Deep genetic substructure within bonobos

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• dc.contributor.author Han, Sojung
• dc.contributor.author Filippo, Cesare de
• dc.contributor.author Parra Farré, Genís
• dc.contributor.author Meneu, Juan Ramon
• dc.contributor.author Laurent, Romain
• dc.contributor.author Frandsen, Peter
• dc.contributor.author Hvilsom, Christina
• dc.contributor.author Gronau, Ilan
• dc.contributor.author Marquès i Bonet, Tomàs, 1975-
• dc.contributor.author Kuhlwilm, Martin
• dc.contributor.author Andrés Morán, Aida, 1976-
• dc.date.accessioned 2025-01-14T13:55:52Z
• dc.date.available 2025-01-14T13:55:52Z
• dc.date.issued 2024
• dc.description.abstract Establishing the genetic and geographic structure of populations is fundamental, both to understand their evolutionary past and preserve their future. Nevertheless, the patterns of genetic population structure are unknown for most endangered species. This is the case for bonobos (Pan paniscus), which, together with chimpanzees (Pan troglodytes), are humans' closest living relatives. Chimpanzees live across equatorial Africa and are classified into four subspecies,1 with some genetic population substructure even within subspecies. Conversely, bonobos live exclusively in the Democratic Republic of Congo and are considered a homogeneous group with low genetic diversity,2 despite some population structure inferred from mtDNA. Nevertheless, mtDNA aside, their genetic structure remains unknown, hampering our understanding of the species and conservation efforts. Mapping bonobo genetic diversity in space is, however, challenging because, being endangered, only non-invasive sampling is possible for wild individuals. Here, we jointly analyze the exomes and mtDNA from 20 wild-born bonobos, the whole genomes of 10 captive bonobos, and the mtDNA of 136 wild individuals. We identify three genetically distinct bonobo groups of inferred Central, Western, and Far-Western geographic origin within the bonobo range. We estimate the split time between the central and western populations to be ∼145,000 years ago and genetic differentiation to be in the order of that of the closest chimpanzee subspecies. Furthermore, our estimated long-term Ne for Far-West (∼3,000) is among the lowest estimated for any great ape lineage. Our results highlight the need to attend to the bonobo substructure, both in terms of research and conservation.
• dc.description.sponsorship C.d.F. and A.M.A. were supported by intramural funds from the Max Planck Institute for Evolutionary Anthropology (Leipzig, Germany). C.d.F. was also supported by the European Research Council (ERC) grant agreement no. 694707 to Svante Pääbo. A.M.A. was additionally funded by the Wellcome Trust ISSF3 UCL award 204841/Z/16/Z. M.K. was supported by “La Caixa” Foundation (ID 100010434), fellowship code LCF/BQ/PR19/11700002, the Vienna Science and Technology Fund (WWTF) (10.47379/VRG20001), and the Austrian Science Fund (FWF) (FW547002). T.M.-B. was supported by the European Research Council (ERC) grant agreement no. 864203. We would like to thank Svante Pääbo for access to samples and discussions, Mimi Arandjelovic and Martin Surbeck for their valuable comments, Roger Mundry for the R-programming discussions, Hjalmar Kühl for sharing the data of the bonobo’s habitat, and Hiroyuki Takemoto for providing the location of the sampled individuals analyzed for mtDNA. We are grateful to the Life Science Computer Cluster of the University of Vienna.
• dc.format.mimetype application/pdf
• dc.identifier.citation Han S, Filippo C de, Parra G, Meneu JR, Laurent R, Frandsen P, et al. Deep genetic substructure within bonobos. Curr Biol. 2024 Nov 18;34(22):5341-8.e3. DOI: 10.1016/j.cub.2024.09.043
• dc.identifier.doi http://dx.doi.org/10.1016/j.cub.2024.09.043
• dc.identifier.issn 0960-9822
• dc.identifier.uri http://hdl.handle.net/10230/69117
• dc.language.iso eng
• dc.publisher Elsevier
• dc.relation.ispartof Curr Biol. 2024 Nov 18;34(22):5341-8.e3
• dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/694707
• dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/864203
• dc.rights © 2024 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by/4.0/
• dc.subject.keyword Bonobo
• dc.subject.keyword Conservation
• dc.subject.keyword Divergence
• dc.subject.keyword Endangered species
• dc.subject.keyword Exome
• dc.subject.keyword Genetic diversity
• dc.subject.keyword Genome
• dc.subject.keyword Great ape
• dc.subject.keyword Pan paniscus
• dc.subject.keyword Population substructure
• dc.title Deep genetic substructure within bonobos
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion