## 1. Introduction



In this entry, I review briefly the history of ecological genetic
research and its recent integration with molecular genetic methods in
the sub-field of molecular ecology. Most studies in ecological
genetics begin with one or the other of the two most prominent
patterns in nature: 


1. adaptation, the "fit" between an organism and its
environment (see the entry on
 fitness);
 or,
2. polymorphism, the maintenance of two or more phenotypic or genetic
forms within a single population by natural selection.



With the development of molecular ecology, the latter can be
significantly extended to explore phenotypic differences between
species in a phylogenetic context. This permits a more incisive
investigation of the environments that favor adaptive divergence of
phenotypes between species. Moreover, the same molecular methods
useful in phylogenetics can often be modified to identify the genes or
chromosomal regions responsible for those inter-specific phenotypes
(Gibson et al. 2020
 [Other Internet Resources]).



The earliest studies attempted to document the action of natural
selection in wild populations in support of Darwinian's theory.
In so doing, these studies attempted to demonstrate that evolution by
natural selection was not only an historical causal force, but that it
also continued to act on the characteristics of wild populations in
the present day. Under the assumption of gradualism, it was not clear
whether natural selecting acting on phenotypes in wild populations
could be detected, let alone account for between species phenotypic
differences. The starting observations of many of the earliest
ecological genetic investigations, i.e., the phenotypes of most
interest, were conspicuous phenotypic polymorphisms, such as the
spotting patterns on butterfly wings or banding patterns of snail
shells or polymorphisms of chromosomal rearrangements. These were
either known to have a genetic basis or could safely be assumed to
have one.



Although natural selection is the only evolutionary force that can
account for adaptation, several evolutionary forces, acting alone or
in combination, can sustain a genetic polymorphism, at least
transiently. Thus, assigning causal agency to a single evolutionary
force is often a more difficult problem when explaining polymorphism
within species than it is for adaptations. In these studies of
conspicuous polymorphisms, natural selection was
"privileged" among the four evolutionary forces as an
explanation for their maintenance, at least in part, because one of
the founders of ecological genetics, E. B. Ford, collaborated
extensively with R. A. Fisher (see Ford 1975). In the early period
(1928-1950), much of the problem of assigning causal agency to
the maintenance of genetic polymorphism was resolved by definition
rather than by empirical observation (see section 2 below:
 Classical Ecological Genetics and Polymorphism).
 That is, only those polymorphisms where the rarest form was deemed
"too common" to be accounted for by recurrent mutation
were considered suitable for study. Moreover, if the species was
abundant, then random genetic drift could similarly be eliminated as a
relevant process. Indeed, the longest standing controversies in
ecological genetics centered on whether natural selection could
account for the observed frequencies of polymorphism or whether the
variation in those frequencies indicated a significant role of random
genetic drift (see, for example, Schemske and Bierzychudek [2001]
regarding the interpretation of flower color polymorphism in the
desert annual, *Linanthus parryae*).



In the later period (1966-present), the advent of allozymes and
molecular genetics permitted investigation of a less biased sample of
genetic polymorphism. The modern characterization and analyses of
allozymes and single nucleotide polymorphisms still retains the early
emphasis on natural selection as the single most important
evolutionary force shaping the hereditary material. Differently put,
adaptive explanations for patterns of species divergence tend to be
favored over non-adaptive explanations (see recent review of the
causes of the rapid diversification among species of reproductive
genes by Dapper and Wade [2020].)



Ecological genetics began at a time when the major theoretical aspects
of the Modern Synthesis were in place, when the marvels of adaptation
were clear, but when few empirical examples of natural selection in
action were available. Achieving adaptive perfection by gradualism
requires long periods of time wherein 



> 
> 
> ... a very slight selective effect acting for a correspondingly
> long time will be equivalent to a much greater effect acting for a
> proportionately shorter time. (R. A. Fisher 1921, in correspondence
> with S. Wright, quoted by Provine [1986: 247]) 
> 
> 
> 



Very weak natural selection, however, is an impediment to the goal of
ecological genetics to illuminate natural selection in action in the
wild. Thus, the shift in focus toward understanding the role of strong
natural selection in maintaining visible genetic polymorphisms is
understandable. As put by its founder, E. B. Ford, 



> 
> 
> It [ecological genetics] supplies the means, and the only direct
> means, of investigating the actual process of evolution taking place
> in the present time. (1975: 3)
> 
> 
> 



