Abstract
Genome-wide scans for positively selected genes (PSGs) in mammals have provided insight into the dynamics of genome evolution, the genetic basis of differences between species, and the functions of individual genes. However, previous scans have been limited in power and accuracy owing to small numbers of available genomes. Here we present the most comprehensive examination of mammalian PSGs to date, using the six high-coverage genome assemblies now available for eutherian mammals. The increased phylogenetic depth of this dataset results in substantially improved statistical power, and permits several new lineage- and clade-specific tests to be applied. Of ∼16,500 human genes with high-confidence orthologs in at least two other species, 400 genes showed significant evidence of positive selection (FDR<0.05), according to a standard likelihood ratio test. An additional 144 genes showed evidence of positive selection on particular lineages or clades. As in previous studies, the identified PSGs were enriched for roles in defense/immunity, chemosensory perception, and reproduction, but enrichments were also evident for more specific functions, such as complement-mediated immunity and taste perception. Several pathways were strongly enriched for PSGs, suggesting possible co-evolution of interacting genes. A novel Bayesian analysis of the possible “selection histories” of each gene indicated that most PSGs have switched multiple times between positive selection and nonselection, suggesting that positive selection is often episodic. A detailed analysis of Affymetrix exon array data indicated that PSGs are expressed at significantly lower levels, and in a more tissue-specific manner, than non-PSGs. Genes that are specifically expressed in the spleen, testes, liver, and breast are significantly enriched for PSGs, but no evidence was found for an enrichment for PSGs among brain-specific genes. This study provides additional evidence for widespread positive selection in mammalian evolution and new genome-wide insights into the functional implications of positive selection.
Highlights
Positive darwinian selection is an important source of evolutionary innovation and a major force behind the divergence of species
Genes involved in immunity and defense are a well-known example; rapid evolution in these genes presumably occurs because new mutations help organisms to prevail in evolutionary ‘‘arms races’’ with pathogens
Many mammalian genes show evidence of positive selection, but open questions remain about the overall impact of positive selection in mammals
Summary
Positive darwinian selection is an important source of evolutionary innovation and a major force behind the divergence of species. A wide variety of methods for detecting positively selected genes (PSGs) have been introduced, including comparative or phylogenetic methods, which make use of patterns of substitutions between species, and population genetic methods, which primarily rely on patterns of intraspecies polymorphism [2,3]. Using these techniques, strong evidence of positive selection has been found for various genes in various organisms, including many genes involved in sensory perception, immunity, host-pathogen interactions, and reproduction (reviewed in [1,3])
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