Evidence that viruses, particularly SIV, drove genetic adaptation in natural populations of eastern chimpanzees

Abstract

All four subspecies of chimpanzees are endangered. Differing in their demographic histories and geographical ranges within sub-Saharan Africa, they have likely adapted to different environmental factors. We show that highly differentiated SNPs in eastern chimpanzees are uniquely enriched in genic sites in a way that is expected under recent adaptation. These sites are enriched for genes that differentiate the immune response to infection by simian immunodeficiency virus (SIV) in natural vs. non-natural host species. Conversely, central chimpanzees exhibit selective sweeps at the cytokine receptors CCR3, CCR9 and CXCR6 - paralogs of CCR5 and CXCR4, the two major receptors utilized by HIV to enter human cells. Thus, we infer that SIV may be eliciting distinctive adaptive responses in different chimpanzee subspecies. Since central chimpanzee SIV is the source of the global HIV/AIDS pandemic, understanding the mechanisms that limit pathogenicity of SIV in chimpanzees can broaden our understanding of HIV infection in humans.