The focus of traditional ecological genetic research on the current
action of natural selection has been broadened in several ways over
the last two decades. First, whereas the early studies tended to focus
on evolution in single populations, there is now a significant
emphasis in ecological genetics on the population genetic structure of
metapopulations and the roles of migration, extinction, and
colonization on evolutionary and adaptive processes (e.g., Goodacre
2002). Secondly, whereas the earliest studies emphasized conspicuous
polymorphisms or chromosomal rearrangements and their influence on
fitness, the advent of biochemical genetics in the late 1960s
significantly broadened the phenotype, beginning with the application
of electrophoretic methods to population studies. These studies
revealed abundant "hidden polymorphism" in the new,
biochemical phenotype of enzyme mobility. These methods extended the
domain of ecological genetics from the classic "conspicuous
phenotypic polymorphisms" in color, shape and behavior to the
physiological domain of enzyme function. The new emphasis on
functional biochemical phenotypes, however, did not change the
explanatory or causal framework of the field. Determining the role of
natural selection in maintaining enzyme polymorphisms, such as the
fast/slow polymorphisms of alcohol dehydrogenase (an enzyme involved
in the detoxification of environmental alcohols), superoxide dismutase
(which catalyzes the removal of free oxygen radicals), or the
esterases (which are involved in the detoxification of pesticides in
many insects), became a primary focus of investigation with the goal
of finding a *selective* basis for the enzyme variants in terms
of differences in their physical and kinetic properties. Indeed, the
roots of controversy between the selectionist and neutralist schools
over the maintenance of "balanced" polymorphisms (see
Lewontin 1974) lie in the controversy over random genetic drift versus
natural selection in early ecological genetic research (see
below).



The more recent advent of DNA sequencing initiated the growth of
molecular phylogenetics and molecular ecology. The new technology
added not only a new phenotype, but also a more pronounced historical
(phylogenetic) dimension to ecological genetic research. Molecular
phylogenics and comparative sequence analysis have become the primary
modern tools for the investigation of the evolutionary patterns and
processes that shape DNA sequences. These methods have strengthened
inferences regarding biogeography, speciation, and adaptation,
especially in regard to the diversification of taxonomic lineages that
attends ecological release and adaptive radiations. They have shifted
the focus from polymorphism within species to diversification among
clades (e.g., Kostyun et al. 2019) and permitted the investigation of
the history of individual genes (Gibson et al. 2020
 [Other Internet Resources]).
 For example, ecological genomic data have permitted the
reconstruction of the invasion of the Galapagos Islands by the wild
tomato species, *Solanum pimpinellifolium*, through
hybridization and introgression with a closely related endemic
species, *Solanum cheesmaniae*. Moreover, an adaptive
phenotype, orange fruit color similar to the endemic species, is
associated with two introgressed regions of the *Solanum*
genome which contain known fruit color loci, supporting the inference
that adaptive convergence was genetically facilitated by introgression
(Gibson et al. 2020
 [Other Internet Resources]).



Two new patterns in particular have been recognized by these DNA-based
methods. The first is the preponderance of "purifying
selection", wherein the conservative power of natural selection
is seen as a barrier to diversity. It is this conservative aspect of
natural selection acting at the molecular level that lends power to
the investigation of the genetic architecture of model organisms
*vis a vis* human genetics. The second pattern is the
discovery of the existence of *ancient polymorphisms*,
molecular genetic variation whose age may be greater than that of the
species or taxon in which it occurs. Natural selection remains the
privileged explanatory force in modern sequence studies. Indeed, the
search for, characterization, and explanation of uniquely molecular
patterns, such as codon bias (Behura & Severson 2013) and
selective sweeps, has, if anything, elevated the focal explanatory
power of natural selection in evolutionary studies. That is, nonrandom
or biased use of redundant codons in DNA sequences is seen as evidence
that, although they have no effect on amino acid sequence, redundant
codons are not all functionally equivalent in that some permit more
efficient gene expression. This is taken as evidence that natural
selection is all powerful, reaching down into the genome to affect
even the smallest and least significant components of the hereditary
material.



In this entry, I review classical ecological genetics and then discuss
the novel kinds of processes and explanations that accompanied the
expansion of the field from single populations to genetically
structured metapopulations and from phenotypic to biochemical and DNA
sequence polymorphisms. I will show that the central early controversy
over the roles of random genetic drift and natural selection in
evolution has continued to this day, despite the apparent
technological refinements afforded by the availability of biochemical
and DNA sequence data. That is, finer scale or more reductionistic
genetic data has not yet led to a resolution of the original
conceptual issues that lie at the foundation of ecological
genetics.


## 2. Classical Ecological Genetics and Polymorphism



Historically, the starting point of ecological genetic research has
been the discovery of variation within a natural population, i.e., a
phenotypic polymorphism. The subsequent goal is three-fold: 


1. determination of whether or not the polymorphism has a genetic
component;
2. determination of the frequency of each of the polymorphic types
and their spatial and temporal variability; and,
3. determination of how natural selection maintains the polymorphism,
either alone or in combination with other evolutionary forces.



