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.

This study has been possible thanks to grant BFU2016-77961-P (AEI/FEDER, UE) awarded by the Agencia Estatal de Investigación (Spain) and with the support of Secretaria d’Universitats i Recerca del Departament d’Economia i Coneixement de la Generalitat de Catalunya (GRC 2014 SGR 866). J.N. was supported by an FI PhD fellowship by Agaur (FI-DGR 2015). M.K. was supported by a DFG fellowship (KU 3467/1-1). T.M.-B. is supported by MINECO BFU2014-55090-P (FEDER), U01 MH106874 grant, Howard Hughes International Early Career and Secretaria d’Universitats i Recerca del Departament d’Economia i Coneixement de la Generalitat de Catalunya.