines of divergence suggest that bacteria (members of the domain Bacteria) diverged from common ancestral species between 2.5 and 3.2 billion years ago, whereas archaea diverged earlier: between 3.1 and 4.1 billion years ago. Eukarya later diverged off the Archaean line. The work further suggests that stromatolites that formed prior to the advent of cyanobacteria (about 2.6 billion years ago) photosynthesized in an anoxic environment and that because of the modifications of the Terrabacteria for land (resistance to drying and the possession of compounds that protect the organism from excess light), photosynthesis using oxygen may be closely linked to adaptations to survive on land.
Summary
Prokaryotes (domains Archaea and Bacteria) are single-celled organisms lacking a nucleus. They have a single piece of circular DNA in the nucleoid area of the cell. Most prokaryotes have a cell wall that lies outside the boundary of the plasma membrane. Some prokaryotes may have additional structures such as a capsule, flagella, and pili. Bacteria and Archaea differ in the lipid composition of their cell membranes and the characteristics of the cell wall. In archaeal membranes, phytanyl units, rather than fatty acids, are linked to glycerol. Some archaeal membranes are lipid monolayers instead of bilayers.
The cell wall is located outside the cell membrane and prevents osmotic lysis. The chemical composition of cell walls varies between species. Bacterial cell walls contain peptidoglycan. Archaean cell walls do not have peptidoglycan, but they may have pseudopeptidoglycan, polysaccharides, glycoproteins, or protein-based cell walls. Bacteria can be divided into two major groups: Gram positive and Gram negative, based on the Gram stain reaction. Gram-positive organisms have a thick cell wall, together with teichoic acids. Gram-negative organisms have a thin cell wall and an outer envelope containing lipopolysaccharides and lipoproteins.
Art Connections
Figure \(8\): Which of the following statements is true?
1. Gram-positive bacteria have a single cell wall anchored to the cell membrane by lipoteichoic acid.
2. Porins allow entry of substances into both Gram-positive and Gram-negative bacteria.
3. The cell wall of Gram-negative bacteria is thick, and the cell wall of Gram-positive bacteria is thin.
4. Gram-negative bacteria have a cell wall made of peptidoglycan, whereas Gram-positive bacteria have a cell wall made of lipoteichoic acid.
Answer
A
Footnotes
1. 1 Battistuzzi, FU, Feijao, A, and Hedges, SB. A genomic timescale of prokaryote evolution: Insights into the origin of methanogenesis, phototrophy, and the colonization of land. BioMed Central: Evolutionary Biology 4 (2004): 44, doi:10.1186/1471-2148-4-44.
Glossary
capsule
external structure that enables a prokaryote to attach to surfaces and protects it from dehydration
conjugation
process by which prokaryotes move DNA from one individual to another using a pilus
Gram negative
bacterium whose cell wall contains little peptidoglycan but has an outer membrane
Gram positive
bacterium that contains mainly peptidoglycan in its cell walls
peptidoglycan
material composed of polysaccharide chains cross-linked to unusual peptides
pilus
surface appendage of some prokaryotes used for attachment to surfaces including other prokaryotes
pseudopeptidoglycan
component of archaea cell walls that is similar to peptidoglycan in morphology but contains different sugars
S-layer
surface-layer protein present on the outside of cell walls of archaea and bacteria
teichoic acid
polymer associated with the cell wall of Gram-positive bacteria
transduction
process by which a bacteriophage moves DNA from one prokaryote to another
transformation
process by which a prokaryote takes in DNA found in its environment that is shed by other prokaryotes | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/27%3A_Prokaryotes/27.02%3A_Prokaryotic_Cell_Structure.txt |
Skills to Develop
• Describe the basic structure of a typical prokaryote
• Describe important differences in structure between Archaea and Bacteria
There are many differences between prokaryotic and eukaryotic cells. However, all cells have four common structures: the plasma membrane, which functions as a barrier for the cell and separates the cell from its environment; the cytoplasm, a jelly-like substance inside the cell; nucleic acids, the genetic material of the cell; and ribosomes, where protein synthesis takes place. Prokaryotes come in various shapes, but many fall into three categories: cocci (spherical), bacilli (rod-shaped), and spirilli (spiral-shaped) (Figure \(1\)).
The Prokaryotic Cell
Recall that prokaryotes (Figure \(2\)) are unicellular organisms that lack organelles or other internal membrane-bound structures. Therefore, they do not have a nucleus but instead generally have a single chromosome—a piece of circular, double-stranded DNA located in an area of the cell called the nucleoid. Most prokaryotes have a cell wall outside the plasma membrane.
Recall that prokaryotes are divided into two different domains, Bacteria and Archaea, which together with Eukarya, comprise the three domains of life (Figure \(3\)).
The composition of the cell wall differs significantly between the domains Bacteria and Archaea. The composition of their cell walls also differs from the eukaryotic cell walls found in plants (cellulose) or fungi and insects (chitin). The cell wall functions as a protective layer, and it is responsible for the organism’s shape. Some bacteria have an outer capsule outside the cell wall. Other structures are present in some prokaryotic species, but not in others (Table \(1\)). For example, the capsule found in some species enables the organism to attach to surfaces, protects it from dehydration and attack by phagocytic cells, and makes pathogens more resistant to our immune responses. Some species also have flagella (singular, flagellum) used for locomotion, and pili (singular, pilus) used for attachment to surfaces. Plasmids, which consist of extra-chromosomal DNA, are also present in many species of bacteria and archaea.
Characteristics of phyla of Bacteria are described in Figure \(4\) and Figure \(5\); Archaea are described in Figure \(6\).
The Plasma Membrane
The plasma membrane is a thin lipid bilayer (6 to 8 nanometers) that completely surrounds the cell and separates the inside from the outside. Its selectively permeable nature keeps ions, proteins, and other molecules within the cell and prevents them from diffusing into the extracellular environment, while other molecules may move through the membrane. Recall that the general structure of a cell membrane is a phospholipid bilayer composed of two layers of lipid molecules. In archaeal cell membranes, isoprene (phytanyl) chains linked to glycerol replace the fatty acids linked to glycerol in bacterial membranes. Some archaeal membranes are lipid monolayers instead of bilayers (Figure \(7\)).
The Cell Wall
The cytoplasm of prokaryotic cells has a high concentration of dissolved solutes. Therefore, the osmotic pressure within the cell is relatively high. The cell wall is a protective layer that surrounds some cells and gives them shape and rigidity. It is located outside the cell membrane and prevents osmotic lysis (bursting due to increasing volume). The chemical composition of the cell walls varies between archaea and bacteria, and also varies between bacterial species.
Bacterial cell walls contain peptidoglycan, composed of polysaccharide chains that are cross-linked by unusual peptides containing both L- and D-amino acids including D-glutamic acid and D-alanine. Proteins normally have only L-amino acids; as a consequence, many of our antibiotics work by mimicking D-amino acids and therefore have specific effects on bacterial cell wall development. There are more than 100 different forms of peptidoglycan. S-layer (surface layer) proteins are also present on the outside of cell walls of both archaea and bacteria.
Bacteria are divided into two major groups: Gram positive and Gram negative, based on their reaction to Gram staining. Note that all Gram-positive bacteria belong to one phylum; bacteria in the other phyla (Proteobacteria, Chlamydias, Spirochetes, Cyanobacteria, and others) are Gram-negative. The Gram staining method is named after its inventor, Danish scientist Hans Christian Gram (1853–1938). The different bacterial responses to the staining procedure are ultimately due to cell wall structure. Gram-positive organisms typically lack the outer membrane found in Gram-negative organisms (Figure \(8\)). Up to 90 percent of the cell wall in Gram-positive bacteria is composed of peptidoglycan, and most of the rest is composed of acidic substances called teichoic acids. Teichoic acids may be covalently linked to lipids in the plasma membrane to form lipoteichoic acids. Lipoteichoic acids anchor the cell wall to the cell membrane. Gram-negative bacteria have a relatively thin cell wall composed of a few layers of peptidoglycan (only 10 percent of the total cell wall), surrounded by an outer envelope containing lipopolysaccharides (LPS) and lipoproteins. This outer envelope is sometimes referred to as a second lipid bilayer. The chemistry of this outer envelope is very different, however, from that of the typical lipid bilayer that forms plasma membranes.
Art Connection
Which of the following statements is true?
1. Gram-positive bacteria have a single cell wall anchored to the cell membrane by lipoteichoic acid.
2. Porins allow entry of substances into both Gram-positive and Gram-negative bacteria.
3. The cell wall of Gram-negative bacteria is thick, and the cell wall of Gram-positive bacteria is thin.
4. Gram-negative bacteria have a cell wall made of peptidoglycan, whereas Gram-positive bacteria have a cell wall made of lipoteichoic acid.
Archaean cell walls do not have peptidoglycan. There are four different types of Archaean cell walls. One type is composed of pseudopeptidoglycan, which is similar to peptidoglycan in morphology but contains different sugars in the polysaccharide chain. The other three types of cell walls are composed of polysaccharides, glycoproteins, or pure protein.
Table \(1\): Structural Differences and Similarities between Bacteria and Archaea
Structural Characteristic Bacteria Archaea
Cell type Prokaryotic Prokaryotic
Cell morphology Variable Variable
Cell wall Contains peptidoglycan Does not contain peptidoglycan
Cell membrane type Lipid bilayer Lipid bilayer or lipid monolayer
Plasma membrane lipids Fatty acids Phytanyl groups
Reproduction
Reproduction in prokaryotes is asexual and usually takes place by binary fission. Recall that the DNA of a prokaryote exists as a single, circular chromosome. Prokaryotes do not undergo mitosis. Rather the chromosome is replicated and the two resulting copies separate from one another, due to the growth of the cell. The prokaryote, now enlarged, is pinched inward at its equator and the two resulting cells, which are clones, separate. Binary fission does not provide an opportunity for genetic recombination or genetic diversity, but prokaryotes can share genes by three other mechanisms.
In transformation, the prokaryote takes in DNA found in its environment that is shed by other prokaryotes. If a nonpathogenic bacterium takes up DNA for a toxin gene from a pathogen and incorporates the new DNA into its own chromosome, it too may become pathogenic. In transduction, bacteriophages, the viruses that infect bacteria, sometimes also move short pieces of chromosomal DNA from one bacterium to another. Transduction results in a recombinant organism. Archaea are not affected by bacteriophages but instead have their own viruses that translocate genetic material from one individual to another. In conjugation, DNA is transferred from one prokaryote to another by means of a pilus, which brings the organisms into contact with one another. The DNA transferred can be in the form of a plasmid or as a hybrid, containing both plasmid and chromosomal DNA. These three processes of DNA exchange are shown in Figure \(9\).
Reproduction can be very rapid: a few minutes for some species. This short generation time coupled with mechanisms of genetic recombination and high rates of mutation result in the rapid evolution of prokaryotes, allowing them to respond to environmental changes (such as the introduction of an antibiotic) very quickly.
Evolution Connection: The Evolution of Prokaryotes
How do scientists answer questions about the evolution of prokaryotes? Unlike with animals, artifacts in the fossil record of prokaryotes offer very little information. Fossils of ancient prokaryotes look like tiny bubbles in rock. Some scientists turn to genetics and to the principle of the molecular clock, which holds that the more recently two species have diverged, the more similar their genes (and thus proteins) will be. Conversely, species that diverged long ago will have more genes that are dissimilar.
Scientists at the NASA Astrobiology Institute and at the European Molecular Biology Laboratory collaborated to analyze the molecular evolution of 32 specific proteins common to 72 species of prokaryotes.1 The model they derived from their data indicates that three important groups of bacteria—Actinobacteria, Deinococcus, and Cyanobacteria (which the authors call Terrabacteria)—were the first to colonize land. (Recall that Deinococcus is a genus of prokaryote—a bacterium—that is highly resistant to ionizing radiation.) Cyanobacteria are photosynthesizers, while Actinobacteria are a group of very common bacteria that include species important in decomposition of organic wastes.
The timelines of divergence suggest that bacteria (members of the domain Bacteria) diverged from common ancestral species between 2.5 and 3.2 billion years ago, whereas archaea diverged earlier: between 3.1 and 4.1 billion years ago. Eukarya later diverged off the Archaean line. The work further suggests that stromatolites that formed prior to the advent of cyanobacteria (about 2.6 billion years ago) photosynthesized in an anoxic environment and that because of the modifications of the Terrabacteria for land (resistance to drying and the possession of compounds that protect the organism from excess light), photosynthesis using oxygen may be closely linked to adaptations to survive on land.
Summary
Prokaryotes (domains Archaea and Bacteria) are single-celled organisms lacking a nucleus. They have a single piece of circular DNA in the nucleoid area of the cell. Most prokaryotes have a cell wall that lies outside the boundary of the plasma membrane. Some prokaryotes may have additional structures such as a capsule, flagella, and pili. Bacteria and Archaea differ in the lipid composition of their cell membranes and the characteristics of the cell wall. In archaeal membranes, phytanyl units, rather than fatty acids, are linked to glycerol. Some archaeal membranes are lipid monolayers instead of bilayers.
The cell wall is located outside the cell membrane and prevents osmotic lysis. The chemical composition of cell walls varies between species. Bacterial cell walls contain peptidoglycan. Archaean cell walls do not have peptidoglycan, but they may have pseudopeptidoglycan, polysaccharides, glycoproteins, or protein-based cell walls. Bacteria can be divided into two major groups: Gram positive and Gram negative, based on the Gram stain reaction. Gram-positive organisms have a thick cell wall, together with teichoic acids. Gram-negative organisms have a thin cell wall and an outer envelope containing lipopolysaccharides and lipoproteins.
Art Connections
Figure \(8\): Which of the following statements is true?
1. Gram-positive bacteria have a single cell wall anchored to the cell membrane by lipoteichoic acid.
2. Porins allow entry of substances into both Gram-positive and Gram-negative bacteria.
3. The cell wall of Gram-negative bacteria is thick, and the cell wall of Gram-positive bacteria is thin.
4. Gram-negative bacteria have a cell wall made of peptidoglycan, whereas Gram-positive bacteria have a cell wall made of lipoteichoic acid.
Answer
A
Footnotes
1. 1 Battistuzzi, FU, Feijao, A, and Hedges, SB. A genomic timescale of prokaryote evolution: Insights into the origin of methanogenesis, phototrophy, and the colonization of land. BioMed Central: Evolutionary Biology 4 (2004): 44, doi:10.1186/1471-2148-4-44.
Glossary
capsule
external structure that enables a prokaryote to attach to surfaces and protects it from dehydration
conjugation
process by which prokaryotes move DNA from one individual to another using a pilus
Gram negative
bacterium whose cell wall contains little peptidoglycan but has an outer membrane
Gram positive
bacterium that contains mainly peptidoglycan in its cell walls
peptidoglycan
material composed of polysaccharide chains cross-linked to unusual peptides
pilus
surface appendage of some prokaryotes used for attachment to surfaces including other prokaryotes
pseudopeptidoglycan
component of archaea cell walls that is similar to peptidoglycan in morphology but contains different sugars
S-layer
surface-layer protein present on the outside of cell walls of archaea and bacteria
teichoic acid
polymer associated with the cell wall of Gram-positive bacteria
transduction
process by which a bacteriophage moves DNA from one prokaryote to another
transformation
process by which a prokaryote takes in DNA found in its environment that is shed by other prokaryotes | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/27%3A_Prokaryotes/27.03%3A_Prokaryotic_Genetics.txt |
Skills to Develop
• Identify the macronutrients needed by prokaryotes, and explain their importance
• Describe the ways in which prokaryotes get energy and carbon for life processes
• Describe the roles of prokaryotes in the carbon and nitrogen cycles
Prokaryotes are metabolically diverse organisms. There are many different environments on Earth with various energy and carbon sources, and variable conditions. Prokaryotes have been able to live in every environment by using whatever energy and carbon sources are available. Prokaryotes fill many niches on Earth, including being involved in nutrient cycles such as nitrogen and carbon cycles, decomposing dead organisms, and thriving inside living organisms, including humans. The very broad range of environments that prokaryotes occupy is possible because they have diverse metabolic processes.
Needs of Prokaryotes
The diverse environments and ecosystems on Earth have a wide range of conditions in terms of temperature, available nutrients, acidity, salinity, and energy sources. Prokaryotes are very well equipped to make their living out of a vast array of nutrients and conditions. To live, prokaryotes need a source of energy, a source of carbon, and some additional nutrients.
Macronutrients
Cells are essentially a well-organized assemblage of macromolecules and water. Recall that macromolecules are produced by the polymerization of smaller units called monomers. For cells to build all of the molecules required to sustain life, they need certain substances, collectively called nutrients. When prokaryotes grow in nature, they obtain their nutrients from the environment. Nutrients that are required in large amounts are called macronutrients, whereas those required in smaller or trace amounts are called micronutrients. Just a handful of elements are considered macronutrients—carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulfur. (A mnemonic for remembering these elements is the acronym CHONPS.)
Why are these macronutrients needed in large amounts? They are the components of organic compounds in cells, including water. Carbon is the major element in all macromolecules: carbohydrates, proteins, nucleic acids, lipids, and many other compounds. Carbon accounts for about 50 percent of the composition of the cell. Nitrogen represents 12 percent of the total dry weight of a typical cell and is a component of proteins, nucleic acids, and other cell constituents. Most of the nitrogen available in nature is either atmospheric nitrogen (N2) or another inorganic form. Diatomic (N2) nitrogen, however, can be converted into an organic form only by certain organisms, called nitrogen-fixing organisms. Both hydrogen and oxygen are part of many organic compounds and of water. Phosphorus is required by all organisms for the synthesis of nucleotides and phospholipids. Sulfur is part of the structure of some amino acids such as cysteine and methionine, and is also present in several vitamins and coenzymes. Other important macronutrients are potassium (K), magnesium (Mg), calcium (Ca), and sodium (Na). Although these elements are required in smaller amounts, they are very important for the structure and function of the prokaryotic cell.
Micronutrients
In addition to these macronutrients, prokaryotes require various metallic elements in small amounts. These are referred to as micronutrients or trace elements. For example, iron is necessary for the function of the cytochromes involved in electron-transport reactions. Some prokaryotes require other elements—such as boron (B), chromium (Cr), and manganese (Mn)—primarily as enzyme cofactors.
The Ways in Which Prokaryotes Obtain Energy
Prokaryotes can use different sources of energy to assemble macromolecules from smaller molecules. Phototrophs (or phototrophic organisms) obtain their energy from sunlight. Chemotrophs (or chemosynthetic organisms) obtain their energy from chemical compounds. Chemotrophs that can use organic compounds as energy sources are called chemoorganotrophs. Those that can also use inorganic compounds as energy sources are called chemolitotrophs.
The Ways in Which Prokaryotes Obtain Carbon
Prokaryotes not only can use different sources of energy but also different sources of carbon compounds. Recall that organisms that are able to fix inorganic carbon are called autotrophs. Autotrophic prokaryotes synthesize organic molecules from carbon dioxide. In contrast, heterotrophic prokaryotes obtain carbon from organic compounds. To make the picture more complex, the terms that describe how prokaryotes obtain energy and carbon can be combined. Thus, photoautotrophs use energy from sunlight, and carbon from carbon dioxide and water, whereas chemoheterotrophs obtain energy and carbon from an organic chemical source. Chemolitoautotrophs obtain their energy from inorganic compounds, and they build their complex molecules from carbon dioxide. Table \(1\) summarizes carbon and energy sources in prokaryotes.
Table \(1\): Carbon and Energy Sources in Prokaryotes
Energy Sources Carbon Sources
Light Chemicals Carbon dioxide Organic compounds
Phototrophs Chemotrophs Autotrophs Heterotrophs
Organic chemicals Inorganic chemicals
Chemo-organotrophs Chemolithotrophs
Role of Prokaryotes in Ecosystems
Prokaryotes are ubiquitous: There is no niche or ecosystem in which they are not present. Prokaryotes play many roles in the environments they occupy. The roles they play in the carbon and nitrogen cycles are vital to life on Earth.
Prokaryotes and the Carbon Cycle
Carbon is one of the most important macronutrients, and prokaryotes play an important role in the carbon cycle (Figure \(1\)). Carbon is cycled through Earth’s major reservoirs: land, the atmosphere, aquatic environments, sediments and rocks, and biomass. The movement of carbon is via carbon dioxide, which is removed from the atmosphere by land plants and marine prokaryotes, and is returned to the atmosphere via the respiration of chemoorganotrophic organisms, including prokaryotes, fungi, and animals. Although the largest carbon reservoir in terrestrial ecosystems is in rocks and sediments, that carbon is not readily available.
A large amount of available carbon is found in land plants. Plants, which are producers, use carbon dioxide from the air to synthesize carbon compounds. Related to this, one very significant source of carbon compounds is humus, which is a mixture of organic materials from dead plants and prokaryotes that have resisted decomposition. Consumers such as animals use organic compounds generated by producers and release carbon dioxide to the atmosphere. Then, bacteria and fungi, collectively called decomposers, carry out the breakdown (decomposition) of plants and animals and their organic compounds. The most important contributor of carbon dioxide to the atmosphere is microbial decomposition of dead material (dead animals, plants, and humus) that undergo respiration.
In aqueous environments and their anoxic sediments, there is another carbon cycle taking place. In this case, the cycle is based on one-carbon compounds. In anoxic sediments, prokaryotes, mostly archaea, produce methane (CH4). This methane moves into the zone above the sediment, which is richer in oxygen and supports bacteria called methane oxidizers that oxidize methane to carbon dioxide, which then returns to the atmosphere.
Prokaryotes and the Nitrogen Cycle
Nitrogen is a very important element for life because it is part of proteins and nucleic acids. It is a macronutrient, and in nature, it is recycled from organic compounds to ammonia, ammonium ions, nitrate, nitrite, and nitrogen gas by myriad processes, many of which are carried out only by prokaryotes. As illustrated in Figure \(2\), prokaryotes are key to the nitrogen cycle. The largest pool of nitrogen available in the terrestrial ecosystem is gaseous nitrogen from the air, but this nitrogen is not usable by plants, which are primary producers. Gaseous nitrogen is transformed, or “fixed” into more readily available forms such as ammonia through the process of nitrogen fixation. Ammonia can be used by plants or converted to other forms.
Another source of ammonia is ammonification, the process by which ammonia is released during the decomposition of nitrogen-containing organic compounds. Ammonia released to the atmosphere, however, represents only 15 percent of the total nitrogen released; the rest is as N2 and N2O. Ammonia is catabolized anaerobically by some prokaryotes, yielding N2 as the final product. Nitrification is the conversion of ammonium to nitrite and nitrate. Nitrification in soils is carried out by bacteria belonging to the genera Nitrosomas, Nitrobacter, and Nitrospira. The bacteria performs the reverse process, the reduction of nitrate from the soils to gaseous compounds such as N2O, NO, and N2, a process called denitrification.
Art Connection
Which of the following statements about the nitrogen cycle is false?
1. Nitrogen fixing bacteria exist on the root nodules of legumes and in the soil.
2. Denitrifying bacteria convert nitrates (\(\ce{NO_3^-}\)) into nitrogen gas (\(\ce{N_2}\)).
3. Ammonification is the process by which ammonium ion (\(\ce{NH_4^+}\)) is released from decomposing organic compounds.
4. Nitrification is the process by which nitrites (\(\ce{NO_2^-}\)) are converted to ammonium ion (\(\ce{NH_4^+}\)).
Summary
Prokaryotes are the most metabolically diverse organisms; they flourish in many different environments with various carbon energy and carbon sources, variable temperature, pH, pressure, and water availability. Nutrients required in large amounts are called macronutrients, whereas those required in trace amounts are called micronutrients or trace elements. Macronutrients include C, H, O, N, P, S, K, Mg, Ca, and Na. In addition to these macronutrients, prokaryotes require various metallic elements for growth and enzyme function. Prokaryotes use different sources of energy to assemble macromolecules from smaller molecules. Phototrophs obtain their energy from sunlight, whereas chemotrophs obtain energy from chemical compounds.
Prokaryotes play roles in the carbon and nitrogen cycles. Carbon is returned to the atmosphere by the respiration of animals and other chemoorganotrophic organisms. Consumers use organic compounds generated by producers and release carbon dioxide into the atmosphere. The most important contributor of carbon dioxide to the atmosphere is microbial decomposition of dead material. Nitrogen is recycled in nature from organic compounds to ammonia, ammonium ions, nitrite, nitrate, and nitrogen gas. Gaseous nitrogen is transformed into ammonia through nitrogen fixation. Ammonia is anaerobically catabolized by some prokaryotes, yielding N2 as the final product. Nitrification is the conversion of ammonium into nitrite. Nitrification in soils is carried out by bacteria. Denitrification is also performed by bacteria and transforms nitrate from soils into gaseous nitrogen compounds, such as N2O, NO, and N2.
Art Connections
Figure \(2\): Which of the following statements about the nitrogen cycle is false?
1. Nitrogen fixing bacteria exist on the root nodules of legumes and in the soil.
2. Denitrifying bacteria convert nitrates (NO3-) into nitrogen gas (N2).
3. Ammonification is the process by which ammonium ion (NH4+) is released from decomposing organic compounds.
4. Nitrification is the process by which nitrites (NO2-) are converted to ammonium ion (NH4+).
Answer
D
Glossary
ammonification
process by which ammonia is released during the decomposition of nitrogen-containing organic compounds
chemotroph
organism that obtains energy from chemical compounds
decomposer
organism that carries out the decomposition of dead organisms
denitrification
transformation of nitrate from soil to gaseous nitrogen compounds such as N2O, NO and N2
nitrification
conversion of ammonium into nitrite and nitrate in soils
nitrogen fixation
process by which gaseous nitrogen is transformed, or “fixed” into more readily available forms such as ammonia | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/27%3A_Prokaryotes/27.04%3A_The_Metabolic_Diversity_of_Prokaryotes.txt |
Prokaryotes play vital roles in the movement of carbon dioxide and nitrogen in the carbon and nitrogen cycles.
Learning Objectives
• Give examples of the beneficial roles played by prokaryotes in different ecosystems
Key Points
• Carbon and nitrogen are both macronutrients that are necessary for life on earth; prokaryotes play vital roles in their cycles.
• The carbon cycle is maintained by prokaryotes that remove carbon dioxide and return it to the atmosphere.
• Prokaryotes play a major role in the nitrogen cycle by fixing atomspheric nitrogen into ammonia that plants can use and by converting ammonia into other forms of nitrogen sources.
Key Terms
• carbon cycle: the physical cycle of carbon through the earth’s biosphere, geosphere, hydrosphere, and atmosphere that includes such processes as photosynthesis, decomposition, respiration and carbonification
• nitrogen cycle: the natural circulation of nitrogen, in which atmospheric nitrogen is converted to nitrogen oxides and deposited in the soil, where it is used by organisms or decomposed back to elemental nitrogen
• nitrogen fixation: the conversion of atmospheric nitrogen into ammonia and organic derivatives, by natural means, especially by microorganisms in the soil, into a form that can be assimilated by plants
Role of Prokaryotes in Ecosystems
Prokaryotes are ubiquitous: There is no niche or ecosystem in which they are not present. Prokaryotes play many roles in the environments they occupy, but the roles they play in the carbon and nitrogen cycles are vital to life on earth.
Prokaryotes and the Carbon Cycle
Carbon is one of the most important macronutrients. Prokaryotes play an important role in the carbon cycle. Carbon is cycled through earth’s major reservoirs: land, the atmosphere, aquatic environments, sediments and rocks, and biomass. The movement of carbon is via carbon dioxide, which is removed from the atmosphere by land plants and marine prokaryotes and is returned to the atmosphere via the respiration of chemoorganotrophic organisms, including prokaryotes, fungi, and animals. Although the largest carbon reservoir in terrestrial ecosystems is in rocks and sediments, that carbon is not readily available.
A large amount of available carbon is found in land plants, which are producers that use carbon dioxide from the air to synthesize carbon compounds. Related to this, one very significant source of carbon compounds is humus, which is a mixture of organic materials from dead plants and prokaryotes that have resisted decomposition. Consumers such as animals use organic compounds generated by producers, releasing carbon dioxide to the atmosphere. Then, bacteria and fungi, collectively called decomposers, carry out the breakdown (decomposition) of plants and animals and their organic compounds. The most important contributor of carbon dioxide to the atmosphere is microbial decomposition of dead material (dead animals, plants, and humus).
In aqueous environments and their anoxic sediments, there is another carbon cycle taking place. In this case, the cycle is based on one-carbon compounds. In anoxic sediments, prokaryotes, mostly archaea, produce methane (CH4). This methane moves into the zone above the sediment, which is richer in oxygen and supports bacteria called methane oxidizers that oxidize methane to carbon dioxide, which then returns to the atmosphere.
Prokaryotes and the Nitrogen Cycle
Nitrogen is a very important element for life because it is part of proteins and nucleic acids. As a macronutrient in nature, it is recycled from organic compounds to ammonia, ammonium ions, nitrate, nitrite, and nitrogen gas by myriad processes, many of which are carried out solely by prokaryotes; they are key to the nitrogen cycle. The largest pool of nitrogen available in the terrestrial ecosystem is gaseous nitrogen from the air, but this nitrogen is not usable by plants, which are primary producers. Gaseous nitrogen is transformed, or “fixed,” into more-readily available forms such as ammonia through the process of nitrogen fixation by natural means, especially by microorganisms (prokayotes) in the soil. Ammonia can then be used by plants or converted to other forms.
