Ghost admixture in eastern gorillas

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  • dc.contributor.author Pawar, Harvinder
  • dc.contributor.author Marquès i Bonet, Tomàs, 1975-
  • dc.contributor.author Kuhlwilm, Martin
  • dc.date.accessioned 2023-10-06T06:02:56Z
  • dc.date.available 2023-10-06T06:02:56Z
  • dc.date.issued 2023
  • dc.description.abstract Archaic admixture has had a substantial impact on human evolution with multiple events across different clades, including from extinct hominins such as Neanderthals and Denisovans into modern humans. In great apes, archaic admixture has been identified in chimpanzees and bonobos but the possibility of such events has not been explored in other species. Here, we address this question using high-coverage whole-genome sequences from all four extant gorilla subspecies, including six newly sequenced eastern gorillas from previously unsampled geographic regions. Using approximate Bayesian computation with neural networks to model the demographic history of gorillas, we find a signature of admixture from an archaic 'ghost' lineage into the common ancestor of eastern gorillas but not western gorillas. We infer that up to 3% of the genome of these individuals is introgressed from an archaic lineage that diverged more than 3 million years ago from the common ancestor of all extant gorillas. This introgression event took place before the split of mountain and eastern lowland gorillas, probably more than 40 thousand years ago and may have influenced perception of bitter taste in eastern gorillas. When comparing the introgression landscapes of gorillas, humans and bonobos, we find a consistent depletion of introgressed fragments on the X chromosome across these species. However, depletion in protein-coding content is not detectable in eastern gorillas, possibly as a consequence of stronger genetic drift in this species.
  • dc.description.sponsorship This project has been funded by the Vienna Science and Technology Fund (WWTF) (grant no. 10.47379/VRG20001) to M.K. and the European Research Council under the European Union’s Horizon 2020 research and innovation programme (grant no. 864203), PID2021-126004NB-100 (MINECO/FEDER, UE), Secretaria d’Universitats i Recerca and CERCA Program del Departament d’Economia i Coneixement de la Generalitat de Catalunya (GRC 2021 SGR 00177) to T.M.-B. H.P. was supported by a Formació de Personal Investigador fellowship from Generalitat de Catalunya (FI_B100131). M.A.-E. was supported by a Formación de Personal Investigador PRE2018-083966 from Ministerio de Ciencia, Universidades e Investigación. C.T.-S., Y.X. and J.P.-M. were funded by Wellcome grant no. 098051. K.G. was supported by Swedish Research Council grant no. 2020-03398. J.L.K. received the María de Maeztu Mobility Fellowship. O.D. was supported by a John Templeton Foundation grant no. ID 62178. A.M.A. received funding from UCL’s Wellcome Trust ISSF3 award no. 204841/Z/16/Z. Q.A. is supported by strategic funding from Monash University (STG-000114).
  • dc.format.mimetype application/pdf
  • dc.identifier.citation Pawar H, Rymbekova A, Cuadros-Espinoza S, Huang X, de Manuel M, van der Valk T, et al. Ghost admixture in eastern gorillas. Nat Ecol Evol. 2023 Sep;7(9):1503-14. DOI: 10.1038/s41559-023-02145-2
  • dc.identifier.doi http://dx.doi.org/10.1038/s41559-023-02145-2
  • dc.identifier.issn 2397-334X
  • dc.identifier.uri http://hdl.handle.net/10230/58050
  • dc.language.iso eng
  • dc.publisher Nature Research
  • dc.relation.ispartof Nat Ecol Evol. 2023 Sep;7(9):1503-14
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/864203
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/3PE/PID2021-126004NB-100
  • dc.rights © The Author(s) 2023. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit 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 Evolutionary genetics
  • dc.subject.keyword Phylogenetics
  • dc.subject.keyword Population genetics
  • dc.title Ghost admixture in eastern gorillas
  • dc.type info:eu-repo/semantics/article
  • dc.type.version info:eu-repo/semantics/publishedVersion

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