Selection in the introgressed regions of the chimpanzee genome

Nye, Jessica, 1986-; Laayouni, Hafid, 1968-; Kuhlwilm, Martin; Mondal, Mayukh, 1989-; Marquès i Bonet, Tomàs, 1975-; Bertranpetit, Jaume, 1952-

doi:http://dx.doi.org/10.1093/gbe/evy077

Selection in the introgressed regions of the chimpanzee genome

License

Citation

Nye J, Laayouni H, Kuhlwilm M, Mondal M, Marques-Bonet T, Bertranpetit J. Selection in the introgressed regions of the chimpanzee genome. Genome Biol Evol. 2018; 10(4):1132-1138. DOI 10.1093/gbe/evy077

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.