Historic sampling of a vanishing beast: Population structure and diversity in the black rhinoceros

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• dc.contributor.author Sánchez-Barreiro, Fátima
• dc.contributor.author Cahsan, Binia de
• dc.contributor.author Westbury, Michael V.
• dc.contributor.author Sun, Xin
• dc.contributor.author Margaryan, Ashot
• dc.contributor.author Fontseré Alemany, Clàudia, 1992-
• dc.contributor.author Bruford, Michael W.
• dc.contributor.author Russo, Isa-Rita M.
• dc.contributor.author Kalthoff, Daniela C.
• dc.contributor.author Sicheritz-Ponten, Thomas
• dc.contributor.author Petersen, Bent
• dc.contributor.author Dalén, Love
• dc.contributor.author Zhang, Guojie
• dc.contributor.author Marquès i Bonet, Tomàs, 1975-
• dc.contributor.author Gilbert, M Thomas
• dc.contributor.author Moodley, Yoshan
• dc.date.accessioned 2023-10-17T06:19:21Z
• dc.date.available 2023-10-17T06:19:21Z
• dc.date.issued 2023
• dc.description.abstract The black rhinoceros (Diceros bicornis L.) is a critically endangered species historically distributed across sub-Saharan Africa. Hunting and habitat disturbance have diminished both its numbers and distribution since the 19th century, but a poaching crisis in the late 20th century drove them to the brink of extinction. Genetic and genomic assessments can greatly increase our knowledge of the species and inform management strategies. However, when a species has been severely reduced, with the extirpation and artificial admixture of several populations, it is extremely challenging to obtain an accurate understanding of historic population structure and evolutionary history from extant samples. Therefore, we generated and analyzed whole genomes from 63 black rhinoceros museum specimens collected between 1775 and 1981. Results showed that the black rhinoceros could be genetically structured into six major historic populations (Central Africa, East Africa, Northwestern Africa, Northeastern Africa, Ruvuma, and Southern Africa) within which were nested four further subpopulations (Maasailand, southwestern, eastern rift, and northern rift), largely mirroring geography, with a punctuated north-south cline. However, we detected varying degrees of admixture among groups and found that several geographical barriers, most prominently the Zambezi River, drove population discontinuities. Genomic diversity was high in the middle of the range and decayed toward the periphery. This comprehensive historic portrait also allowed us to ascertain the ancestry of 20 resequenced genomes from extant populations. Lastly, using insights gained from this unique temporal data set, we suggest management strategies, some of which require urgent implementation, for the conservation of the remaining black rhinoceros diversity.
• dc.description.sponsorship This work was supported by ERC Consolidator Grant 681396 “Extinction Genomics” to M.T.P.G. and by EMBO Short-Term Fellowship 7578 to F.S.-B. The authors would like to acknowledge support from Science for Life Laboratory, the National Genomics Infrastructure (NGI), Sweden, the Knut and Alice Wallenberg Foundation, and UPPMAX for providing assistance in massively parallel DNA sequencing and computational infrastructure. T.M.-B. is supported by funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement No. 864203), BFU2017-86471-P (MINECO/FEDER, UE), “Unidad de Excelencia María de Maeztu”, funded by the AEI (CEX2018-000792-M), and NIH 1R01HG010898-01A1. Y.M. acknowledges support from the National Research Foundation of the Republic of South Africa. The authors are very grateful to all the museums who contributed samples to this study: the Natural History Museum London, the Museum of Natural History Berlin, the Powell-Cotton Museum, the Natural History Museum Vienna, the Natural History Museum at the National Museum Praha, the Natural History Museum of Zimbabwe, the Swedish Museum of Natural History, the Royal Museum for Central Africa Tervuren, the Senckenberg Museum Frankfurt, the United States National Museum Washington (or Smithsonian Arts and Industries Building), and the Bavarian State Collection of Zoology. The authors would also like to thank Professor Alfred L. Roca (Department of Animal Sciences, University of Illinois Urbana-Champaign) for insightful comments on the preliminary results of this manuscript. Lastly, it is with great sadness that we acknowledge the death of our friend, colleague, mentor, and coauthor Michael W. Bruford, who succumbed to illness during the resubmission phase of this manuscript. He will be sorely missed far beyond the bounds of just the conservation genetics community.
• dc.format.mimetype application/pdf
• dc.identifier.citation Sánchez-Barreiro F, De Cahsan B, Westbury MV, Sun X, Margaryan A, Fontsere C, Bruford MW, Russo IM, Kalthoff DC, Sicheritz-Pontén T, Petersen B, Dalén L, Zhang G, Marquès-Bonet T, Gilbert MTP, Moodley Y. Historic sampling of a vanishing beast: Population structure and diversity in the black rhinoceros. Mol Biol Evol. 2023 Sep 1;40(9):msad180. DOI: 10.1093/molbev/msad180
• dc.identifier.doi http://dx.doi.org/10.1093/molbev/msad180
• dc.identifier.issn 0737-4038
• dc.identifier.uri http://hdl.handle.net/10230/58076
• dc.language.iso eng
• dc.publisher Oxford University Press
• dc.relation.ispartof Mol Biol Evol. 2023 Sep 1;40(9):msad180
• dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/681396
• dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/864203
• dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/BFU2017-86471-P
• dc.rights © The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://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 Ancient DNA
• dc.subject.keyword Black rhinoceros
• dc.subject.keyword Conservation genomics
• dc.subject.keyword Population genomics
• dc.title Historic sampling of a vanishing beast: Population structure and diversity in the black rhinoceros
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion