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Ancient and modern genomes unravel the evolutionary history of the rhinoceros family

Liu, Shanlin, Westbury, Michael V., Dussex, Nicolas, Mitchell, Kieren J., Sinding, Mikkel-Holger S., Heintzman, Peter D., Duchêne, David A., Kapp, Joshua D., von Seth, Johanna, Heiniger, Holly, Sánchez-Barreiro, Fátima, Margaryan, Ashot, André-Olsen, Remi, De Cahsan, Binia, Meng, Guanliang, Yang, Chentao, Chen, Lei, van der Valk, Tom, Moodley, Yoshan, Rookmaaker, Kees, Bruford, Michael W., Ryder, Oliver, Steiner, Cynthia, Bruins-van Sonsbeek, Linda G.R., Vartanyan, Sergey, Guo, Chunxue, Cooper, Alan, Kosintsev, Pavel, Kirillova, Irina, Lister, Adrian M., Marques-Bonet, Tomas, Gopalakrishnan, Shyam, Dunn, Robert R., Lorenzen, Eline D., Shapiro, Beth, Zhang, Guojie, Antoine, Pierre-Olivier, Dalén, Love and Gilbert, M. Thomas P. 2021. Ancient and modern genomes unravel the evolutionary history of the rhinoceros family. Cell 184 (19) , pp. 4874-4885. 10.1016/j.cell.2021.07.032

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Abstract

Only five species of the once-diverse Rhinocerotidae remain, making the reconstruction of their evolutionary history a challenge to biologists since Darwin. We sequenced genomes from five rhinoceros species (three extinct and two living), which we compared to existing data from the remaining three living species and a range of outgroups. We identify an early divergence between extant African and Eurasian lineages, resolving a key debate regarding the phylogeny of extant rhinoceroses. This early Miocene (∼16 million years ago [mya]) split post-dates the land bridge formation between the Afro-Arabian and Eurasian landmasses. Our analyses also show that while rhinoceros genomes in general exhibit low levels of genome-wide diversity, heterozygosity is lowest and inbreeding is highest in the modern species. These results suggest that while low genetic diversity is a long-term feature of the family, it has been particularly exacerbated recently, likely reflecting recent anthropogenic-driven population declines.

Item Type: Article
Date Type: Publication
Status: Published
Schools: Biosciences
Additional Information: This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
Publisher: Elsevier
ISSN: 0092-8674
Date of First Compliant Deposit: 3 September 2021
Date of Acceptance: 23 July 2021
Last Modified: 12 Oct 2021 13:56
URI: https://orca.cardiff.ac.uk/id/eprint/143863

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