Ford defines *genetic polymorphism* as 



> 
> 
> ...the occurrence together in the same locality of two or more
> discontinuous forms of a species in such proportions that the rarest
> of them cannot be maintained merely by recurrent mutation. (1975: 109;
> and see also Ford 1940) 
> 
> 
> 



Although recurrent mutation can maintain a polymorphism indefinitely
at mutation-selection balance, here Ford is clearly interested in a
more active role for natural selection in the maintenance of
polymorphism. The first task was facilitated by early developments in
population genetic theory, particularly the findings of Fisher (1930).
Ford interpreted these to mean that naturally occurring, discontinuous
phenotypic variation is "nearly always genetic". The
reasoning stems from the theoretical findings that, in large
populations, it is unlikely that the positive and negative fitness
effects of an allele (or chromosomal inversion) will be exactly
balanced. As a result, the number of individuals with a rare neutral
mutation is proportional to the number of generations since its
origin. Furthermore, if truly neutral, such alleles would spread so
slowly through a large population by random genetic drift that the




> 
> 
> delicate equipoise required for their neutrality will have been upset
> by changes in the environment and in the genetic outfit of the
> organism (Ford 1975: 110) 
> 
> 
> 



before a neutral allele reached appreciable frequency. In addition,
recurrent mutation as a cause of persistent polymorphism was
considered most unlikely and, in fact, this evolutionary cause is
explicitly excluded from the definition of genetic polymorphism by
Ford (see above). Hence, neutral genetic polymorphism was considered
an exceptionally rare event by the founders of ecological genetics
and, consequently, such polymorphisms were the hallmark of strong,
active natural selection.



Ford (1940) further distinguished two types of selective polymorphism,
transient polymorphism and balanced polymorphism. *Transient
polymorphism*, caused by a new favorable mutation in the process
of displacing its ancestral allele by natural selection, was
considered unlikely, because "...advantageous genes will
usually have been already incorporated into the genetic constitution
of the species" (Ford 1975: 110). This and statements like it
reflect the viewpoint that organisms in nature are exquisitely adapted
to their environments by the long-acting process of Fisherian
gradualistic natural selection (see the entry on
 natural selection).
 It is a prelude to the more explicitly adaptationist views found in
the current behavioral literature (see review in Shuster & Wade
2003). This view of the evolutionary process as primarily one of
refinement of existing organismal adaptation is an essential part of
the Fisherian theory of evolutionary genetics (Wade & Goodnight
1998).



The presumptions of a genetic basis for discontinuous phenotypic
polymorphism and its maintenance by natural selection are clear from
the writings of Ford cited above but these principles also can be
found together in a single statement: 



> 
> 
> In view of these considerations it is clear that if any unifactorial
> character is at all widespread it must be of some [adaptive] value.
> Indeed, it is probably true that even if it occurs at as low a
> frequency as 1 per cent, it must have been favored by selection. (Ford
> 1975: 110) 
> 
> 
> 



Thus, the primary goal of the ecological geneticist is to discern
exactly how natural selection is acting to maintain a *balanced
polymorphism* by the relative strength of opposing fitness effects
acting on the different sexes, at different stages in the life
history, at different localities or at different times in the lifetime
of the organism.



The existence of males and females was discussed by Ford as a prime
example of a balanced polymorphism because, 



> 
> 
> It is obvious that any tendency for the males to increase at the
> expense of the females, or the reverse, would be opposed by selection.
> (Ford 1975: 111) 
> 
> 
> 



Fisher (1930) first argued that, because every individual has a mother
and a father, the mean fitness of males must be equal to the mean
fitness of females multiplied by the sex ratio, expressed as the
number of females to males (i.e., the mean number of mates per male;
see also Shuster and Wade 2003, Chapter 1). As a result, fitness
increases with rarity, and, in this circumstance, whenever the
population sex ratio deviates from unity, a gene that increases the
numbers of the minority sex at birth will have a selective advantage.
Thus, a sex ratio of unity is a stable, balanced polymorphism,
achieved in many species by chromosomal determination of sex, which
Ford referred to as a "'built-in' genetic
switch-mechanism", characteristic of other genetic
polymorphisms, like Batesian mimicry. In general, the fitnesses of two
different types constituting a phenotypic polymorphism must be equal
to be maintained within a population by natural selection at a
intermediate equilibrium frequency (a point recognized in Darwin 1871,
Vol. II, Chapter 14). However, the balance of selective forces for
non-sex related (or even sex-linked) polymorphisms is very different
from that required to maintain an equal sex ratio. Using the existence
of the separate sexes as an example of a balanced polymorphism is
misleading or, at least unrepresentative, of the selective forces
necessary to sustain balanced polymorphisms in general.


## 3. Classical Ecological Genetics, Population Size, and Natural Selection



The founding ecological geneticists dismissed any significant role for
random genetic drift in evolution (see the entry on
 genetic drift).
 The theoretical interaction of random genetic drift and natural
selection for single genes with constant effects can be seen in
 Figure 1. Fisher in his evolutionary theory
 assumed that natural populations achieved or sustained very large
 sizes as seen in his correspondence with S. Wright (letter from
 R. A. Fisher to S. Wright, August 13, 1929, as quoted in Provine
 1986: 255) where he stated that "I believe *N* must
 usually be the total population on the planet, enumerated at sexual
 maturity". Similarly, according to his intellectual biographer
 W. Ewens: 



> 
> 
> Fisher never paid much attention to the concept [effective population
> size] as he should have ... and used extremely high population
> sizes (up to \(10^{12})\) in his analyses, surely far too large in
> general. (2000: 33) 
> 
> 
> 



For such extremely large population sizes, the threshold between
selection and drift (see
 Fig. 1),
 which is determined by the effective population size, \(N\_e\), is too
lower to matter evolutionarily. That is, the strength of random
genetic drift, which is proportional to (1/\(2N\_e)\), is very, very
weak and even genes with very small values of \(s\) have their
evolutionary fate determined entirely by selection. This is the
essence of "*Fisherian gradualism*"--very
small selective forces given sufficient time can have effects on
adaptation similar to those of genes with much larger effects acting
over a shorter time period. With very large \(N\_e\), the domain of
random genetic drift is greatly restricted even as that of natural
selection is expanded (see
 Fig. 1).




