Nye, Jessica, 1986-Laayouni, Hafid, 1968-Kuhlwilm, MartinMondal, Mayukh, 1989-Marquès i Bonet, Tomàs, 1975-Bertranpetit, Jaume, 1952-2019-01-282019-01-282018Nye 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/evy0771759-6653http://hdl.handle.net/10230/36441During 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.application/pdfeng© The Author(s) 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.cominfo:eu-repo/semantics/articlehttp://dx.doi.org/10.1093/gbe/evy077ChimpanzeeIntrogressionNatural selectionBalancing selectioninfo:eu-repo/semantics/openAccess