Abstract
Consistent patterns of positive selection in functionally similar genes can suggest a common selective pressure across a group of species. We use alignments of orthologous protein-coding genes from 39 species of birds to estimate parameters related to positive selection for 11,000 genes conserved across birds. We show that functional pathways related to the immune system, recombination, lipid metabolism, and phototransduction are enriched for positively selected genes. By comparing our results with mammalian data, we find a significant enrichment for positively selected genes shared between taxa, and that these shared selected genes are enriched for viral immune pathways. Using pathogen-challenge transcriptome data, we show that genes up-regulated in response to pathogens are also enriched for positively selected genes. Together, our results suggest that pathogens, particularly viruses, consistently target the same genes across divergent clades, and that these genes are hotspots of host-pathogen conflict over deep evolutionary time.
Highlights
Central to the study of evolutionary biology is the desire to understand how natural selection operates across a diverse set of populations and species
Recent studies of mammals show that proteins that interact with viruses experience about twice as many amino acid changes compared to proteins that do not (Enard et al, 2016) and proteins that interact with Plasmodium experience elevated rates of adaptation (Ebel et al, 2017)
We find that the strongest signatures of selection are concentrated in four general categories: immune system genes, genes involved in recombination and replication, genes involved in lipid metabolism, and phototransduction genes
Summary
Central to the study of evolutionary biology is the desire to understand how natural selection operates across a diverse set of populations and species. Comparative genomic studies on primates, mammals, bees, ants, Drosophila and other organisms (Schlenke and Begun, 2003; Sackton et al, 2007; Kosiol et al, 2008; Barreiro and Quintana-Murci, 2010; Roux et al, 2014) that included unbiased selection scans identified immune system pathways as common targets of natural selection. This implies that pathogens, which elicit the immune response, may be strong and consistent selective forces across species.
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