Selection in the Introgressed Regions of the Chimpanzee Genome

Abstract

During the demographic history of the Pan clade, there has been gene-flow between species, likely >200,000 years ago. Bonobo haplotypes in three subspecies of chimpanzee have been identified to be segregating in modern-day chimpanzee populations, suggesting that these haplotypes, with increased differentiation, may be a target of natural selection. Here, we investigate signatures of adaptive introgression within the bonobo-like haplotypes in chimpanzees using site frequency spectrum-based tests. We find evidence for subspecies-specific adaptations in introgressed regions involved with male reproduction in central chimpanzees, the immune system in eastern chimpanzees, female reproduction and the nervous system in Nigeria-Cameroon chimpanzees. Furthermore, our results indicate signatures of balancing selection in some of the putatively introgressed regions. This might be the product of long-term balancing selection resulting in a similar genomic signature as introgression, or possibly balancing selection acting on alleles reintroduced through gene flow.

Fig. 1.

—Statistical distribution of Tajima’s D, Fu and Li’s D and F. Black represents the whole genome and yellow represents the introgressed regions. (A) Pan troglodytes troglodytes. (B) Pan troglodytes schweinfurthii. (C) Pan troglodytes ellioti.

Fig. 2.

—Proportion of genes in or nearest to each introgressed region with DEPICT tissue enrichment analysis through a literature search. (A) Pan troglodytes troglodytes. (B) Pan troglodytes schweinfurthii. (C) Pan troglodytes ellioti.