![a diagram: link to extended description below](figure1.svg)

Figure 1. The interaction of Random
Genetic Drift and Natural Selection. The strength of selection is
measured by the selective effect, \(s\), of a single gene and the
strength of random genetic drift is indicated by \((1/2N\_e)\), where
the population has effective size, \(N\_e\). When \(s\) exceeds
\((1/2N\_e)\), then the evolutionary fate of a gene is determined
primarily by Natural Selection. When \(s\) is less than \((1/2N\_e)\),
then the evolutionary fate of a gene is determined primarily by Random
Genetic Drift. Thus, the evolutionary domains of natural selection
(upper) and random genetic drift (lower) are separated by the wavy
boundary determined by the effective population size. [An
 extended description of figure 1
 is in the supplement.]




However, ecological geneticists did *not* entirely dismiss
random genetic drift as a significant evolutionary force for the same
reasons that Fisher did. Field observations conducted with the
mark-recapture methods developed by ecological geneticists documented
generation-to-generation fluctuations in population size up to or
exceeding an order of magnitude in most natural populations studied
long term. Thus, small local population sizes were not seen as unusual
by ecological geneticists. Indeed, Ford believed that 



> 
> 
> ... organisms automatically generate their own cycles of
> abundance and rarity and that the changes in selection pressure with
> which these are associated many greatly increase the speed of
> evolution; (Ford 1975: 36) 
> 
> 
> 



Despite the not infrequent occurrence of small population sizes where
drift would be expected to be most efficacious, random genetic drift
was still considered an irrelevant evolutionary force in ecological
genetics because natural selection was viewed as being particularly
strong during periods of population decline. That is, the strength of
natural selection was negatively correlated with population density.
Thus, as population size and \(N\_e\) declined owing to environmental
stress, natural selection gained in strength so that the boundary
between domains
 (Fig. 1)
 always favored selection. The smallest populations showed little
phenotypic variation, which was seen as evidence that they were the
most fit or most finely adapted populations. Thus, the lack of
phenotypic variation in small populations was owing to it having been
eliminated by natural selection during the immediately prior period of
decline. Conversely, under periods of population increase,
environmental stresses were minimal, so that natural selection was
weaker and more permissive of variation. This concept of relaxed
selection provided Ford with a cause for the increase in observations
of rare phenotypic variants in large and growing natural populations.
If selection pressure increases inversely to population size, then the
role of random genetic drift in evolution must be greatly
restricted.



In addition, Ford (1975: 38) believed that ecological genetic research
had clearly demonstrated that the selective advantage of a gene in
nature "... quite commonly exceeds 25 per cent and is
frequently far more...". Referring to
 Figure 1,
 this means that the range for values of \(s\) in natural populations
lies significantly above 0.01, placing genes, even in very small
populations, firmly in the domain governed by natural selection.



Furthermore, Ford considered that not only the strength but also the
nature of selective pressures must frequently change with density
because 



> 
> 
> ... an organism has not the same adaptive requirements when
> abundant as when rare, or when the plant and animal forms which
> impinge on it are so. (Ford 1975: 39) 
> 
> 
> 



Indeed, he thought that the fluctuating selection pressure caused by
variations in abundance "invalidates" Wright's
Shifting Balance Theory of Evolution, which he referred to as
"far-fetched". Interestingly, Ford and his colleagues
believed that genetic subdivision of the sort postulated by Wright
would promote rapid evolution but for reasons very different from
Wright's and by different genetic mechanisms (natural selection
instead of random genetic drift, local selection, and interdemic
selection). Ford (1975: 40-44) argued that subdivision of a
large, geographically extensive population into relatively small
groups promotes rapid evolution because, 



> 
> 
> ... when populations occupy a series of restricted habitats they
> can adapt themselves independently to the local environment in each of
> them, while when spread over a larger area they can be adjusted [by
> natural selection] only to the average of the diverse conditions which
> obtain there. This, however, requires that the adaptations should not
> be constantly broken down by a trickle of immigrants from one small
> colony to another. 
> 
> 
> 



Here, he proposes a trade-off between specialized adaptation to local
conditions in the absence of migration and generalized adaptation to
global conditions in the presence of migration. In modern terms, this
is called genotype-by-environment interaction, where the selective
effect, \(s\), of a gene changes with change in the environment. A
gene might be adaptive in one environmental context (i.e., \(s \gt
0)\) but maladaptive in another (i.e., \(s \lt 0)\). Migration between
local environments mixes the adaptive and maladaptive responses to
selection and reduces the average magnitude of gene frequency change.
In this sense, genotype-by-environment interaction for fitness is
viewed as an evolutionary constraint because it limits the rate of
gene frequency change. The restraint can be removed simply by stopping
gene flow and the mixing of genes across different local environments.
Thus, the fixed selective effect illustrated in
 Figure 1,
 must be considered an *average* of variable selective effects
across environments. Clearly, large local effects of opposite sign
must be averaged when there is gene flow among habitats and the
averaging tends to reduce the magnitude of a gene's selective
effect. Ford also suggests that the genetic mechanism involves
"gene complex[es] balanced to fit their own local
environment". That is, he claimed interactions among genes, or
epistasis, contributes to local adaptation. Thus, Ford invokes
genotype-by-environment interactions for fitness as well as gene-gene
interactions for fitness in his cases of rapid evolution, although
both *reduce* the average selective effect of a gene. This
argument also runs counter to his assertion that the adaptive
advantage of a gene is typically 25 percent in natural populations.
Both kinds of interaction change the depiction of the threshold
separating natural selection from random genetic drift
 (Fig. 1);
 in fact they tend to raise it and thereby increase the domain of
random genetic drift. Before turning to interaction effects, I will
examine a representative discussion of ecological genetics of random
genetic drift using data from a natural population.


## 4. The Sewall Wright Effect



Several wing coloration variants segregating in a small natural
population of the moth, *Panaxia dominula* (Fisher & Ford
1947), were investigated using mark-recapture in one of the longest
continuous studies of a single population in all of evolutionary
research. The goal of Fisher and Ford was to determine whether
year-to-year fluctuations in the frequency of the variants
(*medionigra*, a heterozygote, and *bimaculata*, a
homozygote) were better explained by natural selection or by random
genetic drift. (Banding patterns in the snail, *Cepea
nermoralis were* the topic of similar discussions of the
relative roles of natural selection and genetic drift [Cain &
Shephard 1954; Cain & Provine 1992; Millstein 2008, 2009].) They
inferred from their analysis



> 
> 
> The conclusion that natural populations in general, like that to which
> this study is devoted, are affected by selective action, varying from
> time to time in direction and intensity and of sufficient magnitude to
> cause fluctuating variations in all gene frequencies is in good
> accordance with other studies of observable frequencies in wild
> populations. ... We do not think, however, that it has been
> sufficiently emphasized that this fact is fatal to the theory which
> ascribes particular evolutionary importance to such fluctuations in
> gene ratios as may occur by chance in very small isolated populations.
> ...
> 
> 
> 
> Thus our analysis, the first in which the relative parts played by
> random survival and selection in a wild population can be tested, does
> not support the view that chance fluctuations can be of any
> significance in evolution. (Fisher & Ford 1947: 171, 172; quoted
> in Provine 1986: 423)
> 
> 
> 



With this paper, Fisher and Ford moved the long-standing debate
between Wright and Fisher over the relative roles of natural selection
and random genetic drift in evolution from theory to nature. It is
remarkable that, in the first such study with only eight years of
observations on a single locus with alternative alleles, they are
confident in rejecting Wright's theory and random genetic drift
in its entirety.



In his response to their analyses, Wright (1948) pointed out, first,
that his theory of evolution explicitly involved the simultaneous
action of several forces (selection, drift, mutation, and migration)
and he emphatically rejected the paradigm of Fisher and Ford that
*either* selection or drift alone had to be responsible for all
of the observed fluctuation in gene frequencies (see the entry on
 population genetics).
 Wright noted that, in order to reach their statistical conclusion,
Ford and Fisher had to include gene frequency data from a decade
before the more careful study, notably a period without any estimates
of population size. Without this earlier data point, the average
fluctuations were much smaller and not significant. He pointed out
that, like the mark-recapture estimates of population numbers, the
gene frequencies themselves were estimates whose variation, based on
the reported sample sizes, accounted for more than half (55.2%) of the
observed variance that Fisher and Ford were trying to explain. He then
showed that, if one assumed only the unitary explanation of natural
selection, then the observed gene frequency fluctuations were so large
*even without the sampling variance* that the temporal
variations in the allelic selection coefficients must range from near
lethality (or sterility) to tremendous advantage (i.e., from
[?]0.50 to +0.50). However, Fisher and Ford (1947) provided no
indication of comparable levels of temporal variation in any
environmental factor acting as a selective agent. Wright argued that
the effective population sizes used in the analysis were almost
certainly too large, possibly by an order of magnitude, and that
Fisher and Ford had made no attempt to estimate the factors expected
to reduce effective size, like temporal variation in breeding numbers,
non-random mortality among larvae (mortality clustered within families
as might affect a species which experiences > 85% pupal mortality
owing to viral infection), or other causes of the variance in
offspring numbers (such as variation among females in egg numbers or
variation among males in mate numbers). In an unyielding reply, Fisher
and Ford (1950) labeled chance or random fluctuations in gene
frequency, the *Sewall Wright Effect*, a term which has endured
to the present day as a synonym for random genetic drift.



With a larger data set covering several more years, Ford (1975: 146)
revisited this exchange and argued that Wright remained wrong on each
count. Ford also showed that the selective advantage for the rarer of
the genes varied widely, from [?]0.10 to +0.20, and that there was
no evidence of heterozygote advantage. He did not find, however, the
expected negative correlation between strength of selection and
population size in these data. In the intervening decades, data from a
variety of other organisms and natural population had become available
and its review led Ford to conclude: 



> 
> 
> As a result, it is no longer possible to attribute to random genetic
> drift or to mutation any significant part in the control of evolution.
> (1975: 389) 
> 
> 
> 



Thus, throughout its founding period, ecological genetics was
relentlessly supportive of natural selection as unitary explanation
for evolutionary change. (Later laboratory research has shown that the
expression of the color patterns is sensitive or plastic to the
thermal environment during development and thus the gene frequency
estimates may be subject to significant measurement error, owing to
the misclassification of genotypes. This is yet another source of
variation, not accounted for in the Ford analyses. It tends to weaken
the link between genotype and phenotype and thereby weaken the
relationship between selection acting on phenotypes and the underlying
genotypes. In addition, empirical evidence has found, as Wright
expected, that temporal fluctuations in population size, large
variance among females in fecundity, and sexual selection reduce the
effective number to less than half the Fisher-Ford estimate. In
addition, more careful studies have reduced Ford's estimates of
the magnitude of the average genic selection coefficient by about two
thirds [see Cook & Jones 1996].)


## 5. Interactions and their Effect on the Threshold between Natural Selection and Random Drift



The existence of either genotype-by-environment interaction \((\rG
\times \rE)\) or gene-by-gene interaction (epistasis or \(\rG \times
\rG\)) greatly complicates the estimation of selection coefficients.
Ecological geneticists like Ford postulated interactions of the sort
that could change the sign of genic selection coefficients with
changes in the environment (including density) or in the genetic
background. This kind of reversal of selective effect requires what is
known as a "crossing-type" norm of reaction for \(\rG
\times \rE\) or additive-by-additive epistasis for \(\rG \times \rG\)
(Wade 2002). The simplest model of crossing-type \(\rG \times \rE\),
consists of additive selection (i.e., genotypic fitnesses of \(1 + 2s,
1 + s\), and 1 for genotypes AA, Aa, and aa, in one environment and
the opposite order in the second environment) in each of two
alternative environments, \(E\_1\) and \(E\_2\), with frequencies,
\(f\_{E\_1}\) and \(f\_{E\_2}\), respectively. As the two environments
fluctuate in frequency, spatially or temporally, the selective effect
of an A allele changes in both magnitude and sign (see
 Fig. 2).
 Depending upon the relative frequencies of the alternative
environments and the amount of gene flow or migration between them,
the A allele on average can be a "good" gene or a
"bad" gene with respect to fitness, a gene of major effect
or minor effect on fitness, or even a neutral gene if the two
environments are equally abundant. The smaller the amount of migration
between the environments, the greater is the degree of local
adaptation to each as theory and
 Ford suggested (see above).
 However, the *average* selective effect of the gene in the
sense of Fisher's theory must be smaller than the average
observation in a particular locality at a particular time because the
long-term average contains both positive and negative values of \(s\).
Furthermore, to the extent that the local value of \(s\) changes sign
owing to continuous fluctuations in local environmental conditions,
the average effect on fitness A allele will also move downwards, from
the domain of selection to the domain of drift as Wright suggested.
Thus, the very kind of population subdivision imagined by Ford, with
selection acting in every locality albeit in different directions,
creates, rather than eliminates, an increased opportunity for random
genetic drift. 




![a diagram: link to extended description below](figure2.svg)

Figure 2. The interaction of Random
Genetic Drift and Natural Selection, when there is either
genotype-by-environment interaction or additive-by-additive epistasis
(see text). The selective effect, \(s\), of a single gene changes
magnitude as the frequency of the alternative environments,
\(f\_{E\_1}\) and \(f\_{E\_2}\), connected by gene flow, changes
*or* as the frequency of alternative alleles, \(p\_B\) and
\(p\_b\), change at an interacting locus. Thus, neither the selective
effect of a gene nor the effective population size remains constant.
As a result, relative to
 Figure 1,
 the threshold boundary between the domains of Natural Selection and
Random Genetic Drift is greatly widened, meaning that both forces play
more or less equal evolutionary roles over a broad range of values of
\(s\) and \(N\_e\). Furthermore, interactions of this sort open the
possibility that changes in the relative frequencies of alternative
environments or alternative alleles at other loci can move a
gene's selective effect from the domain of selection that of
drift or vice versa during the course of its evolution. [An
 extended description of figure 2
 is in the supplement.] 




