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Whole genome analysis of clouded leopard species reveals an ancient divergence and distinct demographic histories

Bursell, Madeline G., Dikow, Rebecca B., Figueiró, Henrique V., Dudchenko, Olga, Flanagan, Joseph P., Aiden, Erez Lieberman, Goossens, Benoit ORCID:, Nathan, Senthilvel K.S.S., Johnson, Warren E., Koepfli, Klaus-Peter and Frandsen, Paul B. 2022. Whole genome analysis of clouded leopard species reveals an ancient divergence and distinct demographic histories. iScience , 105647. 10.1016/j.isci.2022.105647

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Similar to other apex predator species, populations of mainland (Neofelis nebulosa) and Sunda (Neofelis diardi) clouded leopards are declining. Understanding their patterns of genetic variation can provide critical insights on past genetic erosion and a baseline for understanding their long-term conservation needs. As a step toward this goal, we present draft genome assemblies for the two clouded leopard species to quantify their phylogenetic divergence, genome-wide diversity, and historical population trends. We estimate that the two species diverged 5.1 Mya, much earlier than previous estimates of 1.41 Mya and 2.86 Mya, suggesting they separated when Sundaland was becoming increasingly isolated from mainland Southeast Asia. The Sunda clouded leopard displays a distinct and reduced effective population size trajectory, consistent with a lower genome-wide heterozygosity and SNP density, relative to the mainland clouded leopard. Our results provide new insights into the evolutionary history and genetic health of this unique lineage of felids.

Item Type: Article
Date Type: Published Online
Status: Published
Schools: Biosciences
Publisher: Cell Press
ISSN: 2589-0042
Date of First Compliant Deposit: 16 December 2022
Date of Acceptance: 18 November 2022
Last Modified: 16 May 2023 04:46

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