Another source of ammonia is ammonification, the process by which ammonia is released during the decomposition of nitrogen-containing organic compounds. Ammonia released to the atmosphere, however, represents only 15 percent of the total nitrogen released; the rest is as N2 and N2O. Ammonia is catabolized anaerobically by some prokaryotes, yielding N2 as the final product. Nitrification is the conversion of ammonium to nitrite and nitrate. Nitrification in soils is carried out by bacteria belonging to the genera Nitrosomas, Nitrobacter, and Nitrospira. The bacteria perform the reverse process, the reduction of nitrate from the soils to gaseous compounds such as N2O, NO, and N2, a process called denitrification. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/27%3A_Prokaryotes/27.05%3A_Microbial_Ecology.txt |
Skills to Develop
• Identify bacterial diseases that caused historically important plagues and epidemics
• Describe the link between biofilms and foodborne diseases
• Explain how overuse of antibiotic may be creating “super bugs”
• Explain the importance of MRSA with respect to the problems of antibiotic resistance
Devastating pathogen-borne diseases and plagues, both viral and bacterial in nature, have affected humans since the beginning of human history. The true cause of these diseases was not understood at the time, and some people thought that diseases were a spiritual punishment. Over time, people came to realize that staying apart from afflicted persons, and disposing of the corpses and personal belongings of victims of illness, reduced their own chances of getting sick.
Epidemiologists study how diseases affect a population. An epidemic is a disease that occurs in an unusually high number of individuals in a population at the same time. A pandemic is a widespread, usually worldwide, epidemic. An endemic disease is a disease that is constantly present, usually at low incidence, in a population.
Long History of Bacterial Disease
There are records about infectious diseases as far back as 3000 B.C. A number of significant pandemics caused by bacteria have been documented over several hundred years. Some of the most memorable pandemics led to the decline of cities and nations.
In the 21st century, infectious diseases remain among the leading causes of death worldwide, despite advances made in medical research and treatments in recent decades. A disease spreads when the pathogen that causes it is passed from one person to another. For a pathogen to cause disease, it must be able to reproduce in the host’s body and damage the host in some way.
The Plague of Athens
In 430 B.C., the Plague of Athens killed one-quarter of the Athenian troops that were fighting in the great Peloponnesian War and weakened Athens’ dominance and power. The plague impacted people living in overcrowded Athens as well as troops aboard ships that had to return to Athens. The source of the plague may have been identified recently when researchers from the University of Athens were able to use DNA from teeth recovered from a mass grave. The scientists identified nucleotide sequences from a pathogenic bacterium, Salmonella enterica serovar Typhi (Figure \(1\)), which causes typhoid fever.1 This disease is commonly seen in overcrowded areas and has caused epidemics throughout recorded history.
Bubonic Plagues
From 541 to 750, an outbreak of what was likely a bubonic plague (the Plague of Justinian), eliminated one-quarter to one-half of the human population in the eastern Mediterranean region. The population in Europe dropped by 50 percent during this outbreak. Bubonic plague would strike Europe more than once.
One of the most devastating pandemics was the Black Death (1346 to 1361) that is believed to have been another outbreak of bubonic plague caused by the bacterium Yersinia pestis. It is thought to have originated initially in China and spread along the Silk Road, a network of land and sea trade routes, to the Mediterranean region and Europe, carried by rat fleas living on black rats that were always present on ships. The Black Death reduced the world’s population from an estimated 450 million to about 350 to 375 million. Bubonic plague struck London hard again in the mid-1600s (Figure \(2\)). In modern times, approximately 1,000 to 3,000 cases of plague arise globally each year. Although contracting bubonic plague before antibiotics meant almost certain death, the bacterium responds to several types of modern antibiotics, and mortality rates from plague are now very low.
Link to Learning
Watch a video on the modern understanding of the Black Death—bubonic plague in Europe during the 14th century.
Migration of Diseases to New Populations
Over the centuries, Europeans tended to develop genetic immunity to endemic infectious diseases, but when European conquerors reached the western hemisphere, they brought with them disease-causing bacteria and viruses, which triggered epidemics that completely devastated populations of Native Americans, who had no natural resistance to many European diseases. It has been estimated that up to 90 percent of Native Americans died from infectious diseases after the arrival of Europeans, making conquest of the New World a foregone conclusion.
Emerging and Re-emerging Diseases
The distribution of a particular disease is dynamic. Therefore, changes in the environment, the pathogen, or the host population can dramatically impact the spread of a disease. According to the World Health Organization (WHO) an emerging disease (Figure \(3\)) is one that has appeared in a population for the first time, or that may have existed previously but is rapidly increasing in incidence or geographic range. This definition also includes re-emerging diseases that were previously under control. Approximately 75 percent of recently emerging infectious diseases affecting humans are zoonotic diseases, zoonoses, diseases that primarily infect animals and are transmitted to humans; some are of viral origin and some are of bacterial origin. Brucellosis is an example of a prokaryotic zoonosis that is re-emerging in some regions, and necrotizing fasciitis (commonly known as flesh-eating bacteria) has been increasing in virulence for the last 80 years for unknown reasons.
Some of the present emerging diseases are not actually new, but are diseases that were catastrophic in the past (Figure \(4\)). They devastated populations and became dormant for a while, just to come back, sometimes more virulent than before, as was the case with bubonic plague. Other diseases, like tuberculosis, were never eradicated but were under control in some regions of the world until coming back, mostly in urban centers with high concentrations of immunocompromised people. The WHO has identified certain diseases whose worldwide re-emergence should be monitored. Among these are two viral diseases (dengue fever and yellow fever), and three bacterial diseases (diphtheria, cholera, and bubonic plague). The war against infectious diseases has no foreseeable end.
Biofilms and Disease
Recall that biofilms are microbial communities that are very difficult to destroy. They are responsible for diseases such as infections in patients with cystic fibrosis, Legionnaires’ disease, and otitis media. They produce dental plaque and colonize catheters, prostheses, transcutaneous and orthopedic devices, contact lenses, and internal devices such as pacemakers. They also form in open wounds and burned tissue. In healthcare environments, biofilms grow on hemodialysis machines, mechanical ventilators, shunts, and other medical equipment. In fact, 65 percent of all infections acquired in the hospital (nosocomial infections) are attributed to biofilms. Biofilms are also related to diseases contracted from food because they colonize the surfaces of vegetable leaves and meat, as well as food-processing equipment that isn’t adequately cleaned.
Biofilm infections develop gradually; sometimes, they do not cause symptoms immediately. They are rarely resolved by host defense mechanisms. Once an infection by a biofilm is established, it is very difficult to eradicate, because biofilms tend to be resistant to most of the methods used to control microbial growth, including antibiotics. Biofilms respond poorly or only temporarily to antibiotics; it has been said that they can resist up to 1,000 times the antibiotic concentrations used to kill the same bacteria when they are free-living or planktonic. An antibiotic dose that large would harm the patient; therefore, scientists are working on new ways to get rid of biofilms.
Antibiotics: Are We Facing a Crisis?
The word antibiotic comes from the Greek anti meaning “against” and bios meaning “life.” An antibiotic is a chemical, produced either by microbes or synthetically, that is hostile to the growth of other organisms. Today’s news and media often address concerns about an antibiotic crisis. Are the antibiotics that easily treated bacterial infections in the past becoming obsolete? Are there new “superbugs”—bacteria that have evolved to become more resistant to our arsenal of antibiotics? Is this the beginning of the end of antibiotics? All these questions challenge the healthcare community.
One of the main causes of resistant bacteria is the abuse of antibiotics. The imprudent and excessive use of antibiotics has resulted in the natural selection of resistant forms of bacteria. The antibiotic kills most of the infecting bacteria, and therefore only the resistant forms remain. These resistant forms reproduce, resulting in an increase in the proportion of resistant forms over non-resistant ones. Another major misuse of antibiotics is in patients with colds or the flu, for which antibiotics are useless. Another problem is the excessive use of antibiotics in livestock. The routine use of antibiotics in animal feed promotes bacterial resistance as well. In the United States, 70 percent of the antibiotics produced are fed to animals. These antibiotics are given to livestock in low doses, which maximize the probability of resistance developing, and these resistant bacteria are readily transferred to humans.
Link to Learning
Watch a recent news report on the problem of routine antibiotic administration to livestock and antibiotic-resistant bacteria.
One of the Superbugs: MRSA
The imprudent use of antibiotics has paved the way for bacteria to expand populations of resistant forms. For example, Staphylococcus aureus, often called “staph,” is a common bacterium that can live in the human body and is usually easily treated with antibiotics. A very dangerous strain, however, methicillin-resistant Staphylococcus aureus (MRSA) has made the news over the past few years (Figure \(5\)). This strain is resistant to many commonly used antibiotics, including methicillin, amoxicillin, penicillin, and oxacillin. MRSA can cause infections of the skin, but it can also infect the bloodstream, lungs, urinary tract, or sites of injury. While MRSA infections are common among people in healthcare facilities, they have also appeared in healthy people who haven’t been hospitalized but who live or work in tight populations (like military personnel and prisoners). Researchers have expressed concern about the way this latter source of MRSA targets a much younger population than those residing in care facilities. The Journal of the American Medical Association reported that, among MRSA-afflicted persons in healthcare facilities, the average age is 68, whereas people with “community-associated MRSA” (CA-MRSA) have an average age of 23.2
In summary, the medical community is facing an antibiotic crisis. Some scientists believe that after years of being protected from bacterial infections by antibiotics, we may be returning to a time in which a simple bacterial infection could again devastate the human population. Researchers are developing new antibiotics, but it takes many years to of research and clinical trials, plus financial investments in the millions of dollars, to generate an effective and approved drug.
Foodborne Diseases
Prokaryotes are everywhere: They readily colonize the surface of any type of material, and food is not an exception. Most of the time, prokaryotes colonize food and food-processing equipment in the form of a biofilm. Outbreaks of bacterial infection related to food consumption are common. A foodborne disease (colloquially called “food poisoning”) is an illness resulting from the consumption the pathogenic bacteria, viruses, or other parasites that contaminate food. Although the United States has one of the safest food supplies in the world, the U.S. Centers for Disease Control and Prevention (CDC) has reported that “76 million people get sick, more than 300,000 are hospitalized, and 5,000 Americans die each year from foodborne illness.”
The characteristics of foodborne illnesses have changed over time. In the past, it was relatively common to hear about sporadic cases of botulism, the potentially fatal disease produced by a toxin from the anaerobic bacterium Clostridium botulinum. Some of the most common sources for this bacterium were non-acidic canned foods, homemade pickles, and processed meat and sausages. The can, jar, or package created a suitable anaerobic environment where Clostridium could grow. Proper sterilization and canning procedures have reduced the incidence of this disease.
While people may tend to think of foodborne illnesses as associated with animal-based foods, most cases are now linked to produce. There have been serious, produce-related outbreaks associated with raw spinach in the United States and with vegetable sprouts in Germany, and these types of outbreaks have become more common. The raw spinach outbreak in 2006 was produced by the bacterium E. coli serotype O157:H7. A serotype is a strain of bacteria that carries a set of similar antigens on its cell surface, and there are often many different serotypes of a bacterial species. Most E. coli are not particularly dangerous to humans, but serotype O157:H7 can cause bloody diarrhea and is potentially fatal.
All types of food can potentially be contaminated with bacteria. Recent outbreaks of Salmonella reported by the CDC occurred in foods as diverse as peanut butter, alfalfa sprouts, and eggs. A deadly outbreak in Germany in 2010 was caused by E. coli contamination of vegetable sprouts (Figure \(6\)). The strain that caused the outbreak was found to be a new serotype not previously involved in other outbreaks, which indicates that E. coli is continuously evolving.
Career Connection: Epidemiologist
Epidemiology is the study of the occurrence, distribution, and determinants of health and disease in a population. It is, therefore, part of public health. An epidemiologist studies the frequency and distribution of diseases within human populations and environments.
Epidemiologists collect data about a particular disease and track its spread to identify the original mode of transmission. They sometimes work in close collaboration with historians to try to understand the way a disease evolved geographically and over time, tracking the natural history of pathogens. They gather information from clinical records, patient interviews, surveillance, and any other available means. That information is used to develop strategies, such as vaccinations (Figure \(7\)), and design public health policies to reduce the incidence of a disease or to prevent its spread. Epidemiologists also conduct rapid investigations in case of an outbreak to recommend immediate measures to control it.
An epidemiologist has a bachelor’s degree, plus a master’s degree in public health (MPH). Many epidemiologists are also physicians (and have an M.D.), or they have a Ph.D. in an associated field, such as biology or microbiology.
Summary
Devastating diseases and plagues have been among us since early times. There are records about microbial diseases as far back as 3000 B.C. Infectious diseases remain among the leading causes of death worldwide. Emerging diseases are those rapidly increasing in incidence or geographic range. They can be new or re-emerging diseases (previously under control). Many emerging diseases affecting humans, such as brucellosis, are zoonoses. The WHO has identified a group of diseases whose re-emergence should be monitored: Those caused by bacteria include bubonic plague, diphtheria, and cholera.
Biofilms are considered responsible for diseases such as bacterial infections in patients with cystic fibrosis, Legionnaires’ disease, and otitis media. They produce dental plaque; colonize catheters, prostheses, transcutaneous, and orthopedic devices; and infect contact lenses, open wounds, and burned tissue. Biofilms also produce foodborne diseases because they colonize the surfaces of food and food-processing equipment. Biofilms are resistant to most of the methods used to control microbial growth. The excessive use of antibiotics has resulted in a major global problem, since resistant forms of bacteria have been selected over time. A very dangerous strain, methicillin-resistant Staphylococcus aureus (MRSA), has wreaked havoc recently. Foodborne diseases result from the consumption of contaminated food, pathogenic bacteria, viruses, or parasites that contaminate food.
Footnotes
1. 1 Papagrigorakis MJ, Synodinos PN, and Yapijakis C. Ancient typhoid epidemic reveals possible ancestral strain of Salmonella enterica serovar Typhi. Infect Genet Evol 7 (2007): 126–7, Epub 2006 Jun.
2. 2 Naimi, TS, LeDell, KH, Como-Sabetti, K, et al. Comparison of community- and health care-associated methicillin-resistant Staphylococcus aureus infection. JAMA 290 (2003): 2976–84, doi: 10.1001/jama.290.22.2976.
Glossary
antibiotic
biological substance that, in low concentration, is antagonistic to the growth of prokaryotes
Black Death
devastating pandemic that is believed to have been an outbreak of bubonic plague caused by the bacterium Yersinia pestis
botulism
disease produce by the toxin of the anaerobic bacterium Clostridium botulinum
CA-MRSA
MRSA acquired in the community rather than in a hospital setting
emerging disease
disease making an initial appearance in a population or that is increasing in incidence or geographic range
endemic disease
disease that is constantly present, usually at low incidence, in a population
epidemic
disease that occurs in an unusually high number of individuals in a population at the same time
foodborne disease
any illness resulting from the consumption of contaminated food, or of the pathogenic bacteria, viruses, or other parasites that contaminate food
MRSA
(methicillin-resistant Staphylococcus aureus) very dangerous Staphylococcus aureus strain resistant to multiple antibiotics
pandemic
widespread, usually worldwide, epidemic disease
serotype
strain of bacteria that carries a set of similar antigens on its cell surface, often many in a bacterial species
zoonosis
disease that primarily infects animals that is transmitted to humans | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/27%3A_Prokaryotes/27.06%3A_Bacterial_Diseases_of_Humans.txt |
• 28.1: Eukaryotic Origins and Endosymbiosis
Living things fall into three large groups: Archaea, Bacteria, and Eukarya. The first two have prokaryotic cells, and the third contains all eukaryotes. A relatively sparse fossil record is available to help discern what the first members of each of these lineages looked like, so it is possible that all the events that led to the last common ancestor of extant eukaryotes will remain unknown. However, comparative biology of extant organisms and the limited fossil record provide some insight into
• 28.2: Overview of Protists
In the span of several decades, the Kingdom Protista has been disassembled because sequence analyses have revealed new genetic (and therefore evolutionary) relationships among these eukaryotes. Moreover, protists that exhibit similar morphological features may have evolved analogous structures because of similar selective pressures—rather than because of recent common ancestry. This phenomenon, called convergent evolution, is one reason why protist classification is so challenging.
• 28.3: Characteristics of Excavata
In the span of several decades, the Kingdom Protista has been disassembled because sequence analyses have revealed new genetic (and therefore evolutionary) relationships among these eukaryotes. Moreover, protists that exhibit similar morphological features may have evolved analogous structures because of similar selective pressures—rather than because of recent common ancestry. This phenomenon, called convergent evolution, is one reason why protist classification is so challenging.
• 28.4: Characteristics of Chromalveolata
In the span of several decades, the Kingdom Protista has been disassembled because sequence analyses have revealed new genetic (and therefore evolutionary) relationships among these eukaryotes. Moreover, protists that exhibit similar morphological features may have evolved analogous structures because of similar selective pressures—rather than because of recent common ancestry. This phenomenon, called convergent evolution, is one reason why protist classification is so challenging.
• 28.5: Characteristics of Rhizaria
In the span of several decades, the Kingdom Protista has been disassembled because sequence analyses have revealed new genetic (and therefore evolutionary) relationships among these eukaryotes. Moreover, protists that exhibit similar morphological features may have evolved analogous structures because of similar selective pressures—rather than because of recent common ancestry. This phenomenon, called convergent evolution, is one reason why protist classification is so challenging.
• 28.6: Characteristics of Archaeplastidia
In the span of several decades, the Kingdom Protista has been disassembled because sequence analyses have revealed new genetic (and therefore evolutionary) relationships among these eukaryotes. Moreover, protists that exhibit similar morphological features may have evolved analogous structures because of similar selective pressures—rather than because of recent common ancestry. This phenomenon, called convergent evolution, is one reason why protist classification is so challenging.
• 28.7: Characteristics of Amoebozoa
In the span of several decades, the Kingdom Protista has been disassembled because sequence analyses have revealed new genetic (and therefore evolutionary) relationships among these eukaryotes. Moreover, protists that exhibit similar morphological features may have evolved analogous structures because of similar selective pressures—rather than because of recent common ancestry. This phenomenon, called convergent evolution, is one reason why protist classification is so challenging.
• 28.8: Characteristics of Opisthokonta
In the span of several decades, the Kingdom Protista has been disassembled because sequence analyses have revealed new genetic (and therefore evolutionary) relationships among these eukaryotes. Moreover, protists that exhibit similar morphological features may have evolved analogous structures because of similar selective pressures—rather than because of recent common ancestry. This phenomenon, called convergent evolution, is one reason why protist classification is so challenging.
28: Protists
Skills to Develop
• List the unifying characteristics of eukaryotes
• Describe what scientists know about the origins of eukaryotes based on the last common ancestor
• Explain endosymbiotic theory
Living things fall into three large groups: Archaea, Bacteria, and Eukarya. The first two have prokaryotic cells, and the third contains all eukaryotes. A relatively sparse fossil record is available to help discern what the first members of each of these lineages looked like, so it is possible that all the events that led to the last common ancestor of extant eukaryotes will remain unknown. However, comparative biology of extant organisms and the limited fossil record provide some insight into the history of Eukarya.
The earliest fossils found appear to be Bacteria, most likely cyanobacteria. They are about 3.5 billion years old and are recognizable because of their relatively complex structure and, for prokaryotes, relatively large cells. Most other prokaryotes have small cells, 1 or 2 µm in size, and would be difficult to pick out as fossils. Most living eukaryotes have cells measuring 10 µm or greater. Structures this size, which might be fossils, appear in the geological record about 2.1 billion years ago.
Characteristics of Eukaryotes
Data from these fossils have led comparative biologists to the conclusion that living eukaryotes are all descendants of a single common ancestor. Mapping the characteristics found in all major groups of eukaryotes reveals that the following characteristics must have been present in the last common ancestor, because these characteristics are present in at least some of the members of each major lineage.
1. Cells with nuclei surrounded by a nuclear envelope with nuclear pores. This is the single characteristic that is both necessary and sufficient to define an organism as a eukaryote. All extant eukaryotes have cells with nuclei.
2. Mitochondria. Some extant eukaryotes have very reduced remnants of mitochondria in their cells, whereas other members of their lineages have “typical” mitochondria.
3. A cytoskeleton containing the structural and motility components called actin microfilaments and microtubules. All extant eukaryotes have these cytoskeletal elements.
4. Flagella and cilia, organelles associated with cell motility. Some extant eukaryotes lack flagella and/or cilia, but they are descended from ancestors that possessed them.
5. Chromosomes, each consisting of a linear DNA molecule coiled around basic (alkaline) proteins called histones. The few eukaryotes with chromosomes lacking histones clearly evolved from ancestors that had them.
6. Mitosis, a process of nuclear division wherein replicated chromosomes are divided and separated using elements of the cytoskeleton. Mitosis is universally present in eukaryotes.
7. Sex, a process of genetic recombination unique to eukaryotes in which diploid nuclei at one stage of the life cycle undergo meiosis to yield haploid nuclei and subsequent karyogamy, a stage where two haploid nuclei fuse together to create a diploid zygote nucleus.
8. Members of all major lineages have cell walls, and it might be reasonable to conclude that the last common ancestor could make cell walls during some stage of its life cycle. However, not enough is known about eukaryotes’ cell walls and their development to know how much homology exists among them. If the last common ancestor could make cell walls, it is clear that this ability must have been lost in many groups.
Endosymbiosis and the Evolution of Eukaryotes
In order to understand eukaryotic organisms fully, it is necessary to understand that all extant eukaryotes are descendants of a chimeric organism that was a composite of a host cell and the cell(s) of an alpha-proteobacterium that “took up residence” inside it. This major theme in the origin of eukaryotes is known as endosymbiosis, one cell engulfing another such that the engulfed cell survives and both cells benefit. Over many generations, a symbiotic relationship can result in two organisms that depend on each other so completely that neither could survive on its own. Endosymbiotic events likely contributed to the origin of the last common ancestor of today’s eukaryotes and to later diversification in certain lineages of eukaryotes (Figure \(4\)). Before explaining this further, it is necessary to consider metabolism in prokaryotes.
Prokaryotic Metabolism
Many important metabolic processes arose in prokaryotes, and some of these, such as nitrogen fixation, are never found in eukaryotes. The process of aerobic respiration is found in all major lineages of eukaryotes, and it is localized in the mitochondria. Aerobic respiration is also found in many lineages of prokaryotes, but it is not present in all of them, and many forms of evidence suggest that such anaerobic prokaryotes never carried out aerobic respiration nor did their ancestors.
While today’s atmosphere is about one-fifth molecular oxygen (O2), geological evidence shows that it originally lacked O2. Without oxygen, aerobic respiration would not be expected, and living things would have relied on fermentation instead. At some point before, about 3.5 billion years ago, some prokaryotes began using energy from sunlight to power anabolic processes that reduce carbon dioxide to form organic compounds. That is, they evolved the ability to photosynthesize. Hydrogen, derived from various sources, was captured using light-powered reactions to reduce fixed carbon dioxide in the Calvin cycle. The group of Gram-negative bacteria that gave rise to cyanobacteria used water as the hydrogen source and released O2 as a waste product.
Eventually, the amount of photosynthetic oxygen built up in some environments to levels that posed a risk to living organisms, since it can damage many organic compounds. Various metabolic processes evolved that protected organisms from oxygen, one of which, aerobic respiration, also generated high levels of ATP. It became widely present among prokaryotes, including in a group we now call alpha-proteobacteria. Organisms that did not acquire aerobic respiration had to remain in oxygen-free environments. Originally, oxygen-rich environments were likely localized around places where cyanobacteria were active, but by about 2 billion years ago, geological evidence shows that oxygen was building up to higher concentrations in the atmosphere. Oxygen levels similar to today’s levels only arose within the last 700 million years.
Recall that the first fossils that we believe to be eukaryotes date to about 2 billion years old, so they appeared as oxygen levels were increasing. Also, recall that all extant eukaryotes descended from an ancestor with mitochondria. These organelles were first observed by light microscopists in the late 1800s, where they appeared to be somewhat worm-shaped structures that seemed to be moving around in the cell. Some early observers suggested that they might be bacteria living inside host cells, but these hypotheses remained unknown or rejected in most scientific communities.
Endosymbiotic Theory
As cell biology developed in the twentieth century, it became clear that mitochondria were the organelles responsible for producing ATP using aerobic respiration. In the 1960s, American biologist Lynn Margulis developed endosymbiotic theory, which states that eukaryotes may have been a product of one cell engulfing another, one living within another, and evolving over time until the separate cells were no longer recognizable as such. In 1967, Margulis introduced new work on the theory and substantiated her findings through microbiological evidence. Although Margulis’ work initially was met with resistance, this once-revolutionary hypothesis is now widely (but not completely) accepted, with work progressing on uncovering the steps involved in this evolutionary process and the key players involved. Much still remains to be discovered about the origins of the cells that now make up the cells in all living eukaryotes.
Broadly, it has become clear that many of our nuclear genes and the molecular machinery responsible for replication and expression appear closely related to those in Archaea. On the other hand, the metabolic organelles and genes responsible for many energy-harvesting processes had their origins in bacteria. Much remains to be clarified about how this relationship occurred; this continues to be an exciting field of discovery in biology. For instance, it is not known whether the endosymbiotic event that led to mitochondria occurred before or after the host cell had a nucleus. Such organisms would be among the extinct precursors of the last common ancestor of eukaryotes.
Mitochondria
One of the major features distinguishing prokaryotes from eukaryotes is the presence of mitochondria. Eukaryotic cells may contain anywhere from one to several thousand mitochondria, depending on the cell’s level of energy consumption. Each mitochondrion measures 1 to 10 or greater micrometers in length and exists in the cell as an organelle that can be ovoid to worm-shaped to intricately branched (Figure \(1\)). Mitochondria arise from the division of existing mitochondria; they may fuse together; and they may be moved around inside the cell by interactions with the cytoskeleton. However, mitochondria cannot survive outside the cell. As the atmosphere was oxygenated by photosynthesis, and as successful aerobic prokaryotes evolved, evidence suggests that an ancestral cell with some membrane compartmentalization engulfed a free-living aerobic prokaryote, specifically an alpha-proteobacterium, thereby giving the host cell the ability to use oxygen to release energy stored in nutrients. Alpha-proteobacteria are a large group of bacteria that includes species symbiotic with plants, disease organisms that can infect humans via ticks, and many free-living species that use light for energy. Several lines of evidence support that mitochondria are derived from this endosymbiotic event. Most mitochondria are shaped like alpha-proteobacteria and are surrounded by two membranes, which would result when one membrane-bound organism was engulfed into a vacuole by another membrane-bound organism. The mitochondrial inner membrane is extensive and involves substantial infoldings called cristae that resemble the textured, outer surface of alpha-proteobacteria. The matrix and inner membrane are rich with the enzymes necessary for aerobic respiration.
Mitochondria divide independently by a process that resembles binary fission in prokaryotes. Specifically, mitochondria are not formed from scratch (de novo) by the eukaryotic cell; they reproduce within it and are distributed with the cytoplasm when a cell divides or two cells fuse. Therefore, although these organelles are highly integrated into the eukaryotic cell, they still reproduce as if they are independent organisms within the cell. However, their reproduction is synchronized with the activity and division of the cell. Mitochondria have their own (usually) circular DNA chromosome that is stabilized by attachments to the inner membrane and carries genes similar to genes expressed by alpha-proteobacteria. Mitochondria also have special ribosomes and transfer RNAs that resemble these components in prokaryotes. These features all support that mitochondria were once free-living prokaryotes.
Mitochondria that carry out aerobic respiration have their own genomes, with genes similar to those in alpha-proteobacteria. However, many of the genes for respiratory proteins are located in the nucleus. When these genes are compared to those of other organisms, they appear to be of alpha-proteobacterial origin. Additionally, in some eukaryotic groups, such genes are found in the mitochondria, whereas in other groups, they are found in the nucleus. This has been interpreted as evidence that genes have been transferred from the endosymbiont chromosome to the host genome. This loss of genes by the endosymbiont is probably one explanation why mitochondria cannot live without a host.
Some living eukaryotes are anaerobic and cannot survive in the presence of too much oxygen. Some appear to lack organelles that could be recognized as mitochondria. In the 1970s to the early 1990s, many biologists suggested that some of these eukaryotes were descended from ancestors whose lineages had diverged from the lineage of mitochondrion-containing eukaryotes before endosymbiosis occurred. However, later findings suggest that reduced organelles are found in most, if not all, anaerobic eukaryotes, and that all eukaryotes appear to carry some genes in their nuclei that are of mitochondrial origin. In addition to the aerobic generation of ATP, mitochondria have several other metabolic functions. One of these functions is to generate clusters of iron and sulfur that are important cofactors of many enzymes. Such functions are often associated with the reduced mitochondrion-derived organelles of anaerobic eukaryotes. Therefore, most biologists accept that the last common ancestor of eukaryotes had mitochondria.
Plastids
Some groups of eukaryotes are photosynthetic. Their cells contain, in addition to the standard eukaryotic organelles, another kind of organelle called a plastid. When such cells are carrying out photosynthesis, their plastids are rich in the pigment chlorophyll a and a range of other pigments, called accessory pigments, which are involved in harvesting energy from light. Photosynthetic plastids are called chloroplasts (Figure \(2\)).
Like mitochondria, plastids appear to have an endosymbiotic origin. This hypothesis was also championed by Lynn Margulis. Plastids are derived from cyanobacteria that lived inside the cells of an ancestral, aerobic, heterotrophic eukaryote. This is called primary endosymbiosis, and plastids of primary origin are surrounded by two membranes. The best evidence is that this has happened twice in the history of eukaryotes. In one case, the common ancestor of the major lineage/supergroup Archaeplastida took on a cyanobacterial endosymbiont; in the other, the ancestor of the small amoeboid rhizarian taxon, Paulinella, took on a different cyanobacterial endosymbiont. Almost all photosynthetic eukaryotes are descended from the first event, and only a couple of species are derived from the other.
Cyanobacteria are a group of Gram-negative bacteria with all the conventional structures of the group. However, unlike most prokaryotes, they have extensive, internal membrane-bound sacs called thylakoids. Chlorophyll is a component of these membranes, as are many of the proteins of the light reactions of photosynthesis. Cyanobacteria also have the peptidoglycan wall and lipopolysaccharide layer associated with Gram-negative bacteria.
Chloroplasts of primary origin have thylakoids, a circular DNA chromosome, and ribosomes similar to those of cyanobacteria. Each chloroplast is surrounded by two membranes. In the group of Archaeplastida called the glaucophytes and in Paulinella, a thin peptidoglycan layer is present between the outer and inner plastid membranes. All other plastids lack this relictual cyanobacterial wall. The outer membrane surrounding the plastid is thought to be derived from the vacuole in the host, and the inner membrane is thought to be derived from the plasma membrane of the symbiont.