A very similar effect on the "gene"s eye view' of
selection is caused by additive-by-additive epistasis (Goodnight &
Wade 2000; Wade 2001, 2002). The simplest model of this kind of \(\rG
\times \rG\), with interaction between loci A and B, each with
alternative alleles, results in an average genic selection coefficient
acting on the A allele of \(s(p\_B - p\_b)\), where \(p\_B\) and \(p\_b\)
are the frequencies of alternative alleles at the B-locus that
interact in the additive-by-additive model with alleles at the A
locus. The relative frequencies of the alternative alleles at the B
locus, determine whether the A allele is a "good" gene or
a "bad" gene with respect to fitness, a gene of major
effect or minor fitness effect, or even a neutral gene when the
background alleles are equally abundant (i.e., \(p\_B = p\_b)\).
Whenever allele frequencies of its epistatic partner change, either by
drift or selection, the A allele's selective effect also changes
and, like the case of \(\rG \times \rE\), it moves the boundary
between the domains of natural selection and random drift
 (Fig. 2),
 increasing the domain of the latter at the expense of the former.


## 6. Allozyme Variation and the Drift vs Selection Controversy



The central problem with using conspicuous polymorphisms for
investigating the relative roles of the variety of different
evolutionary forces is that they not an unbiased sample of genetic
diversity with respect to either adaptive function or amount of
genetic variation. Indeed, the definition of genetic polymorphism
adopted by Ford (see above) incorporates the essence of both of these
biases. For a period, it was believed that "The solution to our
dilemma lies in the development of molecular genetics" (Lewontin
1974: 99). With the advent of electrophoresis, the amino acid sequence
of a random sample of proteins from almost any organism could be
studied and, for the first time, the level of genetic diversity, in
the form of amino acid substitutions, across the genome could be
quantified.



Two measures of genetic diversity were possible using electrophoresis:



1. the number of loci polymorphic; and,
2. the average heterozygosity per locus per individual.



From studies across a number of species, it was estimated that
15-40% of all loci were polymorphic and the average individual
was heterozygous at 5-15% of its genome. Since this technique
measured primarily amino acid substitutions resulting in charge
changes, i.e., only one third of all possible amino acid
substitutions, one could infer that these were minimal levels of
genetic diversity which significantly underestimated the actual
levels. The conclusion that genetic variation was ubiquitous, with
most genes being polymorphic, was inescapable. The search for the
adaptive function of allozyme variants and balancing selection at the
physiological level ensued, just as it had in the earliest studies in
ecological genetics.



However, the observed levels of genetic polymorphism presented an
insurmountable problem for the mathematical theory of evolutionary
genetics. The amount of genetic variation was much too large to be
explained by the type of balancing selection observed by Ford and his
colleagues for conspicuous phenotypic polymorphisms in natural
populations. The basic problem was that the numbers of selective
deaths necessary to account for the observed levels of allozyme
polymorphism exceeded the reproductive excess of almost all species.
This where the focus on genetics must be coupled with the ecology of
reproduction and viability. Haldane (1957) called this the "cost
of natural selection" and it is also referred to as the
substitutional load. Differently put, the mortality of homozygous
genotypes, if independently selected, (also known as the
"segregation load") would exceed the total numbers of
offspring produced by a population. For this reason, Kimura (1983)
proposed his neutral theory of molecular evolution, founded on the
theoretical observation that the probability of fixation of a novel
mutant allele with selective coefficient, \(s \gt 0\), was
approximately \(2s\) (Wright 1931: 133). Since \(s\) was generally
believed to be in the range of 0.001 to 0.0001, the likelihood of loss
of a new favorable mutation by chance is quite high, only slightly
smaller than the probability of loss by chance for a truly neutral
allele.



Studies of protein structure revealed that the functional,
non-synonymous sites of a protein, which constitute the minority of
its amino acids, evolved several times more slowly than the
non-functional, synonymous or structural sites. Kimura's view
that much, if not most, of evolutionary change at the molecular level
was determined by random genetic drift and not natural selection was
highly controversial. As Kimura noted, 



> 
> 
> ...if a certain doctrine is constantly being spoken of favorably
> by the majority, endorsed by top authorities in their books and taught
> in classes, then a belief is gradually built up in one's mind,
> eventually becoming the guiding principle and the basis of value
> judgment. At any rate, this was the time when the panselectionist or
> "neo-Darwinian" position was most secure in the history of
> biology: the heyday of the traditional "synthetic theory"
> of evolution. (1983: 22)
> 
> 
> 



It was soon recognized that a more reductionistic approach (DNA
sequence studies) might help to resolve the issue of whether or not
every amino acid was of some functional value because the redundant
positions in the code of life were assumed to provide an estimate of
the true "neutral" rate of evolution, owing to random
genetic drift acting in the absence of selection.


## 7. Sequence Variation and the Drift vs Selection Controversy



The neutral theory of evolution is the antithesis of ecological
genetics. It states that random genetic drift, independent of the
environment, rather than natural selection, governs most evolutionary
change at the level of the DNA and proteins. At the same time, it
admits that natural selection predominates in shaping the
morphological and physiological traits that manifest an adaptive fit
with the environment. This is a paradox because most of the DNA
appears to be non-functional while most of the externally observable
phenotype appears to have adaptive function.



Tests of the theory using DNA sequence data consist of comparisons of
the relative evolutionary rates of different kinds of sites (base
pairs) within codons and take advantage of the redundancy in the
genetic code. The rate of neutral evolution is estimated from levels
of polymorphism or numbers of segregating sites within species or the
divergence between species in silent or redundant site substitutions
(e.g., Dapper & Wade 2020). Silent sites are those that do not
result in an amino acid change in the protein and, hence, are
non-functional in the usual sense. In contrast, the rate of selective
change or selective constraint is evaluated relative to the neutral
rate using replacement sites, those base pair changes that result in
amino acid changes. If the rate of substitution or polymorphism is
lower than neutral, it is evidence of selective constraint or
purifying natural selection acting to prevent change and preserve
function in the face of mutational damage. If the rate of substitution
is higher than neutral, then it is evidence of adaptive substitution.




Molecular evolutionary studies also revealed the existence of
*pseudogenes*, non-coding stretches of DNA derived by the
tandem duplication and subsequent inactivation by mutation of single
copy genes. The lack of function of the pseudogene makes all of its
codons effectively neutral and provides another estimate of the rate
of neutral evolution. Importantly, "replacement" sites
that evolve slowly in the functional gene have been shown to evolve
more rapidly in the nonfunctional tandem duplicate pseudogene.



Changes in the pattern of neutral variation in the vicinity of a
selected site(s) are also informative because, during an adaptive
substitution, neutral variants linked to the piece of selected DNA are
carried or "swept" to fixation along with it. This
"selective sweep" temporarily reduces the level of neutral
variation in the vicinity of selected sites until it can be replaced
by mutation. The degree of reduction in neutral variation or the
"footprint of selection" depends upon the strength of
selection, the frequency of recombination during selection, and the
time since the initiation of selection. The footprint is most
conspicuous when a selective sweep is initiated by the advent of a
single, novel favorable mutation. To the extent that novel selection
results from a change of environment and begins to act on existing or
standing variation already in the population, the impact on neutral
polymorphisms may be quite minimal.



Balancing selection of the sort observed by Ford leaves its own unique
"reverse" footprint on neutral diversity (Kreitman &
Di Rienzo 2004) . Because the segments of DNA constituting the
balanced polymorphism are held in the population by selection much
longer than expected based on random drift, these segments have a
higher effective population size (owing to lower variation in
offspring numbers than random). As a result, they have a longer time
to accumulate mutational variation at nearby neutral sites. In some
cases, the time is longer than that required to create new species,
resulting in *trans-specific polymorphisms* (Cho et al. 2006).
Thus, levels of neutral diversity are expected to be enhanced in the
vicinity of a molecular balanced polymorphism. When the mating system
restricts recombination (e.g., selfing or inbreeding species), the
region of elevated neutral diversity in the vicinity of a balanced
polymorphism can be extensive (e.g., *Arabiodopsis thaliana*
[Tian et al. 2002]).



Kimura predicted that silent substitutions would evolve more rapidly
than replacement substitutions *before* sequence data were
available to test his neutral theory of molecular evolution. Molecular
genetic studies have confirmed his prediction: silent sites evolve
several times faster than replacement sites. These studies clearly
show that the primary mode of action of natural selection at the level
of the DNA sequence is purifying selection. It is this highly
conservative aspect of natural selection that permits comparative
molecular evolutionary studies of developmental processes across
species as diverse as humans and flies. At the molecular level, most
genes, though polymorphic in sequence, do not display evidence of
balancing selection and instead manifest patterns of variation that
accord well with neutral theory.



The interaction of selection and random drift across linked regions of
DNA sequence is one of the most active current areas of theoretical
and empirical research in molecular evolution. Theory shows that it
can be difficult to separate cleanly the action of the evolutionary
forces of selection and drift except for certain regions of parameter
space, whose generality remains unknown and subject to much debate.
Like the study by Fisher and Ford (1947), most empirical studies
interpret *all* deviations away from strictly the neutral
expectation as evidence of natural selection without addressing the
issue of agency. For example, codon bias is evidence that natural
selection affects even the apparently non-functional components of
genes. Thus, the original ecological genetic view that natural
selection is the only significant evolutionary force characterizes
much of modern molecular evolution, despite progress in theory and the
availability of much more reductionistic genetic methods. The
parallels between the summary statement of Ford
 (1975: 389; see above)
 and that of the molecular evolutionary geneticist, E. Nevo,
twenty-five years later are remarkable: 



> 
> 
> Biodiversity evolution, even in small isolated populations, is
> primarily driven by natural selection, including diversifying,
> balancing, cyclical, and purifying selective regimes, interacting
> with, but ultimately overriding, the effects of mutation, migration,
> and stochasticity [random genetic drift]. (Nevo 2001: 6223)
> 
> 
>