Dataset Information

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

ABSTRACT: 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.

SUBMITTER: Bursell MG

PROVIDER: S-EPMC9801239 | biostudies-literature | 2022 Dec

REPOSITORIES: biostudies-literature

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

Bursell Madeline G MG Dikow Rebecca B RB Figueiró Henrique V HV Dudchenko Olga O Flanagan Joseph P JP Aiden Erez Lieberman EL Goossens Benoit B Nathan Senthilvel K S S SKSS Johnson Warren E WE Koepfli Klaus-Peter KP Frandsen Paul B PB

iScience 20221209 12

Similar to other apex predator species, populations of mainland (<i>Neofelis nebulosa</i>) and Sunda (<i>Neofelis diardi</i>) 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 ...[more]

PMID: 36590460

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Project description:BackgroundRevealing the past and present demographic history of populations is of high importance to evaluate the conservation status of species. Demographic data can be obtained by direct monitoring or by analysing data of historical and recent collections. Although these methods provide the most detailed information they are very time consuming. Another alternative way is to make use of the information accumulated in the species' DNA over its history. Recent development of the coalescent theory makes it possible to reconstruct the demographic history of species using nucleotide polymorphism data. To separate the effect of natural selection and demography, multilocus analysis is needed because these two forces can produce similar patterns of polymorphisms. In this study we investigated the amount and pattern of sequence variability of a Europe wide sample set of two peat moss species (Sphagnum fimbriatum and S. squarrosum) with similar distributions and mating systems but presumably contrasting historical demographies using 3 regions of the nuclear genome (appr. 3000 bps). We aimed to draw inferences concerning demographic, and phylogeographