Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros (Ceratotherium simum)

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• dc.contributor.author Sánchez-Barreiro, Fátima
• dc.contributor.author Gopalakrishnan, Shyam
• dc.contributor.author Ramos-Madrigal, Jazmín
• dc.contributor.author Westbury, Michael V.
• dc.contributor.author Manuel Montero, Marc de, 1991-
• dc.contributor.author Margaryan, Ashot
• dc.contributor.author Ciucani, Marta M.
• dc.contributor.author Vieira, Filipe Garrett
• dc.contributor.author Patramanis, Yannis
• dc.contributor.author Kalthoff, Daniela C.
• dc.contributor.author Timmons, Zena
• dc.contributor.author Sicheritz-Ponten, Thomas
• dc.contributor.author Dalén, Love
• dc.contributor.author Ryder, Oliver A.
• dc.contributor.author Zhang, Guojie
• dc.contributor.author Marquès i Bonet, Tomàs, 1975-
• dc.contributor.author Moodley, Yoshan
• dc.contributor.author Gilbert, M Thomas
• dc.date.accessioned 2021-12-02T06:48:42Z
• dc.date.available 2021-12-02T06:48:42Z
• dc.date.issued 2021
• dc.description.abstract Large vertebrates are extremely sensitive to anthropogenic pressure, and their populations are declining fast. The white rhinoceros (Ceratotherium simum) is a paradigmatic case: this African megaherbivore has suffered a remarkable decline in the last 150 years due to human activities. Its subspecies, the northern (NWR) and the southern white rhinoceros (SWR), however, underwent opposite fates: the NWR vanished quickly, while the SWR recovered after the severe decline. Such demographic events are predicted to have an erosive effect at the genomic level, linked to the extirpation of diversity, and increased genetic drift and inbreeding. However, there is little empirical data available to directly reconstruct the subtleties of such processes in light of distinct demographic histories. Therefore, we generated a whole-genome, temporal data set consisting of 52 resequenced white rhinoceros genomes, representing both subspecies at two time windows: before and during/after the bottleneck. Our data reveal previously unknown population structure within both subspecies, as well as quantifiable genomic erosion. Genome-wide heterozygosity decreased significantly by 10% in the NWR and 36% in the SWR, and inbreeding coefficients rose significantly by 11% and 39%, respectively. Despite the remarkable loss of genomic diversity and recent inbreeding it suffered, the only surviving subspecies, the SWR, does not show a significant accumulation of genetic load compared to its historical counterpart. Our data provide empirical support for predictions about the genomic consequences of shrinking populations, and our findings have the potential to inform the conservation efforts of the remaining white rhinoceroses.
• 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. The authors are very grateful to all the museums who provided samples for this study: the American Museum of Natural History, the National Museums Scotland, the Natural History Museum at the National Museum Praha, the Natural History Museum Vienna, the Powell-Cotton Museum, the Royal Museum for Central Africa Tervuren, and the Swedish Museum of Natural History.
• dc.format.mimetype application/pdf
• dc.identifier.citation Sánchez-Barreiro F, Gopalakrishnan S, Ramos-Madrigal J, Westbury MV, de Manuel M, Margaryan A, Ciucani MM, Vieira FG, Patramanis Y, Kalthoff DC, Timmons Z, Sicheritz-Pontén T, Dalén L, Ryder OA, Zhang G, Marquès-Bonet T, Moodley Y, Gilbert MTP. Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros (Ceratotherium simum). Mol Ecol. 2021;30(23):6355-69. DOI: 10.1111/mec.16043
• dc.identifier.doi http://dx.doi.org/10.1111/mec.16043
• dc.identifier.issn 0962-1083
• dc.identifier.uri http://hdl.handle.net/10230/49129
• dc.language.iso eng
• dc.publisher Wiley
• dc.relation.ispartof Mol Ecol. 2021;30(23):6355-69
• dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/681396
• dc.rights © 2021 The Authors. Molecular Ecology published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by-nc/4.0/
• dc.subject.keyword Conservation genomics
• dc.subject.keyword Genomic erosion
• dc.subject.keyword Northern white rhinoceros
• dc.subject.keyword Population decline
• dc.subject.keyword Southern white rhinoceros
• dc.title Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros (Ceratotherium simum)
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion