Genetic variation in pan species is shaped by demographic history and harbors lineage-specific functions
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- dc.contributor.author Han, Sojung
- dc.contributor.author Andrés Morán, Aida, 1976-
- dc.contributor.author Marquès i Bonet, Tomàs, 1975-
- dc.contributor.author Kuhlwilm, Martin
- dc.date.accessioned 2019-06-07T09:51:15Z
- dc.date.available 2019-06-07T09:51:15Z
- dc.date.issued 2019
- dc.description.abstract Chimpanzees (Pan troglodytes) and bonobos (Pan paniscus) are the closest living relatives of humans, but the two species show distinct behavioral and physiological differences, particularly regarding female reproduction. Despite their recent rapid decline, the demographic histories of the two species have been different during the past 1-2 Myr, likely having an impact on their genomic diversity. Here, we analyze the inferred functional consequences of genetic variation across 69 individuals, making use of the most complete data set of genomes in the Pan clade to date. We test to which extent the demographic history influences the efficacy of purifying selection in these species. We find that small historical effective population sizes (Ne) correlate not only with low levels of genetic diversity but also with a larger number of deleterious alleles in homozygosity and an increased proportion of deleterious changes at low frequencies. To investigate the putative genetic basis for phenotypic differences between chimpanzees and bonobos, we exploit the catalog of putatively deleterious protein-coding changes in each lineage. We show that bonobo-specific nonsynonymous changes are enriched in genes related to age at menarche in humans, suggesting that the prominent physiological differences in the female reproductive system between chimpanzees and bonobos might be explained, in part, by putatively adaptive changes on the bonobo lineage.
- dc.description.sponsorship This work was supported by the Max Planck Society (to A.M.A.), BFU2017-86471-P (MINECO/FEDER, UE) (to T.M.-B.), U01 (MH106874 to T.M.-B.), Howard Hughes International Early Career (to T.M.-B.), Obra Social “La Caixa” (to T.M.-B.), Secretaria d’Universitats i Recerca del Departament d’Economia i Coneixement de la Generalitat de Catalunya (to T.M.-B.), and a Deutsche Forschungsgemeinschaft (DFG) fellowship (KU 3467/1-1 to M.K.).
- dc.format.mimetype application/pdf
- dc.identifier.citation Han S, Andrés AM, Marques-Bonet T, Kuhlwilm M. Genetic variation in pan species is shaped by demographic history and harbors lineage-specific functions. Genome Biol Evol. 2019;11(4):1178-91. DOI 10.1093/gbe/evz047
- dc.identifier.doi http://dx.doi.org/10.1093/gbe/evz047
- dc.identifier.issn 1759-6653
- dc.identifier.uri http://hdl.handle.net/10230/41719
- dc.language.iso eng
- dc.publisher Oxford University Press
- dc.relation.ispartof Genome Biology and Evolution. 2019;11(4):1178-91
- dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/BFU2017-86471-P
- dc.rights © The Author(s) 2019. 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 Bonobo genome
- dc.subject.keyword Bonobo reproduction
- dc.subject.keyword Comparative genomics
- dc.subject.keyword Deleteriousness
- dc.title Genetic variation in pan species is shaped by demographic history and harbors lineage-specific functions
- dc.type info:eu-repo/semantics/article
- dc.type.version info:eu-repo/semantics/publishedVersion