There is also, as with the case of mitochondria, strong evidence that many of the genes of the endosymbiont were transferred to the nucleus. Plastids, like mitochondria, cannot live independently outside the host. In addition, like mitochondria, plastids are derived from the division of other plastids and never built from scratch. Researchers have suggested that the endosymbiotic event that led to Archaeplastida occurred 1 to 1.5 billion years ago, at least 5 hundred million years after the fossil record suggests that eukaryotes were present.
Not all plastids in eukaryotes are derived directly from primary endosymbiosis. Some of the major groups of algae became photosynthetic by secondary endosymbiosis, that is, by taking in either green algae or red algae (both from Archaeplastida) as endosymbionts (Figure \(3\)). Numerous microscopic and genetic studies have supported this conclusion. Secondary plastids are surrounded by three or more membranes, and some secondary plastids even have clear remnants of the nucleus of endosymbiotic alga. Others have not “kept” any remnants. There are cases where tertiary or higher-order endosymbiotic events are the best explanations for plastids in some eukaryotes.
Art Connection
What evidence is there that mitochondria were incorporated into the ancestral eukaryotic cell before chloroplasts?
Evolution Connection: Secondary Endosymbiosis in Chlorarachniophytes
Endosymbiosis involves one cell engulfing another to produce, over time, a coevolved relationship in which neither cell could survive alone. The chloroplasts of red and green algae, for instance, are derived from the engulfment of a photosynthetic cyanobacterium by an early prokaryote.
This leads to the question of the possibility of a cell containing an endosymbiont to itself become engulfed, resulting in a secondary endosymbiosis. Molecular and morphological evidence suggest that the chlorarachniophyte protists are derived from a secondary endosymbiotic event. Chlorarachniophytes are rare algae indigenous to tropical seas and sand that can be classified into the rhizarian supergroup. Chlorarachniophytes extend thin cytoplasmic strands, interconnecting themselves with other chlorarachniophytes, in a cytoplasmic network. These protists are thought to have originated when a eukaryote engulfed a green alga, the latter of which had already established an endosymbiotic relationship with a photosynthetic cyanobacterium (Figure \(5\)).
Several lines of evidence support that chlorarachniophytes evolved from secondary endosymbiosis. The chloroplasts contained within the green algal endosymbionts still are capable of photosynthesis, making chlorarachniophytes photosynthetic. The green algal endosymbiont also exhibits a stunted vestigial nucleus. In fact, it appears that chlorarachniophytes are the products of an evolutionarily recent secondary endosymbiotic event. The plastids of chlorarachniophytes are surrounded by four membranes: The first two correspond to the inner and outer membranes of the photosynthetic cyanobacterium, the third corresponds to the green alga, and the fourth corresponds to the vacuole that surrounded the green alga when it was engulfed by the chlorarachniophyte ancestor. In other lineages that involved secondary endosymbiosis, only three membranes can be identified around plastids. This is currently rectified as a sequential loss of a membrane during the course of evolution.
The process of secondary endosymbiosis is not unique to chlorarachniophytes. In fact, secondary endosymbiosis of green algae also led to euglenid protists, whereas secondary endosymbiosis of red algae led to the evolution of dinoflagellates, apicomplexans, and stramenopiles.
Summary
The oldest fossil evidence of eukaryotes is about 2 billion years old. Fossils older than this all appear to be prokaryotes. It is probable that today’s eukaryotes are descended from an ancestor that had a prokaryotic organization. The last common ancestor of today’s Eukarya had several characteristics, including cells with nuclei that divided mitotically and contained linear chromosomes where the DNA was associated with histones, a cytoskeleton and endomembrane system, and the ability to make cilia/flagella during at least part of its life cycle. It was aerobic because it had mitochondria that were the result of an aerobic alpha-proteobacterium that lived inside a host cell. Whether this host had a nucleus at the time of the initial symbiosis remains unknown. The last common ancestor may have had a cell wall for at least part of its life cycle, but more data are needed to confirm this hypothesis. Today’s eukaryotes are very diverse in their shapes, organization, life cycles, and number of cells per individual.
Art Connections
Figure \(4\): What evidence is there that mitochondria were incorporated into the ancestral eukaryotic cell before chloroplasts?
Answer
All eukaryotic cells have mitochondria, but not all eukaryotic cells have chloroplasts.
Glossary
endosymbiosis
engulfment of one cell within another such that the engulfed cell survives, and both cells benefit; the process responsible for the evolution of mitochondria and chloroplasts in eukaryotes
endosymbiotic theory
theory that states that eukaryotes may have been a product of one cell engulfing another, one living within another, and evolving over time until the separate cells were no longer recognizable as such
plastid
one of a group of related organelles in plant cells that are involved in the storage of starches, fats, proteins, and pigments | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/28%3A_Protists/28.01%3A_Eukaryotic_Origins_and_Endosymbiosis.txt |
Skills to Develop
• Describe representative protist organisms from each of the six presently recognized supergroups of eukaryotes
• Identify the evolutionary relationships of plants, animals, and fungi within the six presently recognized supergroups of eukaryotes
In the span of several decades, the Kingdom Protista has been disassembled because sequence analyses have revealed new genetic (and therefore evolutionary) relationships among these eukaryotes. Moreover, protists that exhibit similar morphological features may have evolved analogous structures because of similar selective pressures—rather than because of recent common ancestry. This phenomenon, called convergent evolution, is one reason why protist classification is so challenging. The emerging classification scheme groups the entire domain Eukaryota into six “supergroups” that contain all of the protists as well as animals, plants, and fungi that evolved from a common ancestor (Figure \(1\)). The supergroups are believed to be monophyletic, meaning that all organisms within each supergroup are believed to have evolved from a single common ancestor, and thus all members are most closely related to each other than to organisms outside that group. There is still evidence lacking for the monophyly of some groups.
The classification of eukaryotes is still in flux, and the six supergroups may be modified or replaced by a more appropriate hierarchy as genetic, morphological, and ecological data accumulate. Keep in mind that the classification scheme presented here is just one of several hypotheses, and the true evolutionary relationships are still to be determined. When learning about protists, it is helpful to focus less on the nomenclature and more on the commonalities and differences that define the groups themselves.
Excavata
Many of the protist species classified into the supergroup Excavata are asymmetrical, single-celled organisms with a feeding groove “excavated” from one side. This supergroup includes heterotrophic predators, photosynthetic species, and parasites. Its subgroups are the diplomonads, parabasalids, and euglenozoans.
Diplomonads
Among the Excavata are the diplomonads, which include the intestinal parasite, Giardia lamblia (Figure \(2\)). Until recently, these protists were believed to lack mitochondria. Mitochondrial remnant organelles, called mitosomes, have since been identified in diplomonads, but these mitosomes are essentially nonfunctional. Diplomonads exist in anaerobic environments and use alternative pathways, such as glycolysis, to generate energy. Each diplomonad cell has two identical nuclei and uses several flagella for locomotion.
Parabasalids
A second Excavata subgroup, the parabasalids, also exhibits semi-functional mitochondria. In parabasalids, these structures function anaerobically and are called hydrogenosomes because they produce hydrogen gas as a byproduct. Parabasalids move with flagella and membrane rippling. Trichomonas vaginalis, a parabasalid that causes a sexually transmitted disease in humans, employs these mechanisms to transit through the male and female urogenital tracts. T. vaginalis causes trichamoniasis, which appears in an estimated 180 million cases worldwide each year. Whereas men rarely exhibit symptoms during an infection with this protist, infected women may become more susceptible to secondary infection with human immunodeficiency virus (HIV) and may be more likely to develop cervical cancer. Pregnant women infected with T. vaginalis are at an increased risk of serious complications, such as pre-term delivery.
Euglenozoans
Euglenozoans includes parasites, heterotrophs, autotrophs, and mixotrophs, ranging in size from 10 to 500 µm. Euglenoids move through their aquatic habitats using two long flagella that guide them toward light sources sensed by a primitive ocular organ called an eyespot. The familiar genus, Euglena, encompasses some mixotrophic species that display a photosynthetic capability only when light is present. In the dark, the chloroplasts of Euglena shrink up and temporarily cease functioning, and the cells instead take up organic nutrients from their environment.
The human parasite, Trypanosoma brucei, belongs to a different subgroup of Euglenozoa, the kinetoplastids. The kinetoplastid subgroup is named after the kinetoplast, a DNA mass carried within the single, oversized mitochondrion possessed by each of these cells. This subgroup includes several parasites, collectively called trypanosomes, which cause devastating human diseases and infect an insect species during a portion of their life cycle. T. brucei develops in the gut of the tsetse fly after the fly bites an infected human or other mammalian host. The parasite then travels to the insect salivary glands to be transmitted to another human or other mammal when the infected tsetse fly consumes another blood meal. T. brucei is common in central Africa and is the causative agent of African sleeping sickness, a disease associated with severe chronic fatigue, coma, and can be fatal if left untreated.
Trypanosoma brucei
Watch this video to see T. brucei swimming. https://youtu.be/EnsydwITLYk
Chromalveolata
Current evidence suggests that species classified as chromalveolates are derived from a common ancestor that engulfed a photosynthetic red algal cell, which itself had already evolved chloroplasts from an endosymbiotic relationship with a photosynthetic prokaryote. Therefore, the ancestor of chromalveolates is believed to have resulted from a secondary endosymbiotic event. However, some chromalveolates appear to have lost red alga-derived plastid organelles or lack plastid genes altogether. Therefore, this supergroup should be considered a hypothesis-based working group that is subject to change. Chromalveolates include very important photosynthetic organisms, such as diatoms, brown algae, and significant disease agents in animals and plants. The chromalveolates can be subdivided into alveolates and stramenopiles.
Alveolates: Dinoflagellates, Apicomplexians, and Ciliates
A large body of data supports that the alveolates are derived from a shared common ancestor. The alveolates are named for the presence of an alveolus, or membrane-enclosed sac, beneath the cell membrane. The exact function of the alveolus is unknown, but it may be involved in osmoregulation. The alveolates are further categorized into some of the better-known protists: the dinoflagellates, the apicomplexans, and the ciliates.
Dinoflagellates exhibit extensive morphological diversity and can be photosynthetic, heterotrophic, or mixotrophic. Many dinoflagellates are encased in interlocking plates of cellulose. Two perpendicular flagella fit into the grooves between the cellulose plates, with one flagellum extending longitudinally and a second encircling the dinoflagellate (Figure \(4\)). Together, the flagella contribute to the characteristic spinning motion of dinoflagellates. These protists exist in freshwater and marine habitats, and are a component of plankton, the typically microscopic organisms that drift through the water and serve as a crucial food source for larger aquatic organisms.
Some dinoflagellates generate light, called bioluminescence, when they are jarred or stressed. Large numbers of marine dinoflagellates (billions or trillions of cells per wave) can emit light and cause an entire breaking wave to twinkle or take on a brilliant blue color (Figure \(5\)). For approximately 20 species of marine dinoflagellates, population explosions (also called blooms) during the summer months can tint the ocean with a muddy red color. This phenomenon is called a red tide, and it results from the abundant red pigments present in dinoflagellate plastids. In large quantities, these dinoflagellate species secrete an asphyxiating toxin that can kill fish, birds, and marine mammals. Red tides can be massively detrimental to commercial fisheries, and humans who consume these protists may become poisoned.
The apicomplexan protists are so named because their microtubules, fibrin, and vacuoles are asymmetrically distributed at one end of the cell in a structure called an apical complex (Figure \(6\)). The apical complex is specialized for entry and infection of host cells. Indeed, all apicomplexans are parasitic. This group includes the genus Plasmodium, which causes malaria in humans. Apicomplexan life cycles are complex, involving multiple hosts and stages of sexual and asexual reproduction.
The ciliates, which include Paramecium and Tetrahymena, are a group of protists 10 to 3,000 micrometers in length that are covered in rows, tufts, or spirals of tiny cilia. By beating their cilia synchronously or in waves, ciliates can coordinate directed movements and ingest food particles. Certain ciliates have fused cilia-based structures that function like paddles, funnels, or fins. Ciliates also are surrounded by a pellicle, providing protection without compromising agility. The genus Paramecium includes protists that have organized their cilia into a plate-like primitive mouth, called an oral groove, which is used to capture and digest bacteria (Figure \(7\)). Food captured in the oral groove enters a food vacuole, where it combines with digestive enzymes. Waste particles are expelled by an exocytic vesicle that fuses at a specific region on the cell membrane, called the anal pore. In addition to a vacuole-based digestive system, Paramecium also uses contractile vacuoles, which are osmoregulatory vesicles that fill with water as it enters the cell by osmosis and then contract to squeeze water from the cell.
Link to Learning
Watch the video of the contractile vacuole of Paramecium expelling water to keep the cell osmotically balanced.
Paramecium has two nuclei, a macronucleus and a micronucleus, in each cell. The micronucleus is essential for sexual reproduction, whereas the macronucleus directs asexual binary fission and all other biological functions. The process of sexual reproduction in Paramecium underscores the importance of the micronucleus to these protists. Paramecium and most other ciliates reproduce sexually by conjugation. This process begins when two different mating types of Paramecium make physical contact and join with a cytoplasmic bridge (Figure \(8\)). The diploid micronucleus in each cell then undergoes meiosis to produce four haploid micronuclei. Three of these degenerate in each cell, leaving one micronucleus that then undergoes mitosis, generating two haploid micronuclei. The cells each exchange one of these haploid nuclei and move away from each other. A similar process occurs in bacteria that have plasmids. Fusion of the haploid micronuclei generates a completely novel diploid pre-micronucleus in each conjugative cell. This pre-micronucleus undergoes three rounds of mitosis to produce eight copies, and the original macronucleus disintegrates. Four of the eight pre-micronuclei become full-fledged micronuclei, whereas the other four perform multiple rounds of DNA replication and go on to become new macronuclei. Two cell divisions then yield four new Paramecia from each original conjugative cell.
Exercise
Which of the following statements about Paramecium sexual reproduction is false?
1. The macronuclei are derived from micronuclei.
2. Both mitosis and meiosis occur during sexual reproduction.
3. The conjugate pair swaps macronucleii.
4. Each parent produces four daughter cells.
Stramenopiles: Diatoms, Brown Algae, Golden Algae and Oomycetes
The other subgroup of chromalveolates, the stramenopiles, includes photosynthetic marine algae and heterotrophic protists. The unifying feature of this group is the presence of a textured, or “hairy,” flagellum. Many stramenopiles also have an additional flagellum that lacks hair-like projections (Figure \(9\)). Members of this subgroup range in size from single-celled diatoms to the massive and multicellular kelp.
The diatoms are unicellular photosynthetic protists that encase themselves in intricately patterned, glassy cell walls composed of silicon dioxide in a matrix of organic particles (Figure \(10\)). These protists are a component of freshwater and marine plankton. Most species of diatoms reproduce asexually, although some instances of sexual reproduction and sporulation also exist. Some diatoms exhibit a slit in their silica shell, called a raphe. By expelling a stream of mucopolysaccharides from the raphe, the diatom can attach to surfaces or propel itself in one direction.
During periods of nutrient availability, diatom populations bloom to numbers greater than can be consumed by aquatic organisms. The excess diatoms die and sink to the sea floor where they are not easily reached by saprobes that feed on dead organisms. As a result, the carbon dioxide that the diatoms had consumed and incorporated into their cells during photosynthesis is not returned to the atmosphere. In general, this process by which carbon is transported deep into the ocean is described as the biological carbon pump, because carbon is “pumped” to the ocean depths where it is inaccessible to the atmosphere as carbon dioxide. The biological carbon pump is a crucial component of the carbon cycle that maintains lower atmospheric carbon dioxide levels.
Like diatoms, golden algae are largely unicellular, although some species can form large colonies. Their characteristic gold color results from their extensive use of carotenoids, a group of photosynthetic pigments that are generally yellow or orange in color. Golden algae are found in both freshwater and marine environments, where they form a major part of the plankton community.
The brown algae are primarily marine, multicellular organisms that are known colloquially as seaweeds. Giant kelps are a type of brown algae. Some brown algae have evolved specialized tissues that resemble terrestrial plants, with root-like holdfasts, stem-like stipes, and leaf-like blades that are capable of photosynthesis. The stipes of giant kelps are enormous, extending in some cases for 60 meters. A variety of algal life cycles exists, but the most complex is alternation of generations, in which both haploid and diploid stages involve multicellularity. Compare this life cycle to that of humans, for instance. Haploid gametes produced by meiosis (sperm and egg) combine in fertilization to generate a diploid zygote that undergoes many rounds of mitosis to produce a multicellular embryo and then a fetus. However, the individual sperm and egg themselves never become multicellular beings. Terrestrial plants also have evolved alternation of generations. In the brown algae genus Laminaria, haploid spores develop into multicellular gametophytes, which produce haploid gametes that combine to produce diploid organisms that then become multicellular organisms with a different structure from the haploid form (Figure \(11\)). Certain other organisms perform alternation of generations in which both the haploid and diploid forms look the same.
Exercise
Which of the following statements about the Laminaria life cycle is false?
1. 1n zoospores form in the sporangia.
2. The sporophyte is the 2n plant.
3. The gametophyte is diploid.
4. Both the gametophyte and sporophyte stages are multicellular.
The water molds, oomycetes (“egg fungus”), were so-named based on their fungus-like morphology, but molecular data have shown that the water molds are not closely related to fungi. The oomycetes are characterized by a cellulose-based cell wall and an extensive network of filaments that allow for nutrient uptake. As diploid spores, many oomycetes have two oppositely directed flagella (one hairy and one smooth) for locomotion. The oomycetes are nonphotosynthetic and include many saprobes and parasites. The saprobes appear as white fluffy growths on dead organisms (Figure \(12\)). Most oomycetes are aquatic, but some parasitize terrestrial plants. One plant pathogen is Phytophthora infestans, the causative agent of late blight of potatoes, such as occurred in the nineteenth century Irish potato famine.
Rhizaria
The Rhizaria supergroup includes many of the amoebas, most of which have threadlike or needle-like pseudopodia (Figure \(13\)). Pseudopodia function to trap and engulf food particles and to direct movement in rhizarian protists. These pseudopods project outward from anywhere on the cell surface and can anchor to a substrate. The protist then transports its cytoplasm into the pseudopod, thereby moving the entire cell. This type of motion, called cytoplasmic streaming, is used by several diverse groups of protists as a means of locomotion or as a method to distribute nutrients and oxygen.
Link to Learning
Take a look at this video to see cytoplasmic streaming in a green alga.
Forams
Foraminiferans, or forams, are unicellular heterotrophic protists, ranging from approximately 20 micrometers to several centimeters in length, and occasionally resembling tiny snails (Figure \(14\)). As a group, the forams exhibit porous shells, called tests that are built from various organic materials and typically hardened with calcium carbonate. The tests may house photosynthetic algae, which the forams can harvest for nutrition. Foram pseudopodia extend through the pores and allow the forams to move, feed, and gather additional building materials. Typically, forams are associated with sand or other particles in marine or freshwater habitats. Foraminiferans are also useful as indicators of pollution and changes in global weather patterns.
Radiolarians
A second subtype of Rhizaria, the radiolarians, exhibit intricate exteriors of glassy silica with radial or bilateral symmetry (Figure \(15\)). Needle-like pseudopods supported by microtubules radiate outward from the cell bodies of these protists and function to catch food particles. The shells of dead radiolarians sink to the ocean floor, where they may accumulate in 100 meter-thick depths. Preserved, sedimented radiolarians are very common in the fossil record.
Archaeplastida
Red algae and green algae are included in the supergroup Archaeplastida. It was from a common ancestor of these protists that the land plants evolved, since their closest relatives are found in this group. Molecular evidence supports that all Archaeplastida are descendents of an endosymbiotic relationship between a heterotrophic protist and a cyanobacterium. The red and green algae include unicellular, multicellular, and colonial forms.
Red Algae
Red algae, or rhodophytes, are primarily multicellular, lack flagella, and range in size from microscopic, unicellular protists to large, multicellular forms grouped into the informal seaweed category. The red algae life cycle is an alternation of generations. Some species of red algae contain phycoerythrins, photosynthetic accessory pigments that are red in color and outcompete the green tint of chlorophyll, making these species appear as varying shades of red. Other protists classified as red algae lack phycoerythrins and are parasites. Red algae are common in tropical waters where they have been detected at depths of 260 meters. Other red algae exist in terrestrial or freshwater environments.
Green Algae: Chlorophytes and Charophytes
The most abundant group of algae is the green algae. The green algae exhibit similar features to the land plants, particularly in terms of chloroplast structure. That this group of protists shared a relatively recent common ancestor with land plants is well supported. The green algae are subdivided into the chlorophytes and the charophytes. The charophytes are the closest living relatives to land plants and resemble them in morphology and reproductive strategies. Charophytes are common in wet habitats, and their presence often signals a healthy ecosystem.
The chlorophytes exhibit great diversity of form and function. Chlorophytes primarily inhabit freshwater and damp soil, and are a common component of plankton. Chlamydomonas is a simple, unicellular chlorophyte with a pear-shaped morphology and two opposing, anterior flagella that guide this protist toward light sensed by its eyespot. More complex chlorophyte species exhibit haploid gametes and spores that resemble Chlamydomonas.
The chlorophyte Volvox is one of only a few examples of a colonial organism, which behaves in some ways like a collection of individual cells, but in other ways like the specialized cells of a multicellular organism (Figure \(16\)). Volvox colonies contain 500 to 60,000 cells, each with two flagella, contained within a hollow, spherical matrix composed of a gelatinous glycoprotein secretion. Individual Volvox cells move in a coordinated fashion and are interconnected by cytoplasmic bridges. Only a few of the cells reproduce to create daughter colonies, an example of basic cell specialization in this organism.
True multicellular organisms, such as the sea lettuce, Ulva, are represented among the chlorophytes. In addition, some chlorophytes exist as large, multinucleate, single cells. Species in the genus Caulerpa exhibit flattened fern-like foliage and can reach lengths of 3 meters (Figure \(17\)). Caulerpa species undergo nuclear division, but their cells do not complete cytokinesis, remaining instead as massive and elaborate single cells.
Amoebozoa
The amoebozoans characteristically exhibit pseudopodia that extend like tubes or flat lobes, rather than the hair-like pseudopodia of rhizarian amoeba (Figure \(18\)). The Amoebozoa include several groups of unicellular amoeba-like organisms that are free-living or parasites.
Slime Molds
A subset of the amoebozoans, the slime molds, has several morphological similarities to fungi that are thought to be the result of convergent evolution. For instance, during times of stress, some slime molds develop into spore-generating fruiting bodies, much like fungi.
The slime molds are categorized on the basis of their life cycles into plasmodial or cellular types. Plasmodial slime molds are composed of large, multinucleate cells and move along surfaces like an amorphous blob of slime during their feeding stage (Figure \(19\)). Food particles are lifted and engulfed into the slime mold as it glides along. Upon maturation, the plasmodium takes on a net-like appearance with the ability to form fruiting bodies, or sporangia, during times of stress. Haploid spores are produced by meiosis within the sporangia, and spores can be disseminated through the air or water to potentially land in more favorable environments. If this occurs, the spores germinate to form ameboid or flagellate haploid cells that can combine with each other and produce a diploid zygotic slime mold to complete the life cycle.
The cellular slime molds function as independent amoeboid cells when nutrients are abundant (Figure \(20\)). When food is depleted, cellular slime molds pile onto each other into a mass of cells that behaves as a single unit, called a slug. Some cells in the slug contribute to a 2–3-millimeter stalk, drying up and dying in the process. Cells atop the stalk form an asexual fruiting body that contains haploid spores. As with plasmodial slime molds, the spores are disseminated and can germinate if they land in a moist environment. One representative genus of the cellular slime molds is Dictyostelium, which commonly exists in the damp soil of forests.
Link to Learning
View this site to see the formation of a fruiting body by a cellular slime mold.
Opisthokonta
The opisthokonts include the animal-like choanoflagellates, which are believed to resemble the common ancestor of sponges and, in fact, all animals. Choanoflagellates include unicellular and colonial forms, and number about 244 described species. These organisms exhibit a single, apical flagellum that is surrounded by a contractile collar composed of microvilli. The collar uses a similar mechanism to sponges to filter out bacteria for ingestion by the protist. The morphology of choanoflagellates was recognized early on as resembling the collar cells of sponges, and suggesting a possible relationship to animals.
The Mesomycetozoa form a small group of parasites, primarily of fish, and at least one form that can parasitize humans. Their life cycles are poorly understood. These organisms are of special interest, because they appear to be so closely related to animals. In the past, they were grouped with fungi and other protists based on their morphology.
Summary
The process of classifying protists into meaningful groups is ongoing, but genetic data in the past 20 years have clarified many relationships that were previously unclear or mistaken. The majority view at present is to order all eukaryotes into six supergroups: Excavata, Chromalveolata, Rhizaria, Archaeplastida, Amoebozoa, and Opisthokonta. The goal of this classification scheme is to create clusters of species that all are derived from a common ancestor. At present, the monophyly of some of the supergroups are better supported by genetic data than others. Although tremendous variation exists within the supergroups, commonalities at the morphological, physiological, and ecological levels can be identified.
Art Connections
Figure \(8\): Which of the following statements about Paramecium sexual reproduction is false?
1. The macronuclei are derived from micronuclei.
2. Both mitosis and meiosis occur during sexual reproduction.
3. The conjugate pair swaps macronuclei.
4. Each parent produces four daughter cells.
Answer
C
Figure \(11\): Which of the following statements about the Laminaria life cycle is false?
1. 1n zoospores form in the sporangia.
2. The sporophyte is the 2n plant.
3. The gametophyte is diploid.
4. Both the gametophyte and sporophyte stages are multicellular.
Answer
C
Glossary
biological carbon pump
process by which inorganic carbon is fixed by photosynthetic species that then die and fall to the sea floor where they cannot be reached by saprobes and their carbon dioxide consumption cannot be returned to the atmosphere
bioluminescence
generation and emission of light by an organism, as in dinoflagellates
contractile vacuole
vesicle that fills with water (as it enters the cell by osmosis) and then contracts to squeeze water from the cell; an osmoregulatory vesicle
cytoplasmic streaming
movement of cytoplasm into an extended pseudopod such that the entire cell is transported to the site of the pseudopod
hydrogenosome
organelle carried by parabasalids (Excavata) that functions anaerobically and outputs hydrogen gas as a byproduct; likely evolved from mitochondria
kinetoplast
mass of DNA carried within the single, oversized mitochondrion, characteristic of kinetoplastids (phylum: Euglenozoa)
mitosome
nonfunctional organelle carried in the cells of diplomonads (Excavata) that likely evolved from a mitochondrion
plankton
diverse group of mostly microscopic organisms that drift in marine and freshwater systems and serve as a food source for larger aquatic organisms
raphe
slit in the silica shell of diatoms through which the protist secretes a stream of mucopolysaccharides for locomotion and attachment to substrates
test
porous shell of a foram that is built from various organic materials and typically hardened with calcium carbonate | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/28%3A_Protists/28.02%3A_Overview_of_Protists.txt |
Skills to Develop
• Describe representative protist organisms from each of the six presently recognized supergroups of eukaryotes
• Identify the evolutionary relationships of plants, animals, and fungi within the six presently recognized supergroups of eukaryotes
In the span of several decades, the Kingdom Protista has been disassembled because sequence analyses have revealed new genetic (and therefore evolutionary) relationships among these eukaryotes. Moreover, protists that exhibit similar morphological features may have evolved analogous structures because of similar selective pressures—rather than because of recent common ancestry. This phenomenon, called convergent evolution, is one reason why protist classification is so challenging. The emerging classification scheme groups the entire domain Eukaryota into six “supergroups” that contain all of the protists as well as animals, plants, and fungi that evolved from a common ancestor (Figure \(1\)). The supergroups are believed to be monophyletic, meaning that all organisms within each supergroup are believed to have evolved from a single common ancestor, and thus all members are most closely related to each other than to organisms outside that group. There is still evidence lacking for the monophyly of some groups.
The classification of eukaryotes is still in flux, and the six supergroups may be modified or replaced by a more appropriate hierarchy as genetic, morphological, and ecological data accumulate. Keep in mind that the classification scheme presented here is just one of several hypotheses, and the true evolutionary relationships are still to be determined. When learning about protists, it is helpful to focus less on the nomenclature and more on the commonalities and differences that define the groups themselves.
Excavata
Many of the protist species classified into the supergroup Excavata are asymmetrical, single-celled organisms with a feeding groove “excavated” from one side. This supergroup includes heterotrophic predators, photosynthetic species, and parasites. Its subgroups are the diplomonads, parabasalids, and euglenozoans.
Diplomonads
Among the Excavata are the diplomonads, which include the intestinal parasite, Giardia lamblia (Figure \(2\)). Until recently, these protists were believed to lack mitochondria. Mitochondrial remnant organelles, called mitosomes, have since been identified in diplomonads, but these mitosomes are essentially nonfunctional. Diplomonads exist in anaerobic environments and use alternative pathways, such as glycolysis, to generate energy. Each diplomonad cell has two identical nuclei and uses several flagella for locomotion.
Parabasalids
A second Excavata subgroup, the parabasalids, also exhibits semi-functional mitochondria. In parabasalids, these structures function anaerobically and are called hydrogenosomes because they produce hydrogen gas as a byproduct. Parabasalids move with flagella and membrane rippling. Trichomonas vaginalis, a parabasalid that causes a sexually transmitted disease in humans, employs these mechanisms to transit through the male and female urogenital tracts. T. vaginalis causes trichamoniasis, which appears in an estimated 180 million cases worldwide each year. Whereas men rarely exhibit symptoms during an infection with this protist, infected women may become more susceptible to secondary infection with human immunodeficiency virus (HIV) and may be more likely to develop cervical cancer. Pregnant women infected with T. vaginalis are at an increased risk of serious complications, such as pre-term delivery.
