Selection in the introgressed regions of the chimpanzee genome
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- dc.contributor.author Nye, Jessica, 1986-
- dc.contributor.author Laayouni, Hafid, 1968-
- dc.contributor.author Kuhlwilm, Martin
- dc.contributor.author Mondal, Mayukh, 1989-
- dc.contributor.author Marquès i Bonet, Tomàs, 1975-
- dc.contributor.author Bertranpetit, Jaume, 1952-
- dc.date.accessioned 2019-01-28T10:59:56Z
- dc.date.available 2019-01-28T10:59:56Z
- dc.date.issued 2018
- dc.description.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.
- dc.description.sponsorship 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.
- dc.format.mimetype application/pdf
- dc.identifier.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
- dc.identifier.doi http://dx.doi.org/10.1093/gbe/evy077
- dc.identifier.issn 1759-6653
- dc.identifier.uri http://hdl.handle.net/10230/36441
- dc.language.iso eng
- dc.publisher Oxford University Press
- dc.relation.ispartof Genome Biol Evol. 2018; 10(4):1132-1138
- dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BFU2016-77961-P
- dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BFU2014-55090-P
- dc.rights © 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.com
- dc.rights.accessRights info:eu-repo/semantics/openAccess
- dc.rights.uri http://creativecommons.org/licenses/by-nc/4.0/
- dc.subject.keyword Chimpanzee
- dc.subject.keyword Introgression
- dc.subject.keyword Natural selection
- dc.subject.keyword Balancing selection
- dc.title Selection in the introgressed regions of the chimpanzee genome
- dc.type info:eu-repo/semantics/article
- dc.type.version info:eu-repo/semantics/publishedVersion