differences between genes that are similar because of lateral gene transfer and those that are similar because the organisms shared an ancestor. By comparing large numbers of genes or entire genomes among many species, it is possible to identify transferred genes, since these sequences behave differently from what is expected given the taxonomy of the organism. Using these methods, researchers were able to identify over 2,000 metabolic enzymes obtained by various eukaryotic parasites from lateral gene transfer. Gene family evolution The comparison of complete gene sets for a group of organisms allows the identification of events in gene evolution such as gene duplication or gene deletion. Often, such events are evolutionarily relevant. For example, multiple duplications of genes encoding degradative enzymes of certain families is a common adaptation in microbes to new nutrient sources. On the contrary, loss of genes is important in reductive evolution, such as in intracellular parasites or symbionts. Whole genome duplication events, which potentially duplicate all the genes in a genome at once, are drastic evolutionary events with great relevance in the evolution of many clades, and whose signal can be traced with phylogenomic methods. Establishment of evolutionary relationships Traditional single-gene studies are effective in establishing phylogenetic trees among closely related organisms, but have drawbacks when comparing more distantly related organisms or microorganisms. This is because of lateral gene transfer, convergence, and varying rates of evolution for different genes. By using entire genomes in these comparisons, the anomalies created from these factors are overwhelmed by the pattern of evolution indicated by the majority of the data. Through phylogenomics, it has been discovered that most of the photosynthetic eukaryotes are linked and possibly share a single ancestor. Researchers compared 135 genes from 65 different species of photosynthetic organisms. These included plants, alveolates, rhizarians, haptophytes and cryptomonads. This has been referred to as the Plants+HC+SAR megagroup. Using this method, it is theoretically possible to create fully resolved phylogenetic trees, and timing constraints can be recovered more accurately. However, in practice this is not always the case. Due to insufficient data, multiple trees can sometimes be supported by the same data when analyzed using different methods. Databases PhylomeDB See also Archaeopteryx (phylogenomics software) Microbial phylogenetics Phylogenetics Sequence alignment Supertree References Genomics Phylogenetics