Euglenozoans
Euglenozoans includes parasites, heterotrophs, autotrophs, and mixotrophs, ranging in size from 10 to 500 µm. Euglenoids move through their aquatic habitats using two long flagella that guide them toward light sources sensed by a primitive ocular organ called an eyespot. The familiar genus, Euglena, encompasses some mixotrophic species that display a photosynthetic capability only when light is present. In the dark, the chloroplasts of Euglena shrink up and temporarily cease functioning, and the cells instead take up organic nutrients from their environment.
The human parasite, Trypanosoma brucei, belongs to a different subgroup of Euglenozoa, the kinetoplastids. The kinetoplastid subgroup is named after the kinetoplast, a DNA mass carried within the single, oversized mitochondrion possessed by each of these cells. This subgroup includes several parasites, collectively called trypanosomes, which cause devastating human diseases and infect an insect species during a portion of their life cycle. T. brucei develops in the gut of the tsetse fly after the fly bites an infected human or other mammalian host. The parasite then travels to the insect salivary glands to be transmitted to another human or other mammal when the infected tsetse fly consumes another blood meal. T. brucei is common in central Africa and is the causative agent of African sleeping sickness, a disease associated with severe chronic fatigue, coma, and can be fatal if left untreated.
Trypanosoma brucei
Watch this video to see T. brucei swimming. https://youtu.be/EnsydwITLYk
Chromalveolata
Current evidence suggests that species classified as chromalveolates are derived from a common ancestor that engulfed a photosynthetic red algal cell, which itself had already evolved chloroplasts from an endosymbiotic relationship with a photosynthetic prokaryote. Therefore, the ancestor of chromalveolates is believed to have resulted from a secondary endosymbiotic event. However, some chromalveolates appear to have lost red alga-derived plastid organelles or lack plastid genes altogether. Therefore, this supergroup should be considered a hypothesis-based working group that is subject to change. Chromalveolates include very important photosynthetic organisms, such as diatoms, brown algae, and significant disease agents in animals and plants. The chromalveolates can be subdivided into alveolates and stramenopiles.
Alveolates: Dinoflagellates, Apicomplexians, and Ciliates
A large body of data supports that the alveolates are derived from a shared common ancestor. The alveolates are named for the presence of an alveolus, or membrane-enclosed sac, beneath the cell membrane. The exact function of the alveolus is unknown, but it may be involved in osmoregulation. The alveolates are further categorized into some of the better-known protists: the dinoflagellates, the apicomplexans, and the ciliates.
Dinoflagellates exhibit extensive morphological diversity and can be photosynthetic, heterotrophic, or mixotrophic. Many dinoflagellates are encased in interlocking plates of cellulose. Two perpendicular flagella fit into the grooves between the cellulose plates, with one flagellum extending longitudinally and a second encircling the dinoflagellate (Figure \(4\)). Together, the flagella contribute to the characteristic spinning motion of dinoflagellates. These protists exist in freshwater and marine habitats, and are a component of plankton, the typically microscopic organisms that drift through the water and serve as a crucial food source for larger aquatic organisms.
Some dinoflagellates generate light, called bioluminescence, when they are jarred or stressed. Large numbers of marine dinoflagellates (billions or trillions of cells per wave) can emit light and cause an entire breaking wave to twinkle or take on a brilliant blue color (Figure \(5\)). For approximately 20 species of marine dinoflagellates, population explosions (also called blooms) during the summer months can tint the ocean with a muddy red color. This phenomenon is called a red tide, and it results from the abundant red pigments present in dinoflagellate plastids. In large quantities, these dinoflagellate species secrete an asphyxiating toxin that can kill fish, birds, and marine mammals. Red tides can be massively detrimental to commercial fisheries, and humans who consume these protists may become poisoned.
The apicomplexan protists are so named because their microtubules, fibrin, and vacuoles are asymmetrically distributed at one end of the cell in a structure called an apical complex (Figure \(6\)). The apical complex is specialized for entry and infection of host cells. Indeed, all apicomplexans are parasitic. This group includes the genus Plasmodium, which causes malaria in humans. Apicomplexan life cycles are complex, involving multiple hosts and stages of sexual and asexual reproduction.
The ciliates, which include Paramecium and Tetrahymena, are a group of protists 10 to 3,000 micrometers in length that are covered in rows, tufts, or spirals of tiny cilia. By beating their cilia synchronously or in waves, ciliates can coordinate directed movements and ingest food particles. Certain ciliates have fused cilia-based structures that function like paddles, funnels, or fins. Ciliates also are surrounded by a pellicle, providing protection without compromising agility. The genus Paramecium includes protists that have organized their cilia into a plate-like primitive mouth, called an oral groove, which is used to capture and digest bacteria (Figure \(7\)). Food captured in the oral groove enters a food vacuole, where it combines with digestive enzymes. Waste particles are expelled by an exocytic vesicle that fuses at a specific region on the cell membrane, called the anal pore. In addition to a vacuole-based digestive system, Paramecium also uses contractile vacuoles, which are osmoregulatory vesicles that fill with water as it enters the cell by osmosis and then contract to squeeze water from the cell.
Link to Learning
Watch the video of the contractile vacuole of Paramecium expelling water to keep the cell osmotically balanced.
Paramecium has two nuclei, a macronucleus and a micronucleus, in each cell. The micronucleus is essential for sexual reproduction, whereas the macronucleus directs asexual binary fission and all other biological functions. The process of sexual reproduction in Paramecium underscores the importance of the micronucleus to these protists. Paramecium and most other ciliates reproduce sexually by conjugation. This process begins when two different mating types of Paramecium make physical contact and join with a cytoplasmic bridge (Figure \(8\)). The diploid micronucleus in each cell then undergoes meiosis to produce four haploid micronuclei. Three of these degenerate in each cell, leaving one micronucleus that then undergoes mitosis, generating two haploid micronuclei. The cells each exchange one of these haploid nuclei and move away from each other. A similar process occurs in bacteria that have plasmids. Fusion of the haploid micronuclei generates a completely novel diploid pre-micronucleus in each conjugative cell. This pre-micronucleus undergoes three rounds of mitosis to produce eight copies, and the original macronucleus disintegrates. Four of the eight pre-micronuclei become full-fledged micronuclei, whereas the other four perform multiple rounds of DNA replication and go on to become new macronuclei. Two cell divisions then yield four new Paramecia from each original conjugative cell.
Exercise
Which of the following statements about Paramecium sexual reproduction is false?
1. The macronuclei are derived from micronuclei.
2. Both mitosis and meiosis occur during sexual reproduction.
3. The conjugate pair swaps macronucleii.
4. Each parent produces four daughter cells.
Stramenopiles: Diatoms, Brown Algae, Golden Algae and Oomycetes
The other subgroup of chromalveolates, the stramenopiles, includes photosynthetic marine algae and heterotrophic protists. The unifying feature of this group is the presence of a textured, or “hairy,” flagellum. Many stramenopiles also have an additional flagellum that lacks hair-like projections (Figure \(9\)). Members of this subgroup range in size from single-celled diatoms to the massive and multicellular kelp.
The diatoms are unicellular photosynthetic protists that encase themselves in intricately patterned, glassy cell walls composed of silicon dioxide in a matrix of organic particles (Figure \(10\)). These protists are a component of freshwater and marine plankton. Most species of diatoms reproduce asexually, although some instances of sexual reproduction and sporulation also exist. Some diatoms exhibit a slit in their silica shell, called a raphe. By expelling a stream of mucopolysaccharides from the raphe, the diatom can attach to surfaces or propel itself in one direction.
During periods of nutrient availability, diatom populations bloom to numbers greater than can be consumed by aquatic organisms. The excess diatoms die and sink to the sea floor where they are not easily reached by saprobes that feed on dead organisms. As a result, the carbon dioxide that the diatoms had consumed and incorporated into their cells during photosynthesis is not returned to the atmosphere. In general, this process by which carbon is transported deep into the ocean is described as the biological carbon pump, because carbon is “pumped” to the ocean depths where it is inaccessible to the atmosphere as carbon dioxide. The biological carbon pump is a crucial component of the carbon cycle that maintains lower atmospheric carbon dioxide levels.
Like diatoms, golden algae are largely unicellular, although some species can form large colonies. Their characteristic gold color results from their extensive use of carotenoids, a group of photosynthetic pigments that are generally yellow or orange in color. Golden algae are found in both freshwater and marine environments, where they form a major part of the plankton community.
The brown algae are primarily marine, multicellular organisms that are known colloquially as seaweeds. Giant kelps are a type of brown algae. Some brown algae have evolved specialized tissues that resemble terrestrial plants, with root-like holdfasts, stem-like stipes, and leaf-like blades that are capable of photosynthesis. The stipes of giant kelps are enormous, extending in some cases for 60 meters. A variety of algal life cycles exists, but the most complex is alternation of generations, in which both haploid and diploid stages involve multicellularity. Compare this life cycle to that of humans, for instance. Haploid gametes produced by meiosis (sperm and egg) combine in fertilization to generate a diploid zygote that undergoes many rounds of mitosis to produce a multicellular embryo and then a fetus. However, the individual sperm and egg themselves never become multicellular beings. Terrestrial plants also have evolved alternation of generations. In the brown algae genus Laminaria, haploid spores develop into multicellular gametophytes, which produce haploid gametes that combine to produce diploid organisms that then become multicellular organisms with a different structure from the haploid form (Figure \(11\)). Certain other organisms perform alternation of generations in which both the haploid and diploid forms look the same.
Exercise
Which of the following statements about the Laminaria life cycle is false?
1. 1n zoospores form in the sporangia.
2. The sporophyte is the 2n plant.
3. The gametophyte is diploid.
4. Both the gametophyte and sporophyte stages are multicellular.
The water molds, oomycetes (“egg fungus”), were so-named based on their fungus-like morphology, but molecular data have shown that the water molds are not closely related to fungi. The oomycetes are characterized by a cellulose-based cell wall and an extensive network of filaments that allow for nutrient uptake. As diploid spores, many oomycetes have two oppositely directed flagella (one hairy and one smooth) for locomotion. The oomycetes are nonphotosynthetic and include many saprobes and parasites. The saprobes appear as white fluffy growths on dead organisms (Figure \(12\)). Most oomycetes are aquatic, but some parasitize terrestrial plants. One plant pathogen is Phytophthora infestans, the causative agent of late blight of potatoes, such as occurred in the nineteenth century Irish potato famine.
Rhizaria
The Rhizaria supergroup includes many of the amoebas, most of which have threadlike or needle-like pseudopodia (Figure \(13\)). Pseudopodia function to trap and engulf food particles and to direct movement in rhizarian protists. These pseudopods project outward from anywhere on the cell surface and can anchor to a substrate. The protist then transports its cytoplasm into the pseudopod, thereby moving the entire cell. This type of motion, called cytoplasmic streaming, is used by several diverse groups of protists as a means of locomotion or as a method to distribute nutrients and oxygen.
Link to Learning
Take a look at this video to see cytoplasmic streaming in a green alga.
Forams
Foraminiferans, or forams, are unicellular heterotrophic protists, ranging from approximately 20 micrometers to several centimeters in length, and occasionally resembling tiny snails (Figure \(14\)). As a group, the forams exhibit porous shells, called tests that are built from various organic materials and typically hardened with calcium carbonate. The tests may house photosynthetic algae, which the forams can harvest for nutrition. Foram pseudopodia extend through the pores and allow the forams to move, feed, and gather additional building materials. Typically, forams are associated with sand or other particles in marine or freshwater habitats. Foraminiferans are also useful as indicators of pollution and changes in global weather patterns.
Radiolarians
A second subtype of Rhizaria, the radiolarians, exhibit intricate exteriors of glassy silica with radial or bilateral symmetry (Figure \(15\)). Needle-like pseudopods supported by microtubules radiate outward from the cell bodies of these protists and function to catch food particles. The shells of dead radiolarians sink to the ocean floor, where they may accumulate in 100 meter-thick depths. Preserved, sedimented radiolarians are very common in the fossil record.
Archaeplastida
Red algae and green algae are included in the supergroup Archaeplastida. It was from a common ancestor of these protists that the land plants evolved, since their closest relatives are found in this group. Molecular evidence supports that all Archaeplastida are descendents of an endosymbiotic relationship between a heterotrophic protist and a cyanobacterium. The red and green algae include unicellular, multicellular, and colonial forms.
Red Algae
Red algae, or rhodophytes, are primarily multicellular, lack flagella, and range in size from microscopic, unicellular protists to large, multicellular forms grouped into the informal seaweed category. The red algae life cycle is an alternation of generations. Some species of red algae contain phycoerythrins, photosynthetic accessory pigments that are red in color and outcompete the green tint of chlorophyll, making these species appear as varying shades of red. Other protists classified as red algae lack phycoerythrins and are parasites. Red algae are common in tropical waters where they have been detected at depths of 260 meters. Other red algae exist in terrestrial or freshwater environments.
Green Algae: Chlorophytes and Charophytes
The most abundant group of algae is the green algae. The green algae exhibit similar features to the land plants, particularly in terms of chloroplast structure. That this group of protists shared a relatively recent common ancestor with land plants is well supported. The green algae are subdivided into the chlorophytes and the charophytes. The charophytes are the closest living relatives to land plants and resemble them in morphology and reproductive strategies. Charophytes are common in wet habitats, and their presence often signals a healthy ecosystem.
The chlorophytes exhibit great diversity of form and function. Chlorophytes primarily inhabit freshwater and damp soil, and are a common component of plankton. Chlamydomonas is a simple, unicellular chlorophyte with a pear-shaped morphology and two opposing, anterior flagella that guide this protist toward light sensed by its eyespot. More complex chlorophyte species exhibit haploid gametes and spores that resemble Chlamydomonas.
The chlorophyte Volvox is one of only a few examples of a colonial organism, which behaves in some ways like a collection of individual cells, but in other ways like the specialized cells of a multicellular organism (Figure \(16\)). Volvox colonies contain 500 to 60,000 cells, each with two flagella, contained within a hollow, spherical matrix composed of a gelatinous glycoprotein secretion. Individual Volvox cells move in a coordinated fashion and are interconnected by cytoplasmic bridges. Only a few of the cells reproduce to create daughter colonies, an example of basic cell specialization in this organism.
True multicellular organisms, such as the sea lettuce, Ulva, are represented among the chlorophytes. In addition, some chlorophytes exist as large, multinucleate, single cells. Species in the genus Caulerpa exhibit flattened fern-like foliage and can reach lengths of 3 meters (Figure \(17\)). Caulerpa species undergo nuclear division, but their cells do not complete cytokinesis, remaining instead as massive and elaborate single cells.
Amoebozoa
The amoebozoans characteristically exhibit pseudopodia that extend like tubes or flat lobes, rather than the hair-like pseudopodia of rhizarian amoeba (Figure \(18\)). The Amoebozoa include several groups of unicellular amoeba-like organisms that are free-living or parasites.
Slime Molds
A subset of the amoebozoans, the slime molds, has several morphological similarities to fungi that are thought to be the result of convergent evolution. For instance, during times of stress, some slime molds develop into spore-generating fruiting bodies, much like fungi.
The slime molds are categorized on the basis of their life cycles into plasmodial or cellular types. Plasmodial slime molds are composed of large, multinucleate cells and move along surfaces like an amorphous blob of slime during their feeding stage (Figure \(19\)). Food particles are lifted and engulfed into the slime mold as it glides along. Upon maturation, the plasmodium takes on a net-like appearance with the ability to form fruiting bodies, or sporangia, during times of stress. Haploid spores are produced by meiosis within the sporangia, and spores can be disseminated through the air or water to potentially land in more favorable environments. If this occurs, the spores germinate to form ameboid or flagellate haploid cells that can combine with each other and produce a diploid zygotic slime mold to complete the life cycle.
The cellular slime molds function as independent amoeboid cells when nutrients are abundant (Figure \(20\)). When food is depleted, cellular slime molds pile onto each other into a mass of cells that behaves as a single unit, called a slug. Some cells in the slug contribute to a 2–3-millimeter stalk, drying up and dying in the process. Cells atop the stalk form an asexual fruiting body that contains haploid spores. As with plasmodial slime molds, the spores are disseminated and can germinate if they land in a moist environment. One representative genus of the cellular slime molds is Dictyostelium, which commonly exists in the damp soil of forests.
Link to Learning
View this site to see the formation of a fruiting body by a cellular slime mold.
Opisthokonta
The opisthokonts include the animal-like choanoflagellates, which are believed to resemble the common ancestor of sponges and, in fact, all animals. Choanoflagellates include unicellular and colonial forms, and number about 244 described species. These organisms exhibit a single, apical flagellum that is surrounded by a contractile collar composed of microvilli. The collar uses a similar mechanism to sponges to filter out bacteria for ingestion by the protist. The morphology of choanoflagellates was recognized early on as resembling the collar cells of sponges, and suggesting a possible relationship to animals.
The Mesomycetozoa form a small group of parasites, primarily of fish, and at least one form that can parasitize humans. Their life cycles are poorly understood. These organisms are of special interest, because they appear to be so closely related to animals. In the past, they were grouped with fungi and other protists based on their morphology.
Summary
The process of classifying protists into meaningful groups is ongoing, but genetic data in the past 20 years have clarified many relationships that were previously unclear or mistaken. The majority view at present is to order all eukaryotes into six supergroups: Excavata, Chromalveolata, Rhizaria, Archaeplastida, Amoebozoa, and Opisthokonta. The goal of this classification scheme is to create clusters of species that all are derived from a common ancestor. At present, the monophyly of some of the supergroups are better supported by genetic data than others. Although tremendous variation exists within the supergroups, commonalities at the morphological, physiological, and ecological levels can be identified.
Art Connections
Figure \(8\): Which of the following statements about Paramecium sexual reproduction is false?
1. The macronuclei are derived from micronuclei.
2. Both mitosis and meiosis occur during sexual reproduction.
3. The conjugate pair swaps macronuclei.
4. Each parent produces four daughter cells.
Answer
C
Figure \(11\): Which of the following statements about the Laminaria life cycle is false?
1. 1n zoospores form in the sporangia.
2. The sporophyte is the 2n plant.
3. The gametophyte is diploid.
4. Both the gametophyte and sporophyte stages are multicellular.
Answer
C
Glossary
biological carbon pump
process by which inorganic carbon is fixed by photosynthetic species that then die and fall to the sea floor where they cannot be reached by saprobes and their carbon dioxide consumption cannot be returned to the atmosphere
bioluminescence
generation and emission of light by an organism, as in dinoflagellates
contractile vacuole
vesicle that fills with water (as it enters the cell by osmosis) and then contracts to squeeze water from the cell; an osmoregulatory vesicle
cytoplasmic streaming
movement of cytoplasm into an extended pseudopod such that the entire cell is transported to the site of the pseudopod
hydrogenosome
organelle carried by parabasalids (Excavata) that functions anaerobically and outputs hydrogen gas as a byproduct; likely evolved from mitochondria
kinetoplast
mass of DNA carried within the single, oversized mitochondrion, characteristic of kinetoplastids (phylum: Euglenozoa)
mitosome
nonfunctional organelle carried in the cells of diplomonads (Excavata) that likely evolved from a mitochondrion
plankton
diverse group of mostly microscopic organisms that drift in marine and freshwater systems and serve as a food source for larger aquatic organisms
raphe
slit in the silica shell of diatoms through which the protist secretes a stream of mucopolysaccharides for locomotion and attachment to substrates
test
porous shell of a foram that is built from various organic materials and typically hardened with calcium carbonate | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/28%3A_Protists/28.03%3A_Characteristics_of_Excavata.txt |
Skills to Develop
• Describe representative protist organisms from each of the six presently recognized supergroups of eukaryotes
• Identify the evolutionary relationships of plants, animals, and fungi within the six presently recognized supergroups of eukaryotes
In the span of several decades, the Kingdom Protista has been disassembled because sequence analyses have revealed new genetic (and therefore evolutionary) relationships among these eukaryotes. Moreover, protists that exhibit similar morphological features may have evolved analogous structures because of similar selective pressures—rather than because of recent common ancestry. This phenomenon, called convergent evolution, is one reason why protist classification is so challenging. The emerging classification scheme groups the entire domain Eukaryota into six “supergroups” that contain all of the protists as well as animals, plants, and fungi that evolved from a common ancestor (Figure \(1\)). The supergroups are believed to be monophyletic, meaning that all organisms within each supergroup are believed to have evolved from a single common ancestor, and thus all members are most closely related to each other than to organisms outside that group. There is still evidence lacking for the monophyly of some groups.
The classification of eukaryotes is still in flux, and the six supergroups may be modified or replaced by a more appropriate hierarchy as genetic, morphological, and ecological data accumulate. Keep in mind that the classification scheme presented here is just one of several hypotheses, and the true evolutionary relationships are still to be determined. When learning about protists, it is helpful to focus less on the nomenclature and more on the commonalities and differences that define the groups themselves.
Excavata
Many of the protist species classified into the supergroup Excavata are asymmetrical, single-celled organisms with a feeding groove “excavated” from one side. This supergroup includes heterotrophic predators, photosynthetic species, and parasites. Its subgroups are the diplomonads, parabasalids, and euglenozoans.
Diplomonads
Among the Excavata are the diplomonads, which include the intestinal parasite, Giardia lamblia (Figure \(2\)). Until recently, these protists were believed to lack mitochondria. Mitochondrial remnant organelles, called mitosomes, have since been identified in diplomonads, but these mitosomes are essentially nonfunctional. Diplomonads exist in anaerobic environments and use alternative pathways, such as glycolysis, to generate energy. Each diplomonad cell has two identical nuclei and uses several flagella for locomotion.
Parabasalids
A second Excavata subgroup, the parabasalids, also exhibits semi-functional mitochondria. In parabasalids, these structures function anaerobically and are called hydrogenosomes because they produce hydrogen gas as a byproduct. Parabasalids move with flagella and membrane rippling. Trichomonas vaginalis, a parabasalid that causes a sexually transmitted disease in humans, employs these mechanisms to transit through the male and female urogenital tracts. T. vaginalis causes trichamoniasis, which appears in an estimated 180 million cases worldwide each year. Whereas men rarely exhibit symptoms during an infection with this protist, infected women may become more susceptible to secondary infection with human immunodeficiency virus (HIV) and may be more likely to develop cervical cancer. Pregnant women infected with T. vaginalis are at an increased risk of serious complications, such as pre-term delivery.
Euglenozoans
Euglenozoans includes parasites, heterotrophs, autotrophs, and mixotrophs, ranging in size from 10 to 500 µm. Euglenoids move through their aquatic habitats using two long flagella that guide them toward light sources sensed by a primitive ocular organ called an eyespot. The familiar genus, Euglena, encompasses some mixotrophic species that display a photosynthetic capability only when light is present. In the dark, the chloroplasts of Euglena shrink up and temporarily cease functioning, and the cells instead take up organic nutrients from their environment.
The human parasite, Trypanosoma brucei, belongs to a different subgroup of Euglenozoa, the kinetoplastids. The kinetoplastid subgroup is named after the kinetoplast, a DNA mass carried within the single, oversized mitochondrion possessed by each of these cells. This subgroup includes several parasites, collectively called trypanosomes, which cause devastating human diseases and infect an insect species during a portion of their life cycle. T. brucei develops in the gut of the tsetse fly after the fly bites an infected human or other mammalian host. The parasite then travels to the insect salivary glands to be transmitted to another human or other mammal when the infected tsetse fly consumes another blood meal. T. brucei is common in central Africa and is the causative agent of African sleeping sickness, a disease associated with severe chronic fatigue, coma, and can be fatal if left untreated.
Trypanosoma brucei
Watch this video to see T. brucei swimming. https://youtu.be/EnsydwITLYk
Chromalveolata
Current evidence suggests that species classified as chromalveolates are derived from a common ancestor that engulfed a photosynthetic red algal cell, which itself had already evolved chloroplasts from an endosymbiotic relationship with a photosynthetic prokaryote. Therefore, the ancestor of chromalveolates is believed to have resulted from a secondary endosymbiotic event. However, some chromalveolates appear to have lost red alga-derived plastid organelles or lack plastid genes altogether. Therefore, this supergroup should be considered a hypothesis-based working group that is subject to change. Chromalveolates include very important photosynthetic organisms, such as diatoms, brown algae, and significant disease agents in animals and plants. The chromalveolates can be subdivided into alveolates and stramenopiles.
Alveolates: Dinoflagellates, Apicomplexians, and Ciliates
A large body of data supports that the alveolates are derived from a shared common ancestor. The alveolates are named for the presence of an alveolus, or membrane-enclosed sac, beneath the cell membrane. The exact function of the alveolus is unknown, but it may be involved in osmoregulation. The alveolates are further categorized into some of the better-known protists: the dinoflagellates, the apicomplexans, and the ciliates.
Dinoflagellates exhibit extensive morphological diversity and can be photosynthetic, heterotrophic, or mixotrophic. Many dinoflagellates are encased in interlocking plates of cellulose. Two perpendicular flagella fit into the grooves between the cellulose plates, with one flagellum extending longitudinally and a second encircling the dinoflagellate (Figure \(4\)). Together, the flagella contribute to the characteristic spinning motion of dinoflagellates. These protists exist in freshwater and marine habitats, and are a component of plankton, the typically microscopic organisms that drift through the water and serve as a crucial food source for larger aquatic organisms.
Some dinoflagellates generate light, called bioluminescence, when they are jarred or stressed. Large numbers of marine dinoflagellates (billions or trillions of cells per wave) can emit light and cause an entire breaking wave to twinkle or take on a brilliant blue color (Figure \(5\)). For approximately 20 species of marine dinoflagellates, population explosions (also called blooms) during the summer months can tint the ocean with a muddy red color. This phenomenon is called a red tide, and it results from the abundant red pigments present in dinoflagellate plastids. In large quantities, these dinoflagellate species secrete an asphyxiating toxin that can kill fish, birds, and marine mammals. Red tides can be massively detrimental to commercial fisheries, and humans who consume these protists may become poisoned.
The apicomplexan protists are so named because their microtubules, fibrin, and vacuoles are asymmetrically distributed at one end of the cell in a structure called an apical complex (Figure \(6\)). The apical complex is specialized for entry and infection of host cells. Indeed, all apicomplexans are parasitic. This group includes the genus Plasmodium, which causes malaria in humans. Apicomplexan life cycles are complex, involving multiple hosts and stages of sexual and asexual reproduction.
The ciliates, which include Paramecium and Tetrahymena, are a group of protists 10 to 3,000 micrometers in length that are covered in rows, tufts, or spirals of tiny cilia. By beating their cilia synchronously or in waves, ciliates can coordinate directed movements and ingest food particles. Certain ciliates have fused cilia-based structures that function like paddles, funnels, or fins. Ciliates also are surrounded by a pellicle, providing protection without compromising agility. The genus Paramecium includes protists that have organized their cilia into a plate-like primitive mouth, called an oral groove, which is used to capture and digest bacteria (Figure \(7\)). Food captured in the oral groove enters a food vacuole, where it combines with digestive enzymes. Waste particles are expelled by an exocytic vesicle that fuses at a specific region on the cell membrane, called the anal pore. In addition to a vacuole-based digestive system, Paramecium also uses contractile vacuoles, which are osmoregulatory vesicles that fill with water as it enters the cell by osmosis and then contract to squeeze water from the cell.
Link to Learning
Watch the video of the contractile vacuole of Paramecium expelling water to keep the cell osmotically balanced.
Paramecium has two nuclei, a macronucleus and a micronucleus, in each cell. The micronucleus is essential for sexual reproduction, whereas the macronucleus directs asexual binary fission and all other biological functions. The process of sexual reproduction in Paramecium underscores the importance of the micronucleus to these protists. Paramecium and most other ciliates reproduce sexually by conjugation. This process begins when two different mating types of Paramecium make physical contact and join with a cytoplasmic bridge (Figure \(8\)). The diploid micronucleus in each cell then undergoes meiosis to produce four haploid micronuclei. Three of these degenerate in each cell, leaving one micronucleus that then undergoes mitosis, generating two haploid micronuclei. The cells each exchange one of these haploid nuclei and move away from each other. A similar process occurs in bacteria that have plasmids. Fusion of the haploid micronuclei generates a completely novel diploid pre-micronucleus in each conjugative cell. This pre-micronucleus undergoes three rounds of mitosis to produce eight copies, and the original macronucleus disintegrates. Four of the eight pre-micronuclei become full-fledged micronuclei, whereas the other four perform multiple rounds of DNA replication and go on to become new macronuclei. Two cell divisions then yield four new Paramecia from each original conjugative cell.
Exercise
Which of the following statements about Paramecium sexual reproduction is false?
1. The macronuclei are derived from micronuclei.
2. Both mitosis and meiosis occur during sexual reproduction.
3. The conjugate pair swaps macronucleii.
4. Each parent produces four daughter cells.
Stramenopiles: Diatoms, Brown Algae, Golden Algae and Oomycetes
The other subgroup of chromalveolates, the stramenopiles, includes photosynthetic marine algae and heterotrophic protists. The unifying feature of this group is the presence of a textured, or “hairy,” flagellum. Many stramenopiles also have an additional flagellum that lacks hair-like projections (Figure \(9\)). Members of this subgroup range in size from single-celled diatoms to the massive and multicellular kelp.
The diatoms are unicellular photosynthetic protists that encase themselves in intricately patterned, glassy cell walls composed of silicon dioxide in a matrix of organic particles (Figure \(10\)). These protists are a component of freshwater and marine plankton. Most species of diatoms reproduce asexually, although some instances of sexual reproduction and sporulation also exist. Some diatoms exhibit a slit in their silica shell, called a raphe. By expelling a stream of mucopolysaccharides from the raphe, the diatom can attach to surfaces or propel itself in one direction.
During periods of nutrient availability, diatom populations bloom to numbers greater than can be consumed by aquatic organisms. The excess diatoms die and sink to the sea floor where they are not easily reached by saprobes that feed on dead organisms. As a result, the carbon dioxide that the diatoms had consumed and incorporated into their cells during photosynthesis is not returned to the atmosphere. In general, this process by which carbon is transported deep into the ocean is described as the biological carbon pump, because carbon is “pumped” to the ocean depths where it is inaccessible to the atmosphere as carbon dioxide. The biological carbon pump is a crucial component of the carbon cycle that maintains lower atmospheric carbon dioxide levels.
Like diatoms, golden algae are largely unicellular, although some species can form large colonies. Their characteristic gold color results from their extensive use of carotenoids, a group of photosynthetic pigments that are generally yellow or orange in color. Golden algae are found in both freshwater and marine environments, where they form a major part of the plankton community.
The brown algae are primarily marine, multicellular organisms that are known colloquially as seaweeds. Giant kelps are a type of brown algae. Some brown algae have evolved specialized tissues that resemble terrestrial plants, with root-like holdfasts, stem-like stipes, and leaf-like blades that are capable of photosynthesis. The stipes of giant kelps are enormous, extending in some cases for 60 meters. A variety of algal life cycles exists, but the most complex is alternation of generations, in which both haploid and diploid stages involve multicellularity. Compare this life cycle to that of humans, for instance. Haploid gametes produced by meiosis (sperm and egg) combine in fertilization to generate a diploid zygote that undergoes many rounds of mitosis to produce a multicellular embryo and then a fetus. However, the individual sperm and egg themselves never become multicellular beings. Terrestrial plants also have evolved alternation of generations. In the brown algae genus Laminaria, haploid spores develop into multicellular gametophytes, which produce haploid gametes that combine to produce diploid organisms that then become multicellular organisms with a different structure from the haploid form (Figure \(11\)). Certain other organisms perform alternation of generations in which both the haploid and diploid forms look the same.
Exercise
Which of the following statements about the Laminaria life cycle is false?
1. 1n zoospores form in the sporangia.
2. The sporophyte is the 2n plant.
3. The gametophyte is diploid.
4. Both the gametophyte and sporophyte stages are multicellular.
The water molds, oomycetes (“egg fungus”), were so-named based on their fungus-like morphology, but molecular data have shown that the water molds are not closely related to fungi. The oomycetes are characterized by a cellulose-based cell wall and an extensive network of filaments that allow for nutrient uptake. As diploid spores, many oomycetes have two oppositely directed flagella (one hairy and one smooth) for locomotion. The oomycetes are nonphotosynthetic and include many saprobes and parasites. The saprobes appear as white fluffy growths on dead organisms (Figure \(12\)). Most oomycetes are aquatic, but some parasitize terrestrial plants. One plant pathogen is Phytophthora infestans, the causative agent of late blight of potatoes, such as occurred in the nineteenth century Irish potato famine.
Rhizaria
The Rhizaria supergroup includes many of the amoebas, most of which have threadlike or needle-like pseudopodia (Figure \(13\)). Pseudopodia function to trap and engulf food particles and to direct movement in rhizarian protists. These pseudopods project outward from anywhere on the cell surface and can anchor to a substrate. The protist then transports its cytoplasm into the pseudopod, thereby moving the entire cell. This type of motion, called cytoplasmic streaming, is used by several diverse groups of protists as a means of locomotion or as a method to distribute nutrients and oxygen.
Link to Learning
Take a look at this video to see cytoplasmic streaming in a green alga.
Forams
Foraminiferans, or forams, are unicellular heterotrophic protists, ranging from approximately 20 micrometers to several centimeters in length, and occasionally resembling tiny snails (Figure \(14\)). As a group, the forams exhibit porous shells, called tests that are built from various organic materials and typically hardened with calcium carbonate. The tests may house photosynthetic algae, which the forams can harvest for nutrition. Foram pseudopodia extend through the pores and allow the forams to move, feed, and gather additional building materials. Typically, forams are associated with sand or other particles in marine or freshwater habitats. Foraminiferans are also useful as indicators of pollution and changes in global weather patterns.
Radiolarians
A second subtype of Rhizaria, the radiolarians, exhibit intricate exteriors of glassy silica with radial or bilateral symmetry (Figure \(15\)). Needle-like pseudopods supported by microtubules radiate outward from the cell bodies of these protists and function to catch food particles. The shells of dead radiolarians sink to the ocean floor, where they may accumulate in 100 meter-thick depths. Preserved, sedimented radiolarians are very common in the fossil record.
Archaeplastida
Red algae and green algae are included in the supergroup Archaeplastida. It was from a common ancestor of these protists that the land plants evolved, since their closest relatives are found in this group. Molecular evidence supports that all Archaeplastida are descendents of an endosymbiotic relationship between a heterotrophic protist and a cyanobacterium. The red and green algae include unicellular, multicellular, and colonial forms.
Red Algae
Red algae, or rhodophytes, are primarily multicellular, lack flagella, and range in size from microscopic, unicellular protists to large, multicellular forms grouped into the informal seaweed category. The red algae life cycle is an alternation of generations. Some species of red algae contain phycoerythrins, photosynthetic accessory pigments that are red in color and outcompete the green tint of chlorophyll, making these species appear as varying shades of red. Other protists classified as red algae lack phycoerythrins and are parasites. Red algae are common in tropical waters where they have been detected at depths of 260 meters. Other red algae exist in terrestrial or freshwater environments.
Green Algae: Chlorophytes and Charophytes
The most abundant group of algae is the green algae. The green algae exhibit similar features to the land plants, particularly in terms of chloroplast structure. That this group of protists shared a relatively recent common ancestor with land plants is well supported. The green algae are subdivided into the chlorophytes and the charophytes. The charophytes are the closest living relatives to land plants and resemble them in morphology and reproductive strategies. Charophytes are common in wet habitats, and their presence often signals a healthy ecosystem.
The chlorophytes exhibit great diversity of form and function. Chlorophytes primarily inhabit freshwater and damp soil, and are a common component of plankton. Chlamydomonas is a simple, unicellular chlorophyte with a pear-shaped morphology and two opposing, anterior flagella that guide this protist toward light sensed by its eyespot. More complex chlorophyte species exhibit haploid gametes and spores that resemble Chlamydomonas.
The chlorophyte Volvox is one of only a few examples of a colonial organism, which behaves in some ways like a collection of individual cells, but in other ways like the specialized cells of a multicellular organism (Figure \(16\)). Volvox colonies contain 500 to 60,000 cells, each with two flagella, contained within a hollow, spherical matrix composed of a gelatinous glycoprotein secretion. Individual Volvox cells move in a coordinated fashion and are interconnected by cytoplasmic bridges. Only a few of the cells reproduce to create daughter colonies, an example of basic cell specialization in this organism.
True multicellular organisms, such as the sea lettuce, Ulva, are represented among the chlorophytes. In addition, some chlorophytes exist as large, multinucleate, single cells. Species in the genus Caulerpa exhibit flattened fern-like foliage and can reach lengths of 3 meters (Figure \(17\)). Caulerpa species undergo nuclear division, but their cells do not complete cytokinesis, remaining instead as massive and elaborate single cells.
Amoebozoa
The amoebozoans characteristically exhibit pseudopodia that extend like tubes or flat lobes, rather than the hair-like pseudopodia of rhizarian amoeba (Figure \(18\)). The Amoebozoa include several groups of unicellular amoeba-like organisms that are free-living or parasites.
Slime Molds
A subset of the amoebozoans, the slime molds, has several morphological similarities to fungi that are thought to be the result of convergent evolution. For instance, during times of stress, some slime molds develop into spore-generating fruiting bodies, much like fungi.
The slime molds are categorized on the basis of their life cycles into plasmodial or cellular types. Plasmodial slime molds are composed of large, multinucleate cells and move along surfaces like an amorphous blob of slime during their feeding stage (Figure \(19\)). Food particles are lifted and engulfed into the slime mold as it glides along. Upon maturation, the plasmodium takes on a net-like appearance with the ability to form fruiting bodies, or sporangia, during times of stress. Haploid spores are produced by meiosis within the sporangia, and spores can be disseminated through the air or water to potentially land in more favorable environments. If this occurs, the spores germinate to form ameboid or flagellate haploid cells that can combine with each other and produce a diploid zygotic slime mold to complete the life cycle.
The cellular slime molds function as independent amoeboid cells when nutrients are abundant (Figure \(20\)). When food is depleted, cellular slime molds pile onto each other into a mass of cells that behaves as a single unit, called a slug. Some cells in the slug contribute to a 2–3-millimeter stalk, drying up and dying in the process. Cells atop the stalk form an asexual fruiting body that contains haploid spores. As with plasmodial slime molds, the spores are disseminated and can germinate if they land in a moist environment. One representative genus of the cellular slime molds is Dictyostelium, which commonly exists in the damp soil of forests.
Link to Learning
View this site to see the formation of a fruiting body by a cellular slime mold.
Opisthokonta
The opisthokonts include the animal-like choanoflagellates, which are believed to resemble the common ancestor of sponges and, in fact, all animals. Choanoflagellates include unicellular and colonial forms, and number about 244 described species. These organisms exhibit a single, apical flagellum that is surrounded by a contractile collar composed of microvilli. The collar uses a similar mechanism to sponges to filter out bacteria for ingestion by the protist. The morphology of choanoflagellates was recognized early on as resembling the collar cells of sponges, and suggesting a possible relationship to animals.
The Mesomycetozoa form a small group of parasites, primarily of fish, and at least one form that can parasitize humans. Their life cycles are poorly understood. These organisms are of special interest, because they appear to be so closely related to animals. In the past, they were grouped with fungi and other protists based on their morphology.
Summary
The process of classifying protists into meaningful groups is ongoing, but genetic data in the past 20 years have clarified many relationships that were previously unclear or mistaken. The majority view at present is to order all eukaryotes into six supergroups: Excavata, Chromalveolata, Rhizaria, Archaeplastida, Amoebozoa, and Opisthokonta. The goal of this classification scheme is to create clusters of species that all are derived from a common ancestor. At present, the monophyly of some of the supergroups are better supported by genetic data than others. Although tremendous variation exists within the supergroups, commonalities at the morphological, physiological, and ecological levels can be identified.
Art Connections
Figure \(8\): Which of the following statements about Paramecium sexual reproduction is false?
1. The macronuclei are derived from micronuclei.
2. Both mitosis and meiosis occur during sexual reproduction.
3. The conjugate pair swaps macronuclei.
4. Each parent produces four daughter cells.
Answer
C
Figure \(11\): Which of the following statements about the Laminaria life cycle is false?
1. 1n zoospores form in the sporangia.
2. The sporophyte is the 2n plant.
3. The gametophyte is diploid.
4. Both the gametophyte and sporophyte stages are multicellular.
Answer
C
Glossary
biological carbon pump
process by which inorganic carbon is fixed by photosynthetic species that then die and fall to the sea floor where they cannot be reached by saprobes and their carbon dioxide consumption cannot be returned to the atmosphere
bioluminescence
generation and emission of light by an organism, as in dinoflagellates
contractile vacuole
vesicle that fills with water (as it enters the cell by osmosis) and then contracts to squeeze water from the cell; an osmoregulatory vesicle
cytoplasmic streaming
movement of cytoplasm into an extended pseudopod such that the entire cell is transported to the site of the pseudopod
hydrogenosome
organelle carried by parabasalids (Excavata) that functions anaerobically and outputs hydrogen gas as a byproduct; likely evolved from mitochondria
kinetoplast
mass of DNA carried within the single, oversized mitochondrion, characteristic of kinetoplastids (phylum: Euglenozoa)
mitosome
nonfunctional organelle carried in the cells of diplomonads (Excavata) that likely evolved from a mitochondrion
plankton
diverse group of mostly microscopic organisms that drift in marine and freshwater systems and serve as a food source for larger aquatic organisms
raphe
slit in the silica shell of diatoms through which the protist secretes a stream of mucopolysaccharides for locomotion and attachment to substrates
test
porous shell of a foram that is built from various organic materials and typically hardened with calcium carbonate | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/28%3A_Protists/28.04%3A_Characteristics_of_Chromalveolata.txt |
Skills to Develop
• Describe representative protist organisms from each of the six presently recognized supergroups of eukaryotes
• Identify the evolutionary relationships of plants, animals, and fungi within the six presently recognized supergroups of eukaryotes
In the span of several decades, the Kingdom Protista has been disassembled because sequence analyses have revealed new genetic (and therefore evolutionary) relationships among these eukaryotes. Moreover, protists that exhibit similar morphological features may have evolved analogous structures because of similar selective pressures—rather than because of recent common ancestry. This phenomenon, called convergent evolution, is one reason why protist classification is so challenging. The emerging classification scheme groups the entire domain Eukaryota into six “supergroups” that contain all of the protists as well as animals, plants, and fungi that evolved from a common ancestor (Figure \(1\)). The supergroups are believed to be monophyletic, meaning that all organisms within each supergroup are believed to have evolved from a single common ancestor, and thus all members are most closely related to each other than to organisms outside that group. There is still evidence lacking for the monophyly of some groups.
The classification of eukaryotes is still in flux, and the six supergroups may be modified or replaced by a more appropriate hierarchy as genetic, morphological, and ecological data accumulate. Keep in mind that the classification scheme presented here is just one of several hypotheses, and the true evolutionary relationships are still to be determined. When learning about protists, it is helpful to focus less on the nomenclature and more on the commonalities and differences that define the groups themselves.
Excavata
Many of the protist species classified into the supergroup Excavata are asymmetrical, single-celled organisms with a feeding groove “excavated” from one side. This supergroup includes heterotrophic predators, photosynthetic species, and parasites. Its subgroups are the diplomonads, parabasalids, and euglenozoans.
Diplomonads
Among the Excavata are the diplomonads, which include the intestinal parasite, Giardia lamblia (Figure \(2\)). Until recently, these protists were believed to lack mitochondria. Mitochondrial remnant organelles, called mitosomes, have since been identified in diplomonads, but these mitosomes are essentially nonfunctional. Diplomonads exist in anaerobic environments and use alternative pathways, such as glycolysis, to generate energy. Each diplomonad cell has two identical nuclei and uses several flagella for locomotion.
Parabasalids
A second Excavata subgroup, the parabasalids, also exhibits semi-functional mitochondria. In parabasalids, these structures function anaerobically and are called hydrogenosomes because they produce hydrogen gas as a byproduct. Parabasalids move with flagella and membrane rippling. Trichomonas vaginalis, a parabasalid that causes a sexually transmitted disease in humans, employs these mechanisms to transit through the male and female urogenital tracts. T. vaginalis causes trichamoniasis, which appears in an estimated 180 million cases worldwide each year. Whereas men rarely exhibit symptoms during an infection with this protist, infected women may become more susceptible to secondary infection with human immunodeficiency virus (HIV) and may be more likely to develop cervical cancer. Pregnant women infected with T. vaginalis are at an increased risk of serious complications, such as pre-term delivery.
Euglenozoans
Euglenozoans includes parasites, heterotrophs, autotrophs, and mixotrophs, ranging in size from 10 to 500 µm. Euglenoids move through their aquatic habitats using two long flagella that guide them toward light sources sensed by a primitive ocular organ called an eyespot. The familiar genus, Euglena, encompasses some mixotrophic species that display a photosynthetic capability only when light is present. In the dark, the chloroplasts of Euglena shrink up and temporarily cease functioning, and the cells instead take up organic nutrients from their environment.
The human parasite, Trypanosoma brucei, belongs to a different subgroup of Euglenozoa, the kinetoplastids. The kinetoplastid subgroup is named after the kinetoplast, a DNA mass carried within the single, oversized mitochondrion possessed by each of these cells. This subgroup includes several parasites, collectively called trypanosomes, which cause devastating human diseases and infect an insect species during a portion of their life cycle. T. brucei develops in the gut of the tsetse fly after the fly bites an infected human or other mammalian host. The parasite then travels to the insect salivary glands to be transmitted to another human or other mammal when the infected tsetse fly consumes another blood meal. T. brucei is common in central Africa and is the causative agent of African sleeping sickness, a disease associated with severe chronic fatigue, coma, and can be fatal if left untreated.
Trypanosoma brucei
Watch this video to see T. brucei swimming. https://youtu.be/EnsydwITLYk
Chromalveolata
Current evidence suggests that species classified as chromalveolates are derived from a common ancestor that engulfed a photosynthetic red algal cell, which itself had already evolved chloroplasts from an endosymbiotic relationship with a photosynthetic prokaryote. Therefore, the ancestor of chromalveolates is believed to have resulted from a secondary endosymbiotic event. However, some chromalveolates appear to have lost red alga-derived plastid organelles or lack plastid genes altogether. Therefore, this supergroup should be considered a hypothesis-based working group that is subject to change. Chromalveolates include very important photosynthetic organisms, such as diatoms, brown algae, and significant disease agents in animals and plants. The chromalveolates can be subdivided into alveolates and stramenopiles.
Alveolates: Dinoflagellates, Apicomplexians, and Ciliates
A large body of data supports that the alveolates are derived from a shared common ancestor. The alveolates are named for the presence of an alveolus, or membrane-enclosed sac, beneath the cell membrane. The exact function of the alveolus is unknown, but it may be involved in osmoregulation. The alveolates are further categorized into some of the better-known protists: the dinoflagellates, the apicomplexans, and the ciliates.
Dinoflagellates exhibit extensive morphological diversity and can be photosynthetic, heterotrophic, or mixotrophic. Many dinoflagellates are encased in interlocking plates of cellulose. Two perpendicular flagella fit into the grooves between the cellulose plates, with one flagellum extending longitudinally and a second encircling the dinoflagellate (Figure \(4\)). Together, the flagella contribute to the characteristic spinning motion of dinoflagellates. These protists exist in freshwater and marine habitats, and are a component of plankton, the typically microscopic organisms that drift through the water and serve as a crucial food source for larger aquatic organisms.
Some dinoflagellates generate light, called bioluminescence, when they are jarred or stressed. Large numbers of marine dinoflagellates (billions or trillions of cells per wave) can emit light and cause an entire breaking wave to twinkle or take on a brilliant blue color (Figure \(5\)). For approximately 20 species of marine dinoflagellates, population explosions (also called blooms) during the summer months can tint the ocean with a muddy red color. This phenomenon is called a red tide, and it results from the abundant red pigments present in dinoflagellate plastids. In large quantities, these dinoflagellate species secrete an asphyxiating toxin that can kill fish, birds, and marine mammals. Red tides can be massively detrimental to commercial fisheries, and humans who consume these protists may become poisoned.
The apicomplexan protists are so named because their microtubules, fibrin, and vacuoles are asymmetrically distributed at one end of the cell in a structure called an apical complex (Figure \(6\)). The apical complex is specialized for entry and infection of host cells. Indeed, all apicomplexans are parasitic. This group includes the genus Plasmodium, which causes malaria in humans. Apicomplexan life cycles are complex, involving multiple hosts and stages of sexual and asexual reproduction.
The ciliates, which include Paramecium and Tetrahymena, are a group of protists 10 to 3,000 micrometers in length that are covered in rows, tufts, or spirals of tiny cilia. By beating their cilia synchronously or in waves, ciliates can coordinate directed movements and ingest food particles. Certain ciliates have fused cilia-based structures that function like paddles, funnels, or fins. Ciliates also are surrounded by a pellicle, providing protection without compromising agility. The genus Paramecium includes protists that have organized their cilia into a plate-like primitive mouth, called an oral groove, which is used to capture and digest bacteria (Figure \(7\)). Food captured in the oral groove enters a food vacuole, where it combines with digestive enzymes. Waste particles are expelled by an exocytic vesicle that fuses at a specific region on the cell membrane, called the anal pore. In addition to a vacuole-based digestive system, Paramecium also uses contractile vacuoles, which are osmoregulatory vesicles that fill with water as it enters the cell by osmosis and then contract to squeeze water from the cell.
Link to Learning
Watch the video of the contractile vacuole of Paramecium expelling water to keep the cell osmotically balanced.
Paramecium has two nuclei, a macronucleus and a micronucleus, in each cell. The micronucleus is essential for sexual reproduction, whereas the macronucleus directs asexual binary fission and all other biological functions. The process of sexual reproduction in Paramecium underscores the importance of the micronucleus to these protists. Paramecium and most other ciliates reproduce sexually by conjugation. This process begins when two different mating types of Paramecium make physical contact and join with a cytoplasmic bridge (Figure \(8\)). The diploid micronucleus in each cell then undergoes meiosis to produce four haploid micronuclei. Three of these degenerate in each cell, leaving one micronucleus that then undergoes mitosis, generating two haploid micronuclei. The cells each exchange one of these haploid nuclei and move away from each other. A similar process occurs in bacteria that have plasmids. Fusion of the haploid micronuclei generates a completely novel diploid pre-micronucleus in each conjugative cell. This pre-micronucleus undergoes three rounds of mitosis to produce eight copies, and the original macronucleus disintegrates. Four of the eight pre-micronuclei become full-fledged micronuclei, whereas the other four perform multiple rounds of DNA replication and go on to become new macronuclei. Two cell divisions then yield four new Paramecia from each original conjugative cell.
Exercise
Which of the following statements about Paramecium sexual reproduction is false?
1. The macronuclei are derived from micronuclei.
2. Both mitosis and meiosis occur during sexual reproduction.
3. The conjugate pair swaps macronucleii.
4. Each parent produces four daughter cells.
Stramenopiles: Diatoms, Brown Algae, Golden Algae and Oomycetes
The other subgroup of chromalveolates, the stramenopiles, includes photosynthetic marine algae and heterotrophic protists. The unifying feature of this group is the presence of a textured, or “hairy,” flagellum. Many stramenopiles also have an additional flagellum that lacks hair-like projections (Figure \(9\)). Members of this subgroup range in size from single-celled diatoms to the massive and multicellular kelp.
The diatoms are unicellular photosynthetic protists that encase themselves in intricately patterned, glassy cell walls composed of silicon dioxide in a matrix of organic particles (Figure \(10\)). These protists are a component of freshwater and marine plankton. Most species of diatoms reproduce asexually, although some instances of sexual reproduction and sporulation also exist. Some diatoms exhibit a slit in their silica shell, called a raphe. By expelling a stream of mucopolysaccharides from the raphe, the diatom can attach to surfaces or propel itself in one direction.
During periods of nutrient availability, diatom populations bloom to numbers greater than can be consumed by aquatic organisms. The excess diatoms die and sink to the sea floor where they are not easily reached by saprobes that feed on dead organisms. As a result, the carbon dioxide that the diatoms had consumed and incorporated into their cells during photosynthesis is not returned to the atmosphere. In general, this process by which carbon is transported deep into the ocean is described as the biological carbon pump, because carbon is “pumped” to the ocean depths where it is inaccessible to the atmosphere as carbon dioxide. The biological carbon pump is a crucial component of the carbon cycle that maintains lower atmospheric carbon dioxide levels.
Like diatoms, golden algae are largely unicellular, although some species can form large colonies. Their characteristic gold color results from their extensive use of carotenoids, a group of photosynthetic pigments that are generally yellow or orange in color. Golden algae are found in both freshwater and marine environments, where they form a major part of the plankton community.
The brown algae are primarily marine, multicellular organisms that are known colloquially as seaweeds. Giant kelps are a type of brown algae. Some brown algae have evolved specialized tissues that resemble terrestrial plants, with root-like holdfasts, stem-like stipes, and leaf-like blades that are capable of photosynthesis. The stipes of giant kelps are enormous, extending in some cases for 60 meters. A variety of algal life cycles exists, but the most complex is alternation of generations, in which both haploid and diploid stages involve multicellularity. Compare this life cycle to that of humans, for instance. Haploid gametes produced by meiosis (sperm and egg) combine in fertilization to generate a diploid zygote that undergoes many rounds of mitosis to produce a multicellular embryo and then a fetus. However, the individual sperm and egg themselves never become multicellular beings. Terrestrial plants also have evolved alternation of generations. In the brown algae genus Laminaria, haploid spores develop into multicellular gametophytes, which produce haploid gametes that combine to produce diploid organisms that then become multicellular organisms with a different structure from the haploid form (Figure \(11\)). Certain other organisms perform alternation of generations in which both the haploid and diploid forms look the same.
Exercise
Which of the following statements about the Laminaria life cycle is false?
1. 1n zoospores form in the sporangia.
2. The sporophyte is the 2n plant.
3. The gametophyte is diploid.
4. Both the gametophyte and sporophyte stages are multicellular.
The water molds, oomycetes (“egg fungus”), were so-named based on their fungus-like morphology, but molecular data have shown that the water molds are not closely related to fungi. The oomycetes are characterized by a cellulose-based cell wall and an extensive network of filaments that allow for nutrient uptake. As diploid spores, many oomycetes have two oppositely directed flagella (one hairy and one smooth) for locomotion. The oomycetes are nonphotosynthetic and include many saprobes and parasites. The saprobes appear as white fluffy growths on dead organisms (Figure \(12\)). Most oomycetes are aquatic, but some parasitize terrestrial plants. One plant pathogen is Phytophthora infestans, the causative agent of late blight of potatoes, such as occurred in the nineteenth century Irish potato famine.
Rhizaria
The Rhizaria supergroup includes many of the amoebas, most of which have threadlike or needle-like pseudopodia (Figure \(13\)). Pseudopodia function to trap and engulf food particles and to direct movement in rhizarian protists. These pseudopods project outward from anywhere on the cell surface and can anchor to a substrate. The protist then transports its cytoplasm into the pseudopod, thereby moving the entire cell. This type of motion, called cytoplasmic streaming, is used by several diverse groups of protists as a means of locomotion or as a method to distribute nutrients and oxygen.
Link to Learning
Take a look at this video to see cytoplasmic streaming in a green alga.
Forams
Foraminiferans, or forams, are unicellular heterotrophic protists, ranging from approximately 20 micrometers to several centimeters in length, and occasionally resembling tiny snails (Figure \(14\)). As a group, the forams exhibit porous shells, called tests that are built from various organic materials and typically hardened with calcium carbonate. The tests may house photosynthetic algae, which the forams can harvest for nutrition. Foram pseudopodia extend through the pores and allow the forams to move, feed, and gather additional building materials. Typically, forams are associated with sand or other particles in marine or freshwater habitats. Foraminiferans are also useful as indicators of pollution and changes in global weather patterns.
Radiolarians
A second subtype of Rhizaria, the radiolarians, exhibit intricate exteriors of glassy silica with radial or bilateral symmetry (Figure \(15\)). Needle-like pseudopods supported by microtubules radiate outward from the cell bodies of these protists and function to catch food particles. The shells of dead radiolarians sink to the ocean floor, where they may accumulate in 100 meter-thick depths. Preserved, sedimented radiolarians are very common in the fossil record.
Archaeplastida
Red algae and green algae are included in the supergroup Archaeplastida. It was from a common ancestor of these protists that the land plants evolved, since their closest relatives are found in this group. Molecular evidence supports that all Archaeplastida are descendents of an endosymbiotic relationship between a heterotrophic protist and a cyanobacterium. The red and green algae include unicellular, multicellular, and colonial forms.
Red Algae
Red algae, or rhodophytes, are primarily multicellular, lack flagella, and range in size from microscopic, unicellular protists to large, multicellular forms grouped into the informal seaweed category. The red algae life cycle is an alternation of generations. Some species of red algae contain phycoerythrins, photosynthetic accessory pigments that are red in color and outcompete the green tint of chlorophyll, making these species appear as varying shades of red. Other protists classified as red algae lack phycoerythrins and are parasites. Red algae are common in tropical waters where they have been detected at depths of 260 meters. Other red algae exist in terrestrial or freshwater environments.
Green Algae: Chlorophytes and Charophytes
The most abundant group of algae is the green algae. The green algae exhibit similar features to the land plants, particularly in terms of chloroplast structure. That this group of protists shared a relatively recent common ancestor with land plants is well supported. The green algae are subdivided into the chlorophytes and the charophytes. The charophytes are the closest living relatives to land plants and resemble them in morphology and reproductive strategies. Charophytes are common in wet habitats, and their presence often signals a healthy ecosystem.
The chlorophytes exhibit great diversity of form and function. Chlorophytes primarily inhabit freshwater and damp soil, and are a common component of plankton. Chlamydomonas is a simple, unicellular chlorophyte with a pear-shaped morphology and two opposing, anterior flagella that guide this protist toward light sensed by its eyespot. More complex chlorophyte species exhibit haploid gametes and spores that resemble Chlamydomonas.
The chlorophyte Volvox is one of only a few examples of a colonial organism, which behaves in some ways like a collection of individual cells, but in other ways like the specialized cells of a multicellular organism (Figure \(16\)). Volvox colonies contain 500 to 60,000 cells, each with two flagella, contained within a hollow, spherical matrix composed of a gelatinous glycoprotein secretion. Individual Volvox cells move in a coordinated fashion and are interconnected by cytoplasmic bridges. Only a few of the cells reproduce to create daughter colonies, an example of basic cell specialization in this organism.
True multicellular organisms, such as the sea lettuce, Ulva, are represented among the chlorophytes. In addition, some chlorophytes exist as large, multinucleate, single cells. Species in the genus Caulerpa exhibit flattened fern-like foliage and can reach lengths of 3 meters (Figure \(17\)). Caulerpa species undergo nuclear division, but their cells do not complete cytokinesis, remaining instead as massive and elaborate single cells.
Amoebozoa
The amoebozoans characteristically exhibit pseudopodia that extend like tubes or flat lobes, rather than the hair-like pseudopodia of rhizarian amoeba (Figure \(18\)). The Amoebozoa include several groups of unicellular amoeba-like organisms that are free-living or parasites.
Slime Molds
A subset of the amoebozoans, the slime molds, has several morphological similarities to fungi that are thought to be the result of convergent evolution. For instance, during times of stress, some slime molds develop into spore-generating fruiting bodies, much like fungi.
The slime molds are categorized on the basis of their life cycles into plasmodial or cellular types. Plasmodial slime molds are composed of large, multinucleate cells and move along surfaces like an amorphous blob of slime during their feeding stage (Figure \(19\)). Food particles are lifted and engulfed into the slime mold as it glides along. Upon maturation, the plasmodium takes on a net-like appearance with the ability to form fruiting bodies, or sporangia, during times of stress. Haploid spores are produced by meiosis within the sporangia, and spores can be disseminated through the air or water to potentially land in more favorable environments. If this occurs, the spores germinate to form ameboid or flagellate haploid cells that can combine with each other and produce a diploid zygotic slime mold to complete the life cycle.
The cellular slime molds function as independent amoeboid cells when nutrients are abundant (Figure \(20\)). When food is depleted, cellular slime molds pile onto each other into a mass of cells that behaves as a single unit, called a slug. Some cells in the slug contribute to a 2–3-millimeter stalk, drying up and dying in the process. Cells atop the stalk form an asexual fruiting body that contains haploid spores. As with plasmodial slime molds, the spores are disseminated and can germinate if they land in a moist environment. One representative genus of the cellular slime molds is Dictyostelium, which commonly exists in the damp soil of forests.
Link to Learning
View this site to see the formation of a fruiting body by a cellular slime mold.
Opisthokonta
The opisthokonts include the animal-like choanoflagellates, which are believed to resemble the common ancestor of sponges and, in fact, all animals. Choanoflagellates include unicellular and colonial forms, and number about 244 described species. These organisms exhibit a single, apical flagellum that is surrounded by a contractile collar composed of microvilli. The collar uses a similar mechanism to sponges to filter out bacteria for ingestion by the protist. The morphology of choanoflagellates was recognized early on as resembling the collar cells of sponges, and suggesting a possible relationship to animals.
The Mesomycetozoa form a small group of parasites, primarily of fish, and at least one form that can parasitize humans. Their life cycles are poorly understood. These organisms are of special interest, because they appear to be so closely related to animals. In the past, they were grouped with fungi and other protists based on their morphology.
Summary
The process of classifying protists into meaningful groups is ongoing, but genetic data in the past 20 years have clarified many relationships that were previously unclear or mistaken. The majority view at present is to order all eukaryotes into six supergroups: Excavata, Chromalveolata, Rhizaria, Archaeplastida, Amoebozoa, and Opisthokonta. The goal of this classification scheme is to create clusters of species that all are derived from a common ancestor. At present, the monophyly of some of the supergroups are better supported by genetic data than others. Although tremendous variation exists within the supergroups, commonalities at the morphological, physiological, and ecological levels can be identified.
Art Connections
Figure \(8\): Which of the following statements about Paramecium sexual reproduction is false?
1. The macronuclei are derived from micronuclei.
2. Both mitosis and meiosis occur during sexual reproduction.
3. The conjugate pair swaps macronuclei.
4. Each parent produces four daughter cells.
Answer
C
Figure \(11\): Which of the following statements about the Laminaria life cycle is false?
1. 1n zoospores form in the sporangia.
2. The sporophyte is the 2n plant.
3. The gametophyte is diploid.
4. Both the gametophyte and sporophyte stages are multicellular.
Answer
C
Glossary
biological carbon pump
process by which inorganic carbon is fixed by photosynthetic species that then die and fall to the sea floor where they cannot be reached by saprobes and their carbon dioxide consumption cannot be returned to the atmosphere
bioluminescence
generation and emission of light by an organism, as in dinoflagellates
contractile vacuole
vesicle that fills with water (as it enters the cell by osmosis) and then contracts to squeeze water from the cell; an osmoregulatory vesicle
cytoplasmic streaming
movement of cytoplasm into an extended pseudopod such that the entire cell is transported to the site of the pseudopod
hydrogenosome
organelle carried by parabasalids (Excavata) that functions anaerobically and outputs hydrogen gas as a byproduct; likely evolved from mitochondria
kinetoplast
mass of DNA carried within the single, oversized mitochondrion, characteristic of kinetoplastids (phylum: Euglenozoa)
mitosome
nonfunctional organelle carried in the cells of diplomonads (Excavata) that likely evolved from a mitochondrion
plankton
diverse group of mostly microscopic organisms that drift in marine and freshwater systems and serve as a food source for larger aquatic organisms
raphe
slit in the silica shell of diatoms through which the protist secretes a stream of mucopolysaccharides for locomotion and attachment to substrates
test
porous shell of a foram that is built from various organic materials and typically hardened with calcium carbonate | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/28%3A_Protists/28.05%3A_Characteristics_of_Rhizaria.txt |
Skills to Develop
• Describe representative protist organisms from each of the six presently recognized supergroups of eukaryotes
• Identify the evolutionary relationships of plants, animals, and fungi within the six presently recognized supergroups of eukaryotes
In the span of several decades, the Kingdom Protista has been disassembled because sequence analyses have revealed new genetic (and therefore evolutionary) relationships among these eukaryotes. Moreover, protists that exhibit similar morphological features may have evolved analogous structures because of similar selective pressures—rather than because of recent common ancestry. This phenomenon, called convergent evolution, is one reason why protist classification is so challenging. The emerging classification scheme groups the entire domain Eukaryota into six “supergroups” that contain all of the protists as well as animals, plants, and fungi that evolved from a common ancestor (Figure \(1\)). The supergroups are believed to be monophyletic, meaning that all organisms within each supergroup are believed to have evolved from a single common ancestor, and thus all members are most closely related to each other than to organisms outside that group. There is still evidence lacking for the monophyly of some groups.
The classification of eukaryotes is still in flux, and the six supergroups may be modified or replaced by a more appropriate hierarchy as genetic, morphological, and ecological data accumulate. Keep in mind that the classification scheme presented here is just one of several hypotheses, and the true evolutionary relationships are still to be determined. When learning about protists, it is helpful to focus less on the nomenclature and more on the commonalities and differences that define the groups themselves.
Excavata
Many of the protist species classified into the supergroup Excavata are asymmetrical, single-celled organisms with a feeding groove “excavated” from one side. This supergroup includes heterotrophic predators, photosynthetic species, and parasites. Its subgroups are the diplomonads, parabasalids, and euglenozoans.
Diplomonads
Among the Excavata are the diplomonads, which include the intestinal parasite, Giardia lamblia (Figure \(2\)). Until recently, these protists were believed to lack mitochondria. Mitochondrial remnant organelles, called mitosomes, have since been identified in diplomonads, but these mitosomes are essentially nonfunctional. Diplomonads exist in anaerobic environments and use alternative pathways, such as glycolysis, to generate energy. Each diplomonad cell has two identical nuclei and uses several flagella for locomotion.
Parabasalids
A second Excavata subgroup, the parabasalids, also exhibits semi-functional mitochondria. In parabasalids, these structures function anaerobically and are called hydrogenosomes because they produce hydrogen gas as a byproduct. Parabasalids move with flagella and membrane rippling. Trichomonas vaginalis, a parabasalid that causes a sexually transmitted disease in humans, employs these mechanisms to transit through the male and female urogenital tracts. T. vaginalis causes trichamoniasis, which appears in an estimated 180 million cases worldwide each year. Whereas men rarely exhibit symptoms during an infection with this protist, infected women may become more susceptible to secondary infection with human immunodeficiency virus (HIV) and may be more likely to develop cervical cancer. Pregnant women infected with T. vaginalis are at an increased risk of serious complications, such as pre-term delivery.
Euglenozoans
Euglenozoans includes parasites, heterotrophs, autotrophs, and mixotrophs, ranging in size from 10 to 500 µm. Euglenoids move through their aquatic habitats using two long flagella that guide them toward light sources sensed by a primitive ocular organ called an eyespot. The familiar genus, Euglena, encompasses some mixotrophic species that display a photosynthetic capability only when light is present. In the dark, the chloroplasts of Euglena shrink up and temporarily cease functioning, and the cells instead take up organic nutrients from their environment.
The human parasite, Trypanosoma brucei, belongs to a different subgroup of Euglenozoa, the kinetoplastids. The kinetoplastid subgroup is named after the kinetoplast, a DNA mass carried within the single, oversized mitochondrion possessed by each of these cells. This subgroup includes several parasites, collectively called trypanosomes, which cause devastating human diseases and infect an insect species during a portion of their life cycle. T. brucei develops in the gut of the tsetse fly after the fly bites an infected human or other mammalian host. The parasite then travels to the insect salivary glands to be transmitted to another human or other mammal when the infected tsetse fly consumes another blood meal. T. brucei is common in central Africa and is the causative agent of African sleeping sickness, a disease associated with severe chronic fatigue, coma, and can be fatal if left untreated.
Trypanosoma brucei
Watch this video to see T. brucei swimming. https://youtu.be/EnsydwITLYk
Chromalveolata
Current evidence suggests that species classified as chromalveolates are derived from a common ancestor that engulfed a photosynthetic red algal cell, which itself had already evolved chloroplasts from an endosymbiotic relationship with a photosynthetic prokaryote. Therefore, the ancestor of chromalveolates is believed to have resulted from a secondary endosymbiotic event. However, some chromalveolates appear to have lost red alga-derived plastid organelles or lack plastid genes altogether. Therefore, this supergroup should be considered a hypothesis-based working group that is subject to change. Chromalveolates include very important photosynthetic organisms, such as diatoms, brown algae, and significant disease agents in animals and plants. The chromalveolates can be subdivided into alveolates and stramenopiles.
Alveolates: Dinoflagellates, Apicomplexians, and Ciliates
A large body of data supports that the alveolates are derived from a shared common ancestor. The alveolates are named for the presence of an alveolus, or membrane-enclosed sac, beneath the cell membrane. The exact function of the alveolus is unknown, but it may be involved in osmoregulation. The alveolates are further categorized into some of the better-known protists: the dinoflagellates, the apicomplexans, and the ciliates.
Dinoflagellates exhibit extensive morphological diversity and can be photosynthetic, heterotrophic, or mixotrophic. Many dinoflagellates are encased in interlocking plates of cellulose. Two perpendicular flagella fit into the grooves between the cellulose plates, with one flagellum extending longitudinally and a second encircling the dinoflagellate (Figure \(4\)). Together, the flagella contribute to the characteristic spinning motion of dinoflagellates. These protists exist in freshwater and marine habitats, and are a component of plankton, the typically microscopic organisms that drift through the water and serve as a crucial food source for larger aquatic organisms.
Some dinoflagellates generate light, called bioluminescence, when they are jarred or stressed. Large numbers of marine dinoflagellates (billions or trillions of cells per wave) can emit light and cause an entire breaking wave to twinkle or take on a brilliant blue color (Figure \(5\)). For approximately 20 species of marine dinoflagellates, population explosions (also called blooms) during the summer months can tint the ocean with a muddy red color. This phenomenon is called a red tide, and it results from the abundant red pigments present in dinoflagellate plastids. In large quantities, these dinoflagellate species secrete an asphyxiating toxin that can kill fish, birds, and marine mammals. Red tides can be massively detrimental to commercial fisheries, and humans who consume these protists may become poisoned.
The apicomplexan protists are so named because their microtubules, fibrin, and vacuoles are asymmetrically distributed at one end of the cell in a structure called an apical complex (Figure \(6\)). The apical complex is specialized for entry and infection of host cells. Indeed, all apicomplexans are parasitic. This group includes the genus Plasmodium, which causes malaria in humans. Apicomplexan life cycles are complex, involving multiple hosts and stages of sexual and asexual reproduction.
The ciliates, which include Paramecium and Tetrahymena, are a group of protists 10 to 3,000 micrometers in length that are covered in rows, tufts, or spirals of tiny cilia. By beating their cilia synchronously or in waves, ciliates can coordinate directed movements and ingest food particles. Certain ciliates have fused cilia-based structures that function like paddles, funnels, or fins. Ciliates also are surrounded by a pellicle, providing protection without compromising agility. The genus Paramecium includes protists that have organized their cilia into a plate-like primitive mouth, called an oral groove, which is used to capture and digest bacteria (Figure \(7\)). Food captured in the oral groove enters a food vacuole, where it combines with digestive enzymes. Waste particles are expelled by an exocytic vesicle that fuses at a specific region on the cell membrane, called the anal pore. In addition to a vacuole-based digestive system, Paramecium also uses contractile vacuoles, which are osmoregulatory vesicles that fill with water as it enters the cell by osmosis and then contract to squeeze water from the cell.
Link to Learning
Watch the video of the contractile vacuole of Paramecium expelling water to keep the cell osmotically balanced.
Paramecium has two nuclei, a macronucleus and a micronucleus, in each cell. The micronucleus is essential for sexual reproduction, whereas the macronucleus directs asexual binary fission and all other biological functions. The process of sexual reproduction in Paramecium underscores the importance of the micronucleus to these protists. Paramecium and most other ciliates reproduce sexually by conjugation. This process begins when two different mating types of Paramecium make physical contact and join with a cytoplasmic bridge (Figure \(8\)). The diploid micronucleus in each cell then undergoes meiosis to produce four haploid micronuclei. Three of these degenerate in each cell, leaving one micronucleus that then undergoes mitosis, generating two haploid micronuclei. The cells each exchange one of these haploid nuclei and move away from each other. A similar process occurs in bacteria that have plasmids. Fusion of the haploid micronuclei generates a completely novel diploid pre-micronucleus in each conjugative cell. This pre-micronucleus undergoes three rounds of mitosis to produce eight copies, and the original macronucleus disintegrates. Four of the eight pre-micronuclei become full-fledged micronuclei, whereas the other four perform multiple rounds of DNA replication and go on to become new macronuclei. Two cell divisions then yield four new Paramecia from each original conjugative cell.
Exercise
Which of the following statements about Paramecium sexual reproduction is false?
1. The macronuclei are derived from micronuclei.
2. Both mitosis and meiosis occur during sexual reproduction.
3. The conjugate pair swaps macronucleii.
4. Each parent produces four daughter cells.
Stramenopiles: Diatoms, Brown Algae, Golden Algae and Oomycetes
The other subgroup of chromalveolates, the stramenopiles, includes photosynthetic marine algae and heterotrophic protists. The unifying feature of this group is the presence of a textured, or “hairy,” flagellum. Many stramenopiles also have an additional flagellum that lacks hair-like projections (Figure \(9\)). Members of this subgroup range in size from single-celled diatoms to the massive and multicellular kelp.
The diatoms are unicellular photosynthetic protists that encase themselves in intricately patterned, glassy cell walls composed of silicon dioxide in a matrix of organic particles (Figure \(10\)). These protists are a component of freshwater and marine plankton. Most species of diatoms reproduce asexually, although some instances of sexual reproduction and sporulation also exist. Some diatoms exhibit a slit in their silica shell, called a raphe. By expelling a stream of mucopolysaccharides from the raphe, the diatom can attach to surfaces or propel itself in one direction.
During periods of nutrient availability, diatom populations bloom to numbers greater than can be consumed by aquatic organisms. The excess diatoms die and sink to the sea floor where they are not easily reached by saprobes that feed on dead organisms. As a result, the carbon dioxide that the diatoms had consumed and incorporated into their cells during photosynthesis is not returned to the atmosphere. In general, this process by which carbon is transported deep into the ocean is described as the biological carbon pump, because carbon is “pumped” to the ocean depths where it is inaccessible to the atmosphere as carbon dioxide. The biological carbon pump is a crucial component of the carbon cycle that maintains lower atmospheric carbon dioxide levels.
Like diatoms, golden algae are largely unicellular, although some species can form large colonies. Their characteristic gold color results from their extensive use of carotenoids, a group of photosynthetic pigments that are generally yellow or orange in color. Golden algae are found in both freshwater and marine environments, where they form a major part of the plankton community.
The brown algae are primarily marine, multicellular organisms that are known colloquially as seaweeds. Giant kelps are a type of brown algae. Some brown algae have evolved specialized tissues that resemble terrestrial plants, with root-like holdfasts, stem-like stipes, and leaf-like blades that are capable of photosynthesis. The stipes of giant kelps are enormous, extending in some cases for 60 meters. A variety of algal life cycles exists, but the most complex is alternation of generations, in which both haploid and diploid stages involve multicellularity. Compare this life cycle to that of humans, for instance. Haploid gametes produced by meiosis (sperm and egg) combine in fertilization to generate a diploid zygote that undergoes many rounds of mitosis to produce a multicellular embryo and then a fetus. However, the individual sperm and egg themselves never become multicellular beings. Terrestrial plants also have evolved alternation of generations. In the brown algae genus Laminaria, haploid spores develop into multicellular gametophytes, which produce haploid gametes that combine to produce diploid organisms that then become multicellular organisms with a different structure from the haploid form (Figure \(11\)). Certain other organisms perform alternation of generations in which both the haploid and diploid forms look the same.
Exercise
Which of the following statements about the Laminaria life cycle is false?
1. 1n zoospores form in the sporangia.
2. The sporophyte is the 2n plant.
3. The gametophyte is diploid.
4. Both the gametophyte and sporophyte stages are multicellular.
The water molds, oomycetes (“egg fungus”), were so-named based on their fungus-like morphology, but molecular data have shown that the water molds are not closely related to fungi. The oomycetes are characterized by a cellulose-based cell wall and an extensive network of filaments that allow for nutrient uptake. As diploid spores, many oomycetes have two oppositely directed flagella (one hairy and one smooth) for locomotion. The oomycetes are nonphotosynthetic and include many saprobes and parasites. The saprobes appear as white fluffy growths on dead organisms (Figure \(12\)). Most oomycetes are aquatic, but some parasitize terrestrial plants. One plant pathogen is Phytophthora infestans, the causative agent of late blight of potatoes, such as occurred in the nineteenth century Irish potato famine.
Rhizaria
The Rhizaria supergroup includes many of the amoebas, most of which have threadlike or needle-like pseudopodia (Figure \(13\)). Pseudopodia function to trap and engulf food particles and to direct movement in rhizarian protists. These pseudopods project outward from anywhere on the cell surface and can anchor to a substrate. The protist then transports its cytoplasm into the pseudopod, thereby moving the entire cell. This type of motion, called cytoplasmic streaming, is used by several diverse groups of protists as a means of locomotion or as a method to distribute nutrients and oxygen.
Link to Learning
Take a look at this video to see cytoplasmic streaming in a green alga.
Forams
Foraminiferans, or forams, are unicellular heterotrophic protists, ranging from approximately 20 micrometers to several centimeters in length, and occasionally resembling tiny snails (Figure \(14\)). As a group, the forams exhibit porous shells, called tests that are built from various organic materials and typically hardened with calcium carbonate. The tests may house photosynthetic algae, which the forams can harvest for nutrition. Foram pseudopodia extend through the pores and allow the forams to move, feed, and gather additional building materials. Typically, forams are associated with sand or other particles in marine or freshwater habitats. Foraminiferans are also useful as indicators of pollution and changes in global weather patterns.
Radiolarians
A second subtype of Rhizaria, the radiolarians, exhibit intricate exteriors of glassy silica with radial or bilateral symmetry (Figure \(15\)). Needle-like pseudopods supported by microtubules radiate outward from the cell bodies of these protists and function to catch food particles. The shells of dead radiolarians sink to the ocean floor, where they may accumulate in 100 meter-thick depths. Preserved, sedimented radiolarians are very common in the fossil record.
Archaeplastida
Red algae and green algae are included in the supergroup Archaeplastida. It was from a common ancestor of these protists that the land plants evolved, since their closest relatives are found in this group. Molecular evidence supports that all Archaeplastida are descendents of an endosymbiotic relationship between a heterotrophic protist and a cyanobacterium. The red and green algae include unicellular, multicellular, and colonial forms.
Red Algae
Red algae, or rhodophytes, are primarily multicellular, lack flagella, and range in size from microscopic, unicellular protists to large, multicellular forms grouped into the informal seaweed category. The red algae life cycle is an alternation of generations. Some species of red algae contain phycoerythrins, photosynthetic accessory pigments that are red in color and outcompete the green tint of chlorophyll, making these species appear as varying shades of red. Other protists classified as red algae lack phycoerythrins and are parasites. Red algae are common in tropical waters where they have been detected at depths of 260 meters. Other red algae exist in terrestrial or freshwater environments.
Green Algae: Chlorophytes and Charophytes
The most abundant group of algae is the green algae. The green algae exhibit similar features to the land plants, particularly in terms of chloroplast structure. That this group of protists shared a relatively recent common ancestor with land plants is well supported. The green algae are subdivided into the chlorophytes and the charophytes. The charophytes are the closest living relatives to land plants and resemble them in morphology and reproductive strategies. Charophytes are common in wet habitats, and their presence often signals a healthy ecosystem.
The chlorophytes exhibit great diversity of form and function. Chlorophytes primarily inhabit freshwater and damp soil, and are a common component of plankton. Chlamydomonas is a simple, unicellular chlorophyte with a pear-shaped morphology and two opposing, anterior flagella that guide this protist toward light sensed by its eyespot. More complex chlorophyte species exhibit haploid gametes and spores that resemble Chlamydomonas.
The chlorophyte Volvox is one of only a few examples of a colonial organism, which behaves in some ways like a collection of individual cells, but in other ways like the specialized cells of a multicellular organism (Figure \(16\)). Volvox colonies contain 500 to 60,000 cells, each with two flagella, contained within a hollow, spherical matrix composed of a gelatinous glycoprotein secretion. Individual Volvox cells move in a coordinated fashion and are interconnected by cytoplasmic bridges. Only a few of the cells reproduce to create daughter colonies, an example of basic cell specialization in this organism.
True multicellular organisms, such as the sea lettuce, Ulva, are represented among the chlorophytes. In addition, some chlorophytes exist as large, multinucleate, single cells. Species in the genus Caulerpa exhibit flattened fern-like foliage and can reach lengths of 3 meters (Figure \(17\)). Caulerpa species undergo nuclear division, but their cells do not complete cytokinesis, remaining instead as massive and elaborate single cells.
Amoebozoa
The amoebozoans characteristically exhibit pseudopodia that extend like tubes or flat lobes, rather than the hair-like pseudopodia of rhizarian amoeba (Figure \(18\)). The Amoebozoa include several groups of unicellular amoeba-like organisms that are free-living or parasites.
Slime Molds
A subset of the amoebozoans, the slime molds, has several morphological similarities to fungi that are thought to be the result of convergent evolution. For instance, during times of stress, some slime molds develop into spore-generating fruiting bodies, much like fungi.
The slime molds are categorized on the basis of their life cycles into plasmodial or cellular types. Plasmodial slime molds are composed of large, multinucleate cells and move along surfaces like an amorphous blob of slime during their feeding stage (Figure \(19\)). Food particles are lifted and engulfed into the slime mold as it glides along. Upon maturation, the plasmodium takes on a net-like appearance with the ability to form fruiting bodies, or sporangia, during times of stress. Haploid spores are produced by meiosis within the sporangia, and spores can be disseminated through the air or water to potentially land in more favorable environments. If this occurs, the spores germinate to form ameboid or flagellate haploid cells that can combine with each other and produce a diploid zygotic slime mold to complete the life cycle.
The cellular slime molds function as independent amoeboid cells when nutrients are abundant (Figure \(20\)). When food is depleted, cellular slime molds pile onto each other into a mass of cells that behaves as a single unit, called a slug. Some cells in the slug contribute to a 2–3-millimeter stalk, drying up and dying in the process. Cells atop the stalk form an asexual fruiting body that contains haploid spores. As with plasmodial slime molds, the spores are disseminated and can germinate if they land in a moist environment. One representative genus of the cellular slime molds is Dictyostelium, which commonly exists in the damp soil of forests.
Link to Learning
View this site to see the formation of a fruiting body by a cellular slime mold.
Opisthokonta
The opisthokonts include the animal-like choanoflagellates, which are believed to resemble the common ancestor of sponges and, in fact, all animals. Choanoflagellates include unicellular and colonial forms, and number about 244 described species. These organisms exhibit a single, apical flagellum that is surrounded by a contractile collar composed of microvilli. The collar uses a similar mechanism to sponges to filter out bacteria for ingestion by the protist. The morphology of choanoflagellates was recognized early on as resembling the collar cells of sponges, and suggesting a possible relationship to animals.
The Mesomycetozoa form a small group of parasites, primarily of fish, and at least one form that can parasitize humans. Their life cycles are poorly understood. These organisms are of special interest, because they appear to be so closely related to animals. In the past, they were grouped with fungi and other protists based on their morphology.
Summary
The process of classifying protists into meaningful groups is ongoing, but genetic data in the past 20 years have clarified many relationships that were previously unclear or mistaken. The majority view at present is to order all eukaryotes into six supergroups: Excavata, Chromalveolata, Rhizaria, Archaeplastida, Amoebozoa, and Opisthokonta. The goal of this classification scheme is to create clusters of species that all are derived from a common ancestor. At present, the monophyly of some of the supergroups are better supported by genetic data than others. Although tremendous variation exists within the supergroups, commonalities at the morphological, physiological, and ecological levels can be identified.
Art Connections
Figure \(8\): Which of the following statements about Paramecium sexual reproduction is false?
1. The macronuclei are derived from micronuclei.
2. Both mitosis and meiosis occur during sexual reproduction.
3. The conjugate pair swaps macronuclei.
4. Each parent produces four daughter cells.
Answer
C
Figure \(11\): Which of the following statements about the Laminaria life cycle is false?
1. 1n zoospores form in the sporangia.
2. The sporophyte is the 2n plant.
3. The gametophyte is diploid.
4. Both the gametophyte and sporophyte stages are multicellular.
Answer
C
Glossary
biological carbon pump
process by which inorganic carbon is fixed by photosynthetic species that then die and fall to the sea floor where they cannot be reached by saprobes and their carbon dioxide consumption cannot be returned to the atmosphere
bioluminescence
generation and emission of light by an organism, as in dinoflagellates
contractile vacuole
vesicle that fills with water (as it enters the cell by osmosis) and then contracts to squeeze water from the cell; an osmoregulatory vesicle
cytoplasmic streaming
movement of cytoplasm into an extended pseudopod such that the entire cell is transported to the site of the pseudopod
hydrogenosome
organelle carried by parabasalids (Excavata) that functions anaerobically and outputs hydrogen gas as a byproduct; likely evolved from mitochondria
kinetoplast
mass of DNA carried within the single, oversized mitochondrion, characteristic of kinetoplastids (phylum: Euglenozoa)
mitosome
nonfunctional organelle carried in the cells of diplomonads (Excavata) that likely evolved from a mitochondrion
plankton
diverse group of mostly microscopic organisms that drift in marine and freshwater systems and serve as a food source for larger aquatic organisms
raphe
slit in the silica shell of diatoms through which the protist secretes a stream of mucopolysaccharides for locomotion and attachment to substrates
test
porous shell of a foram that is built from various organic materials and typically hardened with calcium carbonate | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/28%3A_Protists/28.06%3A_Characteristics_of_Archaeplastidia.txt |
Skills to Develop
• Describe representative protist organisms from each of the six presently recognized supergroups of eukaryotes
• Identify the evolutionary relationships of plants, animals, and fungi within the six presently recognized supergroups of eukaryotes
In the span of several decades, the Kingdom Protista has been disassembled because sequence analyses have revealed new genetic (and therefore evolutionary) relationships among these eukaryotes. Moreover, protists that exhibit similar morphological features may have evolved analogous structures because of similar selective pressures—rather than because of recent common ancestry. This phenomenon, called convergent evolution, is one reason why protist classification is so challenging. The emerging classification scheme groups the entire domain Eukaryota into six “supergroups” that contain all of the protists as well as animals, plants, and fungi that evolved from a common ancestor (Figure \(1\)). The supergroups are believed to be monophyletic, meaning that all organisms within each supergroup are believed to have evolved from a single common ancestor, and thus all members are most closely related to each other than to organisms outside that group. There is still evidence lacking for the monophyly of some groups.
The classification of eukaryotes is still in flux, and the six supergroups may be modified or replaced by a more appropriate hierarchy as genetic, morphological, and ecological data accumulate. Keep in mind that the classification scheme presented here is just one of several hypotheses, and the true evolutionary relationships are still to be determined. When learning about protists, it is helpful to focus less on the nomenclature and more on the commonalities and differences that define the groups themselves.
Excavata
Many of the protist species classified into the supergroup Excavata are asymmetrical, single-celled organisms with a feeding groove “excavated” from one side. This supergroup includes heterotrophic predators, photosynthetic species, and parasites. Its subgroups are the diplomonads, parabasalids, and euglenozoans.
Diplomonads
Among the Excavata are the diplomonads, which include the intestinal parasite, Giardia lamblia (Figure \(2\)). Until recently, these protists were believed to lack mitochondria. Mitochondrial remnant organelles, called mitosomes, have since been identified in diplomonads, but these mitosomes are essentially nonfunctional. Diplomonads exist in anaerobic environments and use alternative pathways, such as glycolysis, to generate energy. Each diplomonad cell has two identical nuclei and uses several flagella for locomotion.
Parabasalids
A second Excavata subgroup, the parabasalids, also exhibits semi-functional mitochondria. In parabasalids, these structures function anaerobically and are called hydrogenosomes because they produce hydrogen gas as a byproduct. Parabasalids move with flagella and membrane rippling. Trichomonas vaginalis, a parabasalid that causes a sexually transmitted disease in humans, employs these mechanisms to transit through the male and female urogenital tracts. T. vaginalis causes trichamoniasis, which appears in an estimated 180 million cases worldwide each year. Whereas men rarely exhibit symptoms during an infection with this protist, infected women may become more susceptible to secondary infection with human immunodeficiency virus (HIV) and may be more likely to develop cervical cancer. Pregnant women infected with T. vaginalis are at an increased risk of serious complications, such as pre-term delivery.
Euglenozoans
Euglenozoans includes parasites, heterotrophs, autotrophs, and mixotrophs, ranging in size from 10 to 500 µm. Euglenoids move through their aquatic habitats using two long flagella that guide them toward light sources sensed by a primitive ocular organ called an eyespot. The familiar genus, Euglena, encompasses some mixotrophic species that display a photosynthetic capability only when light is present. In the dark, the chloroplasts of Euglena shrink up and temporarily cease functioning, and the cells instead take up organic nutrients from their environment.
The human parasite, Trypanosoma brucei, belongs to a different subgroup of Euglenozoa, the kinetoplastids. The kinetoplastid subgroup is named after the kinetoplast, a DNA mass carried within the single, oversized mitochondrion possessed by each of these cells. This subgroup includes several parasites, collectively called trypanosomes, which cause devastating human diseases and infect an insect species during a portion of their life cycle. T. brucei develops in the gut of the tsetse fly after the fly bites an infected human or other mammalian host. The parasite then travels to the insect salivary glands to be transmitted to another human or other mammal when the infected tsetse fly consumes another blood meal. T. brucei is common in central Africa and is the causative agent of African sleeping sickness, a disease associated with severe chronic fatigue, coma, and can be fatal if left untreated.
Trypanosoma brucei
Watch this video to see T. brucei swimming. https://youtu.be/EnsydwITLYk
Chromalveolata
Current evidence suggests that species classified as chromalveolates are derived from a common ancestor that engulfed a photosynthetic red algal cell, which itself had already evolved chloroplasts from an endosymbiotic relationship with a photosynthetic prokaryote. Therefore, the ancestor of chromalveolates is believed to have resulted from a secondary endosymbiotic event. However, some chromalveolates appear to have lost red alga-derived plastid organelles or lack plastid genes altogether. Therefore, this supergroup should be considered a hypothesis-based working group that is subject to change. Chromalveolates include very important photosynthetic organisms, such as diatoms, brown algae, and significant disease agents in animals and plants. The chromalveolates can be subdivided into alveolates and stramenopiles.
Alveolates: Dinoflagellates, Apicomplexians, and Ciliates
A large body of data supports that the alveolates are derived from a shared common ancestor. The alveolates are named for the presence of an alveolus, or membrane-enclosed sac, beneath the cell membrane. The exact function of the alveolus is unknown, but it may be involved in osmoregulation. The alveolates are further categorized into some of the better-known protists: the dinoflagellates, the apicomplexans, and the ciliates.
Dinoflagellates exhibit extensive morphological diversity and can be photosynthetic, heterotrophic, or mixotrophic. Many dinoflagellates are encased in interlocking plates of cellulose. Two perpendicular flagella fit into the grooves between the cellulose plates, with one flagellum extending longitudinally and a second encircling the dinoflagellate (Figure \(4\)). Together, the flagella contribute to the characteristic spinning motion of dinoflagellates. These protists exist in freshwater and marine habitats, and are a component of plankton, the typically microscopic organisms that drift through the water and serve as a crucial food source for larger aquatic organisms.
Some dinoflagellates generate light, called bioluminescence, when they are jarred or stressed. Large numbers of marine dinoflagellates (billions or trillions of cells per wave) can emit light and cause an entire breaking wave to twinkle or take on a brilliant blue color (Figure \(5\)). For approximately 20 species of marine dinoflagellates, population explosions (also called blooms) during the summer months can tint the ocean with a muddy red color. This phenomenon is called a red tide, and it results from the abundant red pigments present in dinoflagellate plastids. In large quantities, these dinoflagellate species secrete an asphyxiating toxin that can kill fish, birds, and marine mammals. Red tides can be massively detrimental to commercial fisheries, and humans who consume these protists may become poisoned.
The apicomplexan protists are so named because their microtubules, fibrin, and vacuoles are asymmetrically distributed at one end of the cell in a structure called an apical complex (Figure \(6\)). The apical complex is specialized for entry and infection of host cells. Indeed, all apicomplexans are parasitic. This group includes the genus Plasmodium, which causes malaria in humans. Apicomplexan life cycles are complex, involving multiple hosts and stages of sexual and asexual reproduction.
The ciliates, which include Paramecium and Tetrahymena, are a group of protists 10 to 3,000 micrometers in length that are covered in rows, tufts, or spirals of tiny cilia. By beating their cilia synchronously or in waves, ciliates can coordinate directed movements and ingest food particles. Certain ciliates have fused cilia-based structures that function like paddles, funnels, or fins. Ciliates also are surrounded by a pellicle, providing protection without compromising agility. The genus Paramecium includes protists that have organized their cilia into a plate-like primitive mouth, called an oral groove, which is used to capture and digest bacteria (Figure \(7\)). Food captured in the oral groove enters a food vacuole, where it combines with digestive enzymes. Waste particles are expelled by an exocytic vesicle that fuses at a specific region on the cell membrane, called the anal pore. In addition to a vacuole-based digestive system, Paramecium also uses contractile vacuoles, which are osmoregulatory vesicles that fill with water as it enters the cell by osmosis and then contract to squeeze water from the cell.
Link to Learning
Watch the video of the contractile vacuole of Paramecium expelling water to keep the cell osmotically balanced.
Paramecium has two nuclei, a macronucleus and a micronucleus, in each cell. The micronucleus is essential for sexual reproduction, whereas the macronucleus directs asexual binary fission and all other biological functions. The process of sexual reproduction in Paramecium underscores the importance of the micronucleus to these protists. Paramecium and most other ciliates reproduce sexually by conjugation. This process begins when two different mating types of Paramecium make physical contact and join with a cytoplasmic bridge (Figure \(8\)). The diploid micronucleus in each cell then undergoes meiosis to produce four haploid micronuclei. Three of these degenerate in each cell, leaving one micronucleus that then undergoes mitosis, generating two haploid micronuclei. The cells each exchange one of these haploid nuclei and move away from each other. A similar process occurs in bacteria that have plasmids. Fusion of the haploid micronuclei generates a completely novel diploid pre-micronucleus in each conjugative cell. This pre-micronucleus undergoes three rounds of mitosis to produce eight copies, and the original macronucleus disintegrates. Four of the eight pre-micronuclei become full-fledged micronuclei, whereas the other four perform multiple rounds of DNA replication and go on to become new macronuclei. Two cell divisions then yield four new Paramecia from each original conjugative cell.
Exercise
Which of the following statements about Paramecium sexual reproduction is false?
1. The macronuclei are derived from micronuclei.
2. Both mitosis and meiosis occur during sexual reproduction.
3. The conjugate pair swaps macronucleii.
4. Each parent produces four daughter cells.
Stramenopiles: Diatoms, Brown Algae, Golden Algae and Oomycetes
The other subgroup of chromalveolates, the stramenopiles, includes photosynthetic marine algae and heterotrophic protists. The unifying feature of this group is the presence of a textured, or “hairy,” flagellum. Many stramenopiles also have an additional flagellum that lacks hair-like projections (Figure \(9\)). Members of this subgroup range in size from single-celled diatoms to the massive and multicellular kelp.
The diatoms are unicellular photosynthetic protists that encase themselves in intricately patterned, glassy cell walls composed of silicon dioxide in a matrix of organic particles (Figure \(10\)). These protists are a component of freshwater and marine plankton. Most species of diatoms reproduce asexually, although some instances of sexual reproduction and sporulation also exist. Some diatoms exhibit a slit in their silica shell, called a raphe. By expelling a stream of mucopolysaccharides from the raphe, the diatom can attach to surfaces or propel itself in one direction.
During periods of nutrient availability, diatom populations bloom to numbers greater than can be consumed by aquatic organisms. The excess diatoms die and sink to the sea floor where they are not easily reached by saprobes that feed on dead organisms. As a result, the carbon dioxide that the diatoms had consumed and incorporated into their cells during photosynthesis is not returned to the atmosphere. In general, this process by which carbon is transported deep into the ocean is described as the biological carbon pump, because carbon is “pumped” to the ocean depths where it is inaccessible to the atmosphere as carbon dioxide. The biological carbon pump is a crucial component of the carbon cycle that maintains lower atmospheric carbon dioxide levels.
Like diatoms, golden algae are largely unicellular, although some species can form large colonies. Their characteristic gold color results from their extensive use of carotenoids, a group of photosynthetic pigments that are generally yellow or orange in color. Golden algae are found in both freshwater and marine environments, where they form a major part of the plankton community.
The brown algae are primarily marine, multicellular organisms that are known colloquially as seaweeds. Giant kelps are a type of brown algae. Some brown algae have evolved specialized tissues that resemble terrestrial plants, with root-like holdfasts, stem-like stipes, and leaf-like blades that are capable of photosynthesis. The stipes of giant kelps are enormous, extending in some cases for 60 meters. A variety of algal life cycles exists, but the most complex is alternation of generations, in which both haploid and diploid stages involve multicellularity. Compare this life cycle to that of humans, for instance. Haploid gametes produced by meiosis (sperm and egg) combine in fertilization to generate a diploid zygote that undergoes many rounds of mitosis to produce a multicellular embryo and then a fetus. However, the individual sperm and egg themselves never become multicellular beings. Terrestrial plants also have evolved alternation of generations. In the brown algae genus Laminaria, haploid spores develop into multicellular gametophytes, which produce haploid gametes that combine to produce diploid organisms that then become multicellular organisms with a different structure from the haploid form (Figure \(11\)). Certain other organisms perform alternation of generations in which both the haploid and diploid forms look the same.
Exercise
Which of the following statements about the Laminaria life cycle is false?
1. 1n zoospores form in the sporangia.
2. The sporophyte is the 2n plant.
3. The gametophyte is diploid.
4. Both the gametophyte and sporophyte stages are multicellular.
The water molds, oomycetes (“egg fungus”), were so-named based on their fungus-like morphology, but molecular data have shown that the water molds are not closely related to fungi. The oomycetes are characterized by a cellulose-based cell wall and an extensive network of filaments that allow for nutrient uptake. As diploid spores, many oomycetes have two oppositely directed flagella (one hairy and one smooth) for locomotion. The oomycetes are nonphotosynthetic and include many saprobes and parasites. The saprobes appear as white fluffy growths on dead organisms (Figure \(12\)). Most oomycetes are aquatic, but some parasitize terrestrial plants. One plant pathogen is Phytophthora infestans, the causative agent of late blight of potatoes, such as occurred in the nineteenth century Irish potato famine.
Rhizaria
The Rhizaria supergroup includes many of the amoebas, most of which have threadlike or needle-like pseudopodia (Figure \(13\)). Pseudopodia function to trap and engulf food particles and to direct movement in rhizarian protists. These pseudopods project outward from anywhere on the cell surface and can anchor to a substrate. The protist then transports its cytoplasm into the pseudopod, thereby moving the entire cell. This type of motion, called cytoplasmic streaming, is used by several diverse groups of protists as a means of locomotion or as a method to distribute nutrients and oxygen.
Link to Learning
Take a look at this video to see cytoplasmic streaming in a green alga.
Forams
Foraminiferans, or forams, are unicellular heterotrophic protists, ranging from approximately 20 micrometers to several centimeters in length, and occasionally resembling tiny snails (Figure \(14\)). As a group, the forams exhibit porous shells, called tests that are built from various organic materials and typically hardened with calcium carbonate. The tests may house photosynthetic algae, which the forams can harvest for nutrition. Foram pseudopodia extend through the pores and allow the forams to move, feed, and gather additional building materials. Typically, forams are associated with sand or other particles in marine or freshwater habitats. Foraminiferans are also useful as indicators of pollution and changes in global weather patterns.
Radiolarians
A second subtype of Rhizaria, the radiolarians, exhibit intricate exteriors of glassy silica with radial or bilateral symmetry (Figure \(15\)). Needle-like pseudopods supported by microtubules radiate outward from the cell bodies of these protists and function to catch food particles. The shells of dead radiolarians sink to the ocean floor, where they may accumulate in 100 meter-thick depths. Preserved, sedimented radiolarians are very common in the fossil record.
Archaeplastida
Red algae and green algae are included in the supergroup Archaeplastida. It was from a common ancestor of these protists that the land plants evolved, since their closest relatives are found in this group. Molecular evidence supports that all Archaeplastida are descendents of an endosymbiotic relationship between a heterotrophic protist and a cyanobacterium. The red and green algae include unicellular, multicellular, and colonial forms.
Red Algae
Red algae, or rhodophytes, are primarily multicellular, lack flagella, and range in size from microscopic, unicellular protists to large, multicellular forms grouped into the informal seaweed category. The red algae life cycle is an alternation of generations. Some species of red algae contain phycoerythrins, photosynthetic accessory pigments that are red in color and outcompete the green tint of chlorophyll, making these species appear as varying shades of red. Other protists classified as red algae lack phycoerythrins and are parasites. Red algae are common in tropical waters where they have been detected at depths of 260 meters. Other red algae exist in terrestrial or freshwater environments.
Green Algae: Chlorophytes and Charophytes
The most abundant group of algae is the green algae. The green algae exhibit similar features to the land plants, particularly in terms of chloroplast structure. That this group of protists shared a relatively recent common ancestor with land plants is well supported. The green algae are subdivided into the chlorophytes and the charophytes. The charophytes are the closest living relatives to land plants and resemble them in morphology and reproductive strategies. Charophytes are common in wet habitats, and their presence often signals a healthy ecosystem.
The chlorophytes exhibit great diversity of form and function. Chlorophytes primarily inhabit freshwater and damp soil, and are a common component of plankton. Chlamydomonas is a simple, unicellular chlorophyte with a pear-shaped morphology and two opposing, anterior flagella that guide this protist toward light sensed by its eyespot. More complex chlorophyte species exhibit haploid gametes and spores that resemble Chlamydomonas.
The chlorophyte Volvox is one of only a few examples of a colonial organism, which behaves in some ways like a collection of individual cells, but in other ways like the specialized cells of a multicellular organism (Figure \(16\)). Volvox colonies contain 500 to 60,000 cells, each with two flagella, contained within a hollow, spherical matrix composed of a gelatinous glycoprotein secretion. Individual Volvox cells move in a coordinated fashion and are interconnected by cytoplasmic bridges. Only a few of the cells reproduce to create daughter colonies, an example of basic cell specialization in this organism.
True multicellular organisms, such as the sea lettuce, Ulva, are represented among the chlorophytes. In addition, some chlorophytes exist as large, multinucleate, single cells. Species in the genus Caulerpa exhibit flattened fern-like foliage and can reach lengths of 3 meters (Figure \(17\)). Caulerpa species undergo nuclear division, but their cells do not complete cytokinesis, remaining instead as massive and elaborate single cells.
Amoebozoa
The amoebozoans characteristically exhibit pseudopodia that extend like tubes or flat lobes, rather than the hair-like pseudopodia of rhizarian amoeba (Figure \(18\)). The Amoebozoa include several groups of unicellular amoeba-like organisms that are free-living or parasites.
Slime Molds
A subset of the amoebozoans, the slime molds, has several morphological similarities to fungi that are thought to be the result of convergent evolution. For instance, during times of stress, some slime molds develop into spore-generating fruiting bodies, much like fungi.
The slime molds are categorized on the basis of their life cycles into plasmodial or cellular types. Plasmodial slime molds are composed of large, multinucleate cells and move along surfaces like an amorphous blob of slime during their feeding stage (Figure \(19\)). Food particles are lifted and engulfed into the slime mold as it glides along. Upon maturation, the plasmodium takes on a net-like appearance with the ability to form fruiting bodies, or sporangia, during times of stress. Haploid spores are produced by meiosis within the sporangia, and spores can be disseminated through the air or water to potentially land in more favorable environments. If this occurs, the spores germinate to form ameboid or flagellate haploid cells that can combine with each other and produce a diploid zygotic slime mold to complete the life cycle.
The cellular slime molds function as independent amoeboid cells when nutrients are abundant (Figure \(20\)). When food is depleted, cellular slime molds pile onto each other into a mass of cells that behaves as a single unit, called a slug. Some cells in the slug contribute to a 2–3-millimeter stalk, drying up and dying in the process. Cells atop the stalk form an asexual fruiting body that contains haploid spores. As with plasmodial slime molds, the spores are disseminated and can germinate if they land in a moist environment. One representative genus of the cellular slime molds is Dictyostelium, which commonly exists in the damp soil of forests.
Link to Learning
View this site to see the formation of a fruiting body by a cellular slime mold.
Opisthokonta
The opisthokonts include the animal-like choanoflagellates, which are believed to resemble the common ancestor of sponges and, in fact, all animals. Choanoflagellates include unicellular and colonial forms, and number about 244 described species. These organisms exhibit a single, apical flagellum that is surrounded by a contractile collar composed of microvilli. The collar uses a similar mechanism to sponges to filter out bacteria for ingestion by the protist. The morphology of choanoflagellates was recognized early on as resembling the collar cells of sponges, and suggesting a possible relationship to animals.
The Mesomycetozoa form a small group of parasites, primarily of fish, and at least one form that can parasitize humans. Their life cycles are poorly understood. These organisms are of special interest, because they appear to be so closely related to animals. In the past, they were grouped with fungi and other protists based on their morphology.
Summary
The process of classifying protists into meaningful groups is ongoing, but genetic data in the past 20 years have clarified many relationships that were previously unclear or mistaken. The majority view at present is to order all eukaryotes into six supergroups: Excavata, Chromalveolata, Rhizaria, Archaeplastida, Amoebozoa, and Opisthokonta. The goal of this classification scheme is to create clusters of species that all are derived from a common ancestor. At present, the monophyly of some of the supergroups are better supported by genetic data than others. Although tremendous variation exists within the supergroups, commonalities at the morphological, physiological, and ecological levels can be identified.
Art Connections
Figure \(8\): Which of the following statements about Paramecium sexual reproduction is false?
1. The macronuclei are derived from micronuclei.
2. Both mitosis and meiosis occur during sexual reproduction.
3. The conjugate pair swaps macronuclei.
4. Each parent produces four daughter cells.
Answer
C
Figure \(11\): Which of the following statements about the Laminaria life cycle is false?
1. 1n zoospores form in the sporangia.
2. The sporophyte is the 2n plant.
3. The gametophyte is diploid.
4. Both the gametophyte and sporophyte stages are multicellular.
Answer
C
Glossary
biological carbon pump
process by which inorganic carbon is fixed by photosynthetic species that then die and fall to the sea floor where they cannot be reached by saprobes and their carbon dioxide consumption cannot be returned to the atmosphere
bioluminescence
generation and emission of light by an organism, as in dinoflagellates
contractile vacuole
vesicle that fills with water (as it enters the cell by osmosis) and then contracts to squeeze water from the cell; an osmoregulatory vesicle
cytoplasmic streaming
movement of cytoplasm into an extended pseudopod such that the entire cell is transported to the site of the pseudopod
hydrogenosome
organelle carried by parabasalids (Excavata) that functions anaerobically and outputs hydrogen gas as a byproduct; likely evolved from mitochondria
kinetoplast
mass of DNA carried within the single, oversized mitochondrion, characteristic of kinetoplastids (phylum: Euglenozoa)
mitosome
nonfunctional organelle carried in the cells of diplomonads (Excavata) that likely evolved from a mitochondrion
plankton
diverse group of mostly microscopic organisms that drift in marine and freshwater systems and serve as a food source for larger aquatic organisms
raphe
slit in the silica shell of diatoms through which the protist secretes a stream of mucopolysaccharides for locomotion and attachment to substrates
test
porous shell of a foram that is built from various organic materials and typically hardened with calcium carbonate | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/28%3A_Protists/28.07%3A_Characteristics_of_Amoebozoa.txt |
Skills to Develop
• Describe representative protist organisms from each of the six presently recognized supergroups of eukaryotes
• Identify the evolutionary relationships of plants, animals, and fungi within the six presently recognized supergroups of eukaryotes
In the span of several decades, the Kingdom Protista has been disassembled because sequence analyses have revealed new genetic (and therefore evolutionary) relationships among these eukaryotes. Moreover, protists that exhibit similar morphological features may have evolved analogous structures because of similar selective pressures—rather than because of recent common ancestry. This phenomenon, called convergent evolution, is one reason why protist classification is so challenging. The emerging classification scheme groups the entire domain Eukaryota into six “supergroups” that contain all of the protists as well as animals, plants, and fungi that evolved from a common ancestor (Figure \(1\)). The supergroups are believed to be monophyletic, meaning that all organisms within each supergroup are believed to have evolved from a single common ancestor, and thus all members are most closely related to each other than to organisms outside that group. There is still evidence lacking for the monophyly of some groups.
The classification of eukaryotes is still in flux, and the six supergroups may be modified or replaced by a more appropriate hierarchy as genetic, morphological, and ecological data accumulate. Keep in mind that the classification scheme presented here is just one of several hypotheses, and the true evolutionary relationships are still to be determined. When learning about protists, it is helpful to focus less on the nomenclature and more on the commonalities and differences that define the groups themselves.
Excavata
Many of the protist species classified into the supergroup Excavata are asymmetrical, single-celled organisms with a feeding groove “excavated” from one side. This supergroup includes heterotrophic predators, photosynthetic species, and parasites. Its subgroups are the diplomonads, parabasalids, and euglenozoans.
Diplomonads
Among the Excavata are the diplomonads, which include the intestinal parasite, Giardia lamblia (Figure \(2\)). Until recently, these protists were believed to lack mitochondria. Mitochondrial remnant organelles, called mitosomes, have since been identified in diplomonads, but these mitosomes are essentially nonfunctional. Diplomonads exist in anaerobic environments and use alternative pathways, such as glycolysis, to generate energy. Each diplomonad cell has two identical nuclei and uses several flagella for locomotion.
Parabasalids
A second Excavata subgroup, the parabasalids, also exhibits semi-functional mitochondria. In parabasalids, these structures function anaerobically and are called hydrogenosomes because they produce hydrogen gas as a byproduct. Parabasalids move with flagella and membrane rippling. Trichomonas vaginalis, a parabasalid that causes a sexually transmitted disease in humans, employs these mechanisms to transit through the male and female urogenital tracts. T. vaginalis causes trichamoniasis, which appears in an estimated 180 million cases worldwide each year. Whereas men rarely exhibit symptoms during an infection with this protist, infected women may become more susceptible to secondary infection with human immunodeficiency virus (HIV) and may be more likely to develop cervical cancer. Pregnant women infected with T. vaginalis are at an increased risk of serious complications, such as pre-term delivery.
Euglenozoans
Euglenozoans includes parasites, heterotrophs, autotrophs, and mixotrophs, ranging in size from 10 to 500 µm. Euglenoids move through their aquatic habitats using two long flagella that guide them toward light sources sensed by a primitive ocular organ called an eyespot. The familiar genus, Euglena, encompasses some mixotrophic species that display a photosynthetic capability only when light is present. In the dark, the chloroplasts of Euglena shrink up and temporarily cease functioning, and the cells instead take up organic nutrients from their environment.
The human parasite, Trypanosoma brucei, belongs to a different subgroup of Euglenozoa, the kinetoplastids. The kinetoplastid subgroup is named after the kinetoplast, a DNA mass carried within the single, oversized mitochondrion possessed by each of these cells. This subgroup includes several parasites, collectively called trypanosomes, which cause devastating human diseases and infect an insect species during a portion of their life cycle. T. brucei develops in the gut of the tsetse fly after the fly bites an infected human or other mammalian host. The parasite then travels to the insect salivary glands to be transmitted to another human or other mammal when the infected tsetse fly consumes another blood meal. T. brucei is common in central Africa and is the causative agent of African sleeping sickness, a disease associated with severe chronic fatigue, coma, and can be fatal if left untreated.
Trypanosoma brucei
Watch this video to see T. brucei swimming. https://youtu.be/EnsydwITLYk
Chromalveolata
Current evidence suggests that species classified as chromalveolates are derived from a common ancestor that engulfed a photosynthetic red algal cell, which itself had already evolved chloroplasts from an endosymbiotic relationship with a photosynthetic prokaryote. Therefore, the ancestor of chromalveolates is believed to have resulted from a secondary endosymbiotic event. However, some chromalveolates appear to have lost red alga-derived plastid organelles or lack plastid genes altogether. Therefore, this supergroup should be considered a hypothesis-based working group that is subject to change. Chromalveolates include very important photosynthetic organisms, such as diatoms, brown algae, and significant disease agents in animals and plants. The chromalveolates can be subdivided into alveolates and stramenopiles.
Alveolates: Dinoflagellates, Apicomplexians, and Ciliates
A large body of data supports that the alveolates are derived from a shared common ancestor. The alveolates are named for the presence of an alveolus, or membrane-enclosed sac, beneath the cell membrane. The exact function of the alveolus is unknown, but it may be involved in osmoregulation. The alveolates are further categorized into some of the better-known protists: the dinoflagellates, the apicomplexans, and the ciliates.
Dinoflagellates exhibit extensive morphological diversity and can be photosynthetic, heterotrophic, or mixotrophic. Many dinoflagellates are encased in interlocking plates of cellulose. Two perpendicular flagella fit into the grooves between the cellulose plates, with one flagellum extending longitudinally and a second encircling the dinoflagellate (Figure \(4\)). Together, the flagella contribute to the characteristic spinning motion of dinoflagellates. These protists exist in freshwater and marine habitats, and are a component of plankton, the typically microscopic organisms that drift through the water and serve as a crucial food source for larger aquatic organisms.
Some dinoflagellates generate light, called bioluminescence, when they are jarred or stressed. Large numbers of marine dinoflagellates (billions or trillions of cells per wave) can emit light and cause an entire breaking wave to twinkle or take on a brilliant blue color (Figure \(5\)). For approximately 20 species of marine dinoflagellates, population explosions (also called blooms) during the summer months can tint the ocean with a muddy red color. This phenomenon is called a red tide, and it results from the abundant red pigments present in dinoflagellate plastids. In large quantities, these dinoflagellate species secrete an asphyxiating toxin that can kill fish, birds, and marine mammals. Red tides can be massively detrimental to commercial fisheries, and humans who consume these protists may become poisoned.
The apicomplexan protists are so named because their microtubules, fibrin, and vacuoles are asymmetrically distributed at one end of the cell in a structure called an apical complex (Figure \(6\)). The apical complex is specialized for entry and infection of host cells. Indeed, all apicomplexans are parasitic. This group includes the genus Plasmodium, which causes malaria in humans. Apicomplexan life cycles are complex, involving multiple hosts and stages of sexual and asexual reproduction.
The ciliates, which include Paramecium and Tetrahymena, are a group of protists 10 to 3,000 micrometers in length that are covered in rows, tufts, or spirals of tiny cilia. By beating their cilia synchronously or in waves, ciliates can coordinate directed movements and ingest food particles. Certain ciliates have fused cilia-based structures that function like paddles, funnels, or fins. Ciliates also are surrounded by a pellicle, providing protection without compromising agility. The genus Paramecium includes protists that have organized their cilia into a plate-like primitive mouth, called an oral groove, which is used to capture and digest bacteria (Figure \(7\)). Food captured in the oral groove enters a food vacuole, where it combines with digestive enzymes. Waste particles are expelled by an exocytic vesicle that fuses at a specific region on the cell membrane, called the anal pore. In addition to a vacuole-based digestive system, Paramecium also uses contractile vacuoles, which are osmoregulatory vesicles that fill with water as it enters the cell by osmosis and then contract to squeeze water from the cell.
Link to Learning
Watch the video of the contractile vacuole of Paramecium expelling water to keep the cell osmotically balanced.
Paramecium has two nuclei, a macronucleus and a micronucleus, in each cell. The micronucleus is essential for sexual reproduction, whereas the macronucleus directs asexual binary fission and all other biological functions. The process of sexual reproduction in Paramecium underscores the importance of the micronucleus to these protists. Paramecium and most other ciliates reproduce sexually by conjugation. This process begins when two different mating types of Paramecium make physical contact and join with a cytoplasmic bridge (Figure \(8\)). The diploid micronucleus in each cell then undergoes meiosis to produce four haploid micronuclei. Three of these degenerate in each cell, leaving one micronucleus that then undergoes mitosis, generating two haploid micronuclei. The cells each exchange one of these haploid nuclei and move away from each other. A similar process occurs in bacteria that have plasmids. Fusion of the haploid micronuclei generates a completely novel diploid pre-micronucleus in each conjugative cell. This pre-micronucleus undergoes three rounds of mitosis to produce eight copies, and the original macronucleus disintegrates. Four of the eight pre-micronuclei become full-fledged micronuclei, whereas the other four perform multiple rounds of DNA replication and go on to become new macronuclei. Two cell divisions then yield four new Paramecia from each original conjugative cell.
Exercise
Which of the following statements about Paramecium sexual reproduction is false?
1. The macronuclei are derived from micronuclei.
2. Both mitosis and meiosis occur during sexual reproduction.
3. The conjugate pair swaps macronucleii.
4. Each parent produces four daughter cells.
Stramenopiles: Diatoms, Brown Algae, Golden Algae and Oomycetes
The other subgroup of chromalveolates, the stramenopiles, includes photosynthetic marine algae and heterotrophic protists. The unifying feature of this group is the presence of a textured, or “hairy,” flagellum. Many stramenopiles also have an additional flagellum that lacks hair-like projections (Figure \(9\)). Members of this subgroup range in size from single-celled diatoms to the massive and multicellular kelp.
The diatoms are unicellular photosynthetic protists that encase themselves in intricately patterned, glassy cell walls composed of silicon dioxide in a matrix of organic particles (Figure \(10\)). These protists are a component of freshwater and marine plankton. Most species of diatoms reproduce asexually, although some instances of sexual reproduction and sporulation also exist. Some diatoms exhibit a slit in their silica shell, called a raphe. By expelling a stream of mucopolysaccharides from the raphe, the diatom can attach to surfaces or propel itself in one direction.
During periods of nutrient availability, diatom populations bloom to numbers greater than can be consumed by aquatic organisms. The excess diatoms die and sink to the sea floor where they are not easily reached by saprobes that feed on dead organisms. As a result, the carbon dioxide that the diatoms had consumed and incorporated into their cells during photosynthesis is not returned to the atmosphere. In general, this process by which carbon is transported deep into the ocean is described as the biological carbon pump, because carbon is “pumped” to the ocean depths where it is inaccessible to the atmosphere as carbon dioxide. The biological carbon pump is a crucial component of the carbon cycle that maintains lower atmospheric carbon dioxide levels.
Like diatoms, golden algae are largely unicellular, although some species can form large colonies. Their characteristic gold color results from their extensive use of carotenoids, a group of photosynthetic pigments that are generally yellow or orange in color. Golden algae are found in both freshwater and marine environments, where they form a major part of the plankton community.
The brown algae are primarily marine, multicellular organisms that are known colloquially as seaweeds. Giant kelps are a type of brown algae. Some brown algae have evolved specialized tissues that resemble terrestrial plants, with root-like holdfasts, stem-like stipes, and leaf-like blades that are capable of photosynthesis. The stipes of giant kelps are enormous, extending in some cases for 60 meters. A variety of algal life cycles exists, but the most complex is alternation of generations, in which both haploid and diploid stages involve multicellularity. Compare this life cycle to that of humans, for instance. Haploid gametes produced by meiosis (sperm and egg) combine in fertilization to generate a diploid zygote that undergoes many rounds of mitosis to produce a multicellular embryo and then a fetus. However, the individual sperm and egg themselves never become multicellular beings. Terrestrial plants also have evolved alternation of generations. In the brown algae genus Laminaria, haploid spores develop into multicellular gametophytes, which produce haploid gametes that combine to produce diploid organisms that then become multicellular organisms with a different structure from the haploid form (Figure \(11\)). Certain other organisms perform alternation of generations in which both the haploid and diploid forms look the same.
Exercise
Which of the following statements about the Laminaria life cycle is false?
1. 1n zoospores form in the sporangia.
2. The sporophyte is the 2n plant.
3. The gametophyte is diploid.
4. Both the gametophyte and sporophyte stages are multicellular.
The water molds, oomycetes (“egg fungus”), were so-named based on their fungus-like morphology, but molecular data have shown that the water molds are not closely related to fungi. The oomycetes are characterized by a cellulose-based cell wall and an extensive network of filaments that allow for nutrient uptake. As diploid spores, many oomycetes have two oppositely directed flagella (one hairy and one smooth) for locomotion. The oomycetes are nonphotosynthetic and include many saprobes and parasites. The saprobes appear as white fluffy growths on dead organisms (Figure \(12\)). Most oomycetes are aquatic, but some parasitize terrestrial plants. One plant pathogen is Phytophthora infestans, the causative agent of late blight of potatoes, such as occurred in the nineteenth century Irish potato famine.
Rhizaria
The Rhizaria supergroup includes many of the amoebas, most of which have threadlike or needle-like pseudopodia (Figure \(13\)). Pseudopodia function to trap and engulf food particles and to direct movement in rhizarian protists. These pseudopods project outward from anywhere on the cell surface and can anchor to a substrate. The protist then transports its cytoplasm into the pseudopod, thereby moving the entire cell. This type of motion, called cytoplasmic streaming, is used by several diverse groups of protists as a means of locomotion or as a method to distribute nutrients and oxygen.
Link to Learning
Take a look at this video to see cytoplasmic streaming in a green alga.
Forams
Foraminiferans, or forams, are unicellular heterotrophic protists, ranging from approximately 20 micrometers to several centimeters in length, and occasionally resembling tiny snails (Figure \(14\)). As a group, the forams exhibit porous shells, called tests that are built from various organic materials and typically hardened with calcium carbonate. The tests may house photosynthetic algae, which the forams can harvest for nutrition. Foram pseudopodia extend through the pores and allow the forams to move, feed, and gather additional building materials. Typically, forams are associated with sand or other particles in marine or freshwater habitats. Foraminiferans are also useful as indicators of pollution and changes in global weather patterns.
Radiolarians
A second subtype of Rhizaria, the radiolarians, exhibit intricate exteriors of glassy silica with radial or bilateral symmetry (Figure \(15\)). Needle-like pseudopods supported by microtubules radiate outward from the cell bodies of these protists and function to catch food particles. The shells of dead radiolarians sink to the ocean floor, where they may accumulate in 100 meter-thick depths. Preserved, sedimented radiolarians are very common in the fossil record.
Archaeplastida
Red algae and green algae are included in the supergroup Archaeplastida. It was from a common ancestor of these protists that the land plants evolved, since their closest relatives are found in this group. Molecular evidence supports that all Archaeplastida are descendents of an endosymbiotic relationship between a heterotrophic protist and a cyanobacterium. The red and green algae include unicellular, multicellular, and colonial forms.
Red Algae
Red algae, or rhodophytes, are primarily multicellular, lack flagella, and range in size from microscopic, unicellular protists to large, multicellular forms grouped into the informal seaweed category. The red algae life cycle is an alternation of generations. Some species of red algae contain phycoerythrins, photosynthetic accessory pigments that are red in color and outcompete the green tint of chlorophyll, making these species appear as varying shades of red. Other protists classified as red algae lack phycoerythrins and are parasites. Red algae are common in tropical waters where they have been detected at depths of 260 meters. Other red algae exist in terrestrial or freshwater environments.
Green Algae: Chlorophytes and Charophytes
The most abundant group of algae is the green algae. The green algae exhibit similar features to the land plants, particularly in terms of chloroplast structure. That this group of protists shared a relatively recent common ancestor with land plants is well supported. The green algae are subdivided into the chlorophytes and the charophytes. The charophytes are the closest living relatives to land plants and resemble them in morphology and reproductive strategies. Charophytes are common in wet habitats, and their presence often signals a healthy ecosystem.
The chlorophytes exhibit great diversity of form and function. Chlorophytes primarily inhabit freshwater and damp soil, and are a common component of plankton. Chlamydomonas is a simple, unicellular chlorophyte with a pear-shaped morphology and two opposing, anterior flagella that guide this protist toward light sensed by its eyespot. More complex chlorophyte species exhibit haploid gametes and spores that resemble Chlamydomonas.
The chlorophyte Volvox is one of only a few examples of a colonial organism, which behaves in some ways like a collection of individual cells, but in other ways like the specialized cells of a multicellular organism (Figure \(16\)). Volvox colonies contain 500 to 60,000 cells, each with two flagella, contained within a hollow, spherical matrix composed of a gelatinous glycoprotein secretion. Individual Volvox cells move in a coordinated fashion and are interconnected by cytoplasmic bridges. Only a few of the cells reproduce to create daughter colonies, an example of basic cell specialization in this organism.
True multicellular organisms, such as the sea lettuce, Ulva, are represented among the chlorophytes. In addition, some chlorophytes exist as large, multinucleate, single cells. Species in the genus Caulerpa exhibit flattened fern-like foliage and can reach lengths of 3 meters (Figure \(17\)). Caulerpa species undergo nuclear division, but their cells do not complete cytokinesis, remaining instead as massive and elaborate single cells.
Amoebozoa
The amoebozoans characteristically exhibit pseudopodia that extend like tubes or flat lobes, rather than the hair-like pseudopodia of rhizarian amoeba (Figure \(18\)). The Amoebozoa include several groups of unicellular amoeba-like organisms that are free-living or parasites.
Slime Molds
A subset of the amoebozoans, the slime molds, has several morphological similarities to fungi that are thought to be the result of convergent evolution. For instance, during times of stress, some slime molds develop into spore-generating fruiting bodies, much like fungi.
The slime molds are categorized on the basis of their life cycles into plasmodial or cellular types. Plasmodial slime molds are composed of large, multinucleate cells and move along surfaces like an amorphous blob of slime during their feeding stage (Figure \(19\)). Food particles are lifted and engulfed into the slime mold as it glides along. Upon maturation, the plasmodium takes on a net-like appearance with the ability to form fruiting bodies, or sporangia, during times of stress. Haploid spores are produced by meiosis within the sporangia, and spores can be disseminated through the air or water to potentially land in more favorable environments. If this occurs, the spores germinate to form ameboid or flagellate haploid cells that can combine with each other and produce a diploid zygotic slime mold to complete the life cycle.
The cellular slime molds function as independent amoeboid cells when nutrients are abundant (Figure \(20\)). When food is depleted, cellular slime molds pile onto each other into a mass of cells that behaves as a single unit, called a slug. Some cells in the slug contribute to a 2–3-millimeter stalk, drying up and dying in the process. Cells atop the stalk form an asexual fruiting body that contains haploid spores. As with plasmodial slime molds, the spores are disseminated and can germinate if they land in a moist environment. One representative genus of the cellular slime molds is Dictyostelium, which commonly exists in the damp soil of forests.
Link to Learning
View this site to see the formation of a fruiting body by a cellular slime mold.
Opisthokonta
The opisthokonts include the animal-like choanoflagellates, which are believed to resemble the common ancestor of sponges and, in fact, all animals. Choanoflagellates include unicellular and colonial forms, and number about 244 described species. These organisms exhibit a single, apical flagellum that is surrounded by a contractile collar composed of microvilli. The collar uses a similar mechanism to sponges to filter out bacteria for ingestion by the protist. The morphology of choanoflagellates was recognized early on as resembling the collar cells of sponges, and suggesting a possible relationship to animals.
The Mesomycetozoa form a small group of parasites, primarily of fish, and at least one form that can parasitize humans. Their life cycles are poorly understood. These organisms are of special interest, because they appear to be so closely related to animals. In the past, they were grouped with fungi and other protists based on their morphology.
Summary
The process of classifying protists into meaningful groups is ongoing, but genetic data in the past 20 years have clarified many relationships that were previously unclear or mistaken. The majority view at present is to order all eukaryotes into six supergroups: Excavata, Chromalveolata, Rhizaria, Archaeplastida, Amoebozoa, and Opisthokonta. The goal of this classification scheme is to create clusters of species that all are derived from a common ancestor. At present, the monophyly of some of the supergroups are better supported by genetic data than others. Although tremendous variation exists within the supergroups, commonalities at the morphological, physiological, and ecological levels can be identified.
Art Connections
Figure \(8\): Which of the following statements about Paramecium sexual reproduction is false?
1. The macronuclei are derived from micronuclei.
2. Both mitosis and meiosis occur during sexual reproduction.
3. The conjugate pair swaps macronuclei.
4. Each parent produces four daughter cells.
Answer
C
Figure \(11\): Which of the following statements about the Laminaria life cycle is false?
1. 1n zoospores form in the sporangia.
2. The sporophyte is the 2n plant.
3. The gametophyte is diploid.
4. Both the gametophyte and sporophyte stages are multicellular.
Answer
C
Glossary
biological carbon pump
process by which inorganic carbon is fixed by photosynthetic species that then die and fall to the sea floor where they cannot be reached by saprobes and their carbon dioxide consumption cannot be returned to the atmosphere
bioluminescence
generation and emission of light by an organism, as in dinoflagellates
contractile vacuole
vesicle that fills with water (as it enters the cell by osmosis) and then contracts to squeeze water from the cell; an osmoregulatory vesicle
cytoplasmic streaming
movement of cytoplasm into an extended pseudopod such that the entire cell is transported to the site of the pseudopod
hydrogenosome
organelle carried by parabasalids (Excavata) that functions anaerobically and outputs hydrogen gas as a byproduct; likely evolved from mitochondria
kinetoplast
mass of DNA carried within the single, oversized mitochondrion, characteristic of kinetoplastids (phylum: Euglenozoa)
mitosome
nonfunctional organelle carried in the cells of diplomonads (Excavata) that likely evolved from a mitochondrion
plankton
diverse group of mostly microscopic organisms that drift in marine and freshwater systems and serve as a food source for larger aquatic organisms
raphe
slit in the silica shell of diatoms through which the protist secretes a stream of mucopolysaccharides for locomotion and attachment to substrates
test
porous shell of a foram that is built from various organic materials and typically hardened with calcium carbonate | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/28%3A_Protists/28.08%3A_Characteristics_of_Opisthokonta.txt |
Which moved onto land first, plants or animals?
This fossilized fern may be millions of years old. Over 200 million years ago, the first evidence of ferns related to several modern families appeared. The "great fern radiation" occurred in the late-Cretaceous, which ended 65 million years ago, when many modern families of ferns first appeared. And if animals were the first on land, would many have starved?
Evolution of Plants
As shown in Figure below, plants are thought to have evolved from an aquatic green alga protist. Later, they evolved important adaptations for land, including vascular tissues, seeds, and flowers. Each of these major adaptations made plants better suited for life on dry land and much more successful.
From a simple, green alga ancestor that lived in the water, plants eventually evolved several major adaptations for life on land.
The Earliest Plants
The earliest plants were probably similar to the stonewort, an aquatic algae pictured inFigure below. Unlike most modern plants, stoneworts have stalks rather than stiff stems, and they have hair-like structures called rhizoids instead of roots. On the other hand, stoneworts have distinct male and female reproductive structures, which is a plant characteristic. For fertilization to occur, sperm need at least a thin film of moisture to swim to eggs. In all these ways, the first plants may have resembled stoneworts.
Modern stoneworts may be similar to the earliest plants. Shown is a field of modern stoneworts (right), and an example from the Charophyta, a division of green algae that includes the closest relatives of the earliest plants (left).
Life on Land
By the time the earliest plants evolved, animals were already the dominant organisms in the ocean. Plants were also constrained to the upper layer of water that received enough sunlight for photosynthesis. Therefore, plants never became dominant marine organisms. But when plants moved onto land, everything was wide open. Why was the land devoid of other life? Without plants growing on land, there was nothing for other organisms to feed on. Land could not be colonized by other organisms until land plants became established.
Plants may have colonized the land as early as 700 million years ago. The oldest fossils of land plants date back about 470 million years. The first land plants probably resembled modern plants called liverworts, like the one shown in Figure below.
The first land plants may have been similar to liverworts like this one.
Colonization of the land was a huge step in plant evolution. Until then, virtually all life had evolved in the ocean. Dry land was a very different kind of place. The biggest problem was the dryness. Simply absorbing enough water to stay alive was a huge challenge. It kept early plants small and low to the ground. Water was also needed for sexual reproduction, so sperm could swim to eggs. In addition, temperatures on land were extreme and always changing. Sunlight was also strong and dangerous. It put land organisms at high risk of mutations.
Vascular Plants Evolve
Plants evolved a number of adaptations that helped them cope with these problems on dry land. One of the earliest and most important was the evolution of vascular tissues. Vascular tissues form a plant’s “plumbing system.” They carry water and minerals from soil to leaves for photosynthesis. They also carry food (sugar dissolved in water) from photosynthetic cellsto other cells in the plant for growth or storage. The evolution of vascular tissues revolutionized the plant kingdom. The tissues allowed plants to grow large and endure periods of drought in harsh land environments. Early vascular plants probably resembled the fern shown in Figure below.
Early vascular plants may have looked like this modern fern.
In addition to vascular tissues, these early plants evolved other adaptations to life on land, including lignin, leaves, roots, and a change in their life cycle.
• Lignin is a tough carbohydrate molecule that is hydrophobic (“water fearing”). It adds support to vascular tissues in stems. It also waterproofs the tissues so they don’t leak, which makes them more efficient at transporting fluids. Because most other organisms cannot break down lignin, it helps protect plants from herbivores and parasites.
• Leaves are rich in chloroplasts that function as solar collectors and food factories. The first leaves were very small, but leaves became larger over time.
• Roots are vascular organs that can penetrate soil and even rock. They absorb water andminerals from soil and carry them to leaves. They also anchor a plant in the soil. Roots evolved from rhizoids, which nonvascular plants had used for absorption.
• Land plants evolved a dominant diploid sporophyte generation. This was adaptive because diploid individuals are less likely to suffer harmful effects of mutations. They have two copies of each gene, so if a mutation occurs in one gene, they have a backup copy. This is extremely important on land, where there’s a lot of solar radiation.
With all these advantages, it’s easy to see why vascular plants spread quickly and widely on land. Many nonvascular plants went extinct as vascular plants became more numerous. Vascular plants are now the dominant land plants on Earth.
Summary
• The earliest plants are thought to have evolved in the ocean from a green alga ancestor.
• Plants were among the earliest organisms to leave the water and colonize land.
• The evolution of vascular tissues allowed plants to grow larger and thrive on land.
Review
1. What were the first plants to evolve?
2. What are vascular tissues of a plant? What is their function?
3. Explain why life on land was difficult for early plants.
4. Why did plants need to become established on land before animals could colonize the land?
29.01: Origin of Land Plants
Plants adapted to the dehydrating land environment through the development of new physical structures and reproductive mechanisms.
Learning Objectives
• Discuss how lack of water in the terrestrial environment led to significant adaptations in plants
Key Points
• While some plants remain dependent on a moist and humid environment, many have adapted to a more arid climate by developing tolerance or resistance to drought conditions.
• Alternation of generations describes a life cycle in which an organism has both haploid (1n) and diploid (2n) multicellular stages, although in different species the haploid or diploid stage can be dominant.
• The life on land presents significant challenges for plants, including the potential for desiccation, mutagenic radiation from the sun, and a lack of buoyancy from the water.
Key Terms
• desiccation tolerance: the ability of an organism to withstand or endure extreme dryness, or drought-like condition
• alternation of generation: the life cycle of plants with a multicellular sporophyte, which is diploid, that alternates with a multicellular gametophyte, which is haploid
Plant Adaptations to Life on Land
As organisms adapted to life on land, they had to contend with several challenges in the terrestrial environment. The cell ‘s interior is mostly water: in this medium, small molecules dissolve and diffuse and the majority of the chemical reactions of metabolism take place. Desiccation, or drying out, is a constant danger for organisms exposed to air. Even when parts of a plant are close to a source of water, the aerial structures are prone to desiccation. Water also provides buoyancy to organisms. On land, plants need to develop structural support in a medium that does not give the same lift as water. The organism is also subject to bombardment by mutagenic radiation because air does not filter out the ultraviolet rays of sunlight. Additionally, the male gametes must reach the female gametes using new strategies because swimming is no longer possible. As such, both gametes and zygotes must be protected from desiccation. Successful land plants have developed strategies to face all of these challenges. Not all adaptations appeared at once; some species never moved very far from the aquatic environment, although others went on to conquer the driest environments on Earth.
Despite these survival challenges, life on land does offer several advantages. First, sunlight is abundant. Water acts as a filter, altering the spectral quality of light absorbed by the photosynthetic pigment chlorophyll. Second, carbon dioxide is more readily available in air than water since it diffuses faster in air. Third, land plants evolved before land animals; therefore, until dry land was also colonized by animals, no predators threatened plant life. This situation changed as animals emerged from the water and fed on the abundant sources of nutrients in the established flora. In turn, plants developed strategies to deter predation: from spines and thorns to toxic chemicals.
Early land plants, like the early land animals, did not live far from an abundant source of water and developed survival strategies to combat dryness. One of these strategies is called desiccation tolerance. Many mosses can dry out to a brown and brittle mat, but as soon as rain or a flood makes water available, mosses will absorb it and are restored to their healthy green appearance. Another strategy is to colonize environments where droughts are uncommon. Ferns, which are considered an early lineage of plants, thrive in damp and cool places such as the understory of temperate forests. Later, plants moved away from moist or aquatic environments and developed resistance to desiccation, rather than tolerance. These plants, like cacti, minimize the loss of water to such an extent they can survive in extremely dry environments.
The most successful adaptation solution was the development of new structures that gave plants the advantage when colonizing new and dry environments. Four major adaptations are found in all terrestrial plants: the alternation of generations, a sporangium in which the spores are formed, a gametangium that produces haploid cells, and apical meristem tissue in roots and shoots. The evolution of a waxy cuticle and a cell wall with lignin also contributed to the success of land plants. These adaptations are noticeably lacking in the closely-related green algae, which gives reason for the debate over their placement in the plant kingdom.
Alternation of Generations
Alternation of generations describes a life cycle in which an organism has both haploid and diploid multicellular stages (n represents the number of copies of chromosomes). Haplontic refers to a lifecycle in which there is a dominant haploid stage (1n), while diplontic refers to a lifecycle in which the diploid (2n) is the dominant life stage. Humans are diplontic. Most plants exhibit alternation of generations, which is described as haplodiplodontic. The haploid multicellular form, known as a gametophyte, is followed in the development sequence by a multicellular diploid organism: the sporophyte. The gametophyte gives rise to the gametes (reproductive cells) by mitosis. This can be the most obvious phase of the life cycle of the plant, as in the mosses. In fact, the sporophyte stage is barely noticeable in lower plants (the collective term for the plant groups of mosses, liverworts, and lichens). Alternatively, the gametophyte stage can occur in a microscopic structure, such as a pollen grain, in the higher plants (a common collective term for the vascular plants). Towering trees are the diplontic phase in the life cycles of plants such as sequoias and pines.
Protection of the embryo is a major requirement for land plants. The vulnerable embryo must be sheltered from desiccation and other environmental hazards. In both seedless and seed plants, the female gametophyte provides protection and nutrients to the embryo as it develops into the new generation of sporophyte. This distinguishing feature of land plants gave the group its alternate name of embryophytes. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/29%3A_Seedless_Plants/29.01%3A_Origin_of_Land_Plants/29.1C%3A_Plant_Adaptations_to_Life_on_Land.txt |
Bryophytes (liverworts, mosses, and hornworts) are non-vascular plants that appeared on earth over 450 million years ago.
Learning Objectives
• Describe the characteristics of bryophytes
Key Points
• Bryophytes are the closest-living relative of early terrestrial plants; liverworts were the first Bryophytes, probably appearing during the Ordovician period.
• Bryophytes fossil formation is improbable since they do not possess lignin.
• Bryophytes thrive in mostly-damp habitats; however, some species can live in deserts while others can inhabit hostile environments such as the tundra.
• Bryophytes are nonvascular because they do not have tracheids; instead, water and nutrients circulate inside specialized conducting cells.
• In a bryophyte, all the vegetative organs belong to the gametophyte, which is the dominant and most familiar form; the sporophyte appears for only a short period.
• The sporophyte is dependent on the gametophyte and remains permanently attached to it in order to gain nutrition and protection.
Key Terms
• bryophyte: seedless, nonvascular plants that are the closest extant relative of early terrestrial plants
• tracheid: elongated cells in the xylem of vascular plants that serve in the transport of water and mineral salts
• sporangium: a case, capsule, or container in which spores are produced by an organism
Bryophytes
Bryophytes are the group of seedles plants that are the closest-extant relative of early terrestrial plants. The first bryophytes (liverworts) probably appeared in the Ordovician period, about 450 million years ago. However, because they lack of lignin and other resistant structures, bryophyte fossil formation is improbable and the fossil record is poor. Some spores protected by sporopollenin have survived and are attributed to early bryophytes. By the Silurian period, however, vascular plants had spread through the continents. This compelling fact is used as evidence that non-vascular plants must have preceded the Silurian period.
More than 25,000 species of bryophytes thrive in mostly-damp habitats, although some live in deserts. They constitute the major flora of inhospitable environments like the tundra where their small size and tolerance to desiccation offer distinct advantages. They generally lack lignin and do not have actual tracheids (xylem cells specialized for water conduction). Rather, water and nutrients circulate inside specialized conducting cells. Although the term non-tracheophyte is more accurate, bryophytes are commonly called non-vascular plants.
In a bryophyte, all the conspicuous vegetative organs, including the photosynthetic leaf-like structures, the thallus, stem, and the rhizoid that anchors the plant to its substrate, belong to the haploid organism, or gametophyte. The sporophyte is barely noticeable. Thus, the gametophyte is the dominant and most familiar form; the sporophyte appears for only a short period. The gametes formed by bryophytes swim with a flagellum. The sporangium, the multicellular sexual reproductive structure, is present in bryophytes and absent in the majority of algae. The sporophyte embryo also remains attached to the parent plant, which protects and nourishes it. This is a characteristic of land plants. The bryophytes are divided into three phyla: the liverworts (Hepaticophyta), the hornworts (Anthocerotophyta), and the mosses (true Bryophyta).
29.02: Bryophytes Have a Dominant Gametophyte Generation
Bryophytes (liverworts, mosses, and hornworts) are non-vascular plants that appeared on earth over 450 million years ago.
Learning Objectives
• Describe the characteristics of bryophytes
Key Points
• Bryophytes are the closest-living relative of early terrestrial plants; liverworts were the first Bryophytes, probably appearing during the Ordovician period.
• Bryophytes fossil formation is improbable since they do not possess lignin.
• Bryophytes thrive in mostly-damp habitats; however, some species can live in deserts while others can inhabit hostile environments such as the tundra.
• Bryophytes are nonvascular because they do not have tracheids; instead, water and nutrients circulate inside specialized conducting cells.
• In a bryophyte, all the vegetative organs belong to the gametophyte, which is the dominant and most familiar form; the sporophyte appears for only a short period.
• The sporophyte is dependent on the gametophyte and remains permanently attached to it in order to gain nutrition and protection.
Key Terms
• bryophyte: seedless, nonvascular plants that are the closest extant relative of early terrestrial plants
• tracheid: elongated cells in the xylem of vascular plants that serve in the transport of water and mineral salts
• sporangium: a case, capsule, or container in which spores are produced by an organism
Bryophytes
Bryophytes are the group of seedles plants that are the closest-extant relative of early terrestrial plants. The first bryophytes (liverworts) probably appeared in the Ordovician period, about 450 million years ago. However, because they lack of lignin and other resistant structures, bryophyte fossil formation is improbable and the fossil record is poor. Some spores protected by sporopollenin have survived and are attributed to early bryophytes. By the Silurian period, however, vascular plants had spread through the continents. This compelling fact is used as evidence that non-vascular plants must have preceded the Silurian period.
More than 25,000 species of bryophytes thrive in mostly-damp habitats, although some live in deserts. They constitute the major flora of inhospitable environments like the tundra where their small size and tolerance to desiccation offer distinct advantages. They generally lack lignin and do not have actual tracheids (xylem cells specialized for water conduction). Rather, water and nutrients circulate inside specialized conducting cells. Although the term non-tracheophyte is more accurate, bryophytes are commonly called non-vascular plants.
In a bryophyte, all the conspicuous vegetative organs, including the photosynthetic leaf-like structures, the thallus, stem, and the rhizoid that anchors the plant to its substrate, belong to the haploid organism, or gametophyte. The sporophyte is barely noticeable. Thus, the gametophyte is the dominant and most familiar form; the sporophyte appears for only a short period. The gametes formed by bryophytes swim with a flagellum. The sporangium, the multicellular sexual reproductive structure, is present in bryophytes and absent in the majority of algae. The sporophyte embryo also remains attached to the parent plant, which protects and nourishes it. This is a characteristic of land plants. The bryophytes are divided into three phyla: the liverworts (Hepaticophyta), the hornworts (Anthocerotophyta), and the mosses (true Bryophyta). | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/29%3A_Seedless_Plants/29.02%3A_Bryophytes_Have_a_Dominant_Gametophyte_Generation/29.2A%3A_Bryophytes.txt |
Liverworts and hornworts are both bryophytes, but aspects of their structures and development are different.
Learning Objectives
• Describe the distinguishing traits of hornworts and liverworts
Key Points
• The leaves of liverworts are lobate green structures similar to the lobes of the liver, while hornworts have narrow, pipe-like structures.
• The gametophyte stage is the dominant stage in both liverworts and hornworts; however, liverwort sporophytes do not contain stomata, while hornwort sporophytes do.
• The life cycle of liverworts and hornworts follows alternation of generations: spores germinate into gametophytes, the zygote develops into a sporophyte that releases spores, and then spores produce new gametophytes.
• Liverworts develop short, small sporophytes, whereas hornworts develop long, slender sporophytes.
• To aid in spore dispersal, liverworts utilize elaters, whereas hornworts utilize pseudoelaters.
• Liverworts and hornworts can reproduce asexually through the fragmentation of leaves into gemmae that disperse and develop into gametophytes.
Key Terms
• alternation of generation: the life cycle of plants with a multicellular sporophyte, which is diploid, that alternates with a multicellular gametophyte, which is haploid
• pseudoelater: single-celled structure that aids in spore dispersal
• gemmae: small, intact, complete pieces of plant that are produced in a cup on the surface of the thallus and develop into gametophytes through asexual reproduction
Liverworts
Liverworts (Hepaticophyta) are viewed as the plants most closely related to the ancestor that moved to land. Liverworts have colonized every terrestrial habitat on earth and diversified to more than 7000 existing species. Liverwort gametophytes (the dominant stage of the life cycle) form lobate green structures. The shape of these leaves are similar to the lobes of the liver; hence, providing the origin of the name given to the phylum. Openings that allow the movement of gases may be observed in liverworts. However, these are not stomata because they do not actively open and close. The plant takes up water over its entire surface and has no cuticle to prevent desiccation.
The liverwort’s life cycle begins with the release of haploid spores from the sporangium that developed on the sporophyte. Spores disseminated by wind or water germinate into flattened thalli gametophytes attached to the substrate by thin, single-celled filaments. Male and female gametangia develop on separate, individual plants. Once released, male gametes swim with the aid of their flagella to the female gametangium (the archegonium), and fertilization ensues. The zygote grows into a small sporophyte still attached to the parent gametophyte and develops spore-producing cells and elaters. The spore-producing cells undergo meiosis to form spores, which disperse (with the help of elaters), giving rise to new gametophytes. Thus, the life cycle of liverworts follows the pattern of alternation of generations.
Liverwort plants can also reproduce asexually by the breaking of branches or the spreading of leaf fragments called gemmae. In this latter type of reproduction, the gemmae (small, intact, complete pieces of plant that are produced in a cup on the surface of the thallus ) are splashed out of the cup by raindrops. The gemmae then land nearby and develop into gametophytes.
Hornworts
The hornworts (Anthocerotophyta) belong to the broad bryophyte group that have colonized a variety of habitats on land, although they are never far from a source of moisture. The short, blue-green gametophyte is the dominant phase of the lifecycle of a hornwort. The narrow, pipe-like sporophyte is the defining characteristic of the group. The sporophytes emerge from the parent gametophyte and continue to grow throughout the life of the plant. Stomata appear in the hornworts and are abundant on the sporophyte. Photosynthetic cells in the thallus contain a single chloroplast. Meristem cells at the base of the plant keep dividing and adding to its height. Many hornworts establish symbiotic relationships with cyanobacteria that fix nitrogen from the environment.
The life cycle of hornworts also follows the general pattern of alternation of generations and has a similar life cycle to liverworts. The gametophytes grow as flat thalli on the soil with embedded gametangia. Flagellated sperm swim to the archegonia and fertilize eggs. However, unlike liverworts, the zygote develops into a long and slender sporophyte that eventually splits open, releasing spores. Additionally, thin cells called pseudoelaters surround the spores and help propel them further in the environment. Unlike the elaters observed in liverworts, the hornwort pseudoelaters are single-celled structures. The haploid spores germinate and produce the next generation of gametophytes. Like liverworts, some hornworts may also produce asexually through fragmentation. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/29%3A_Seedless_Plants/29.02%3A_Bryophytes_Have_a_Dominant_Gametophyte_Generation/29.2B%3A_Liverworts_and_Hornworts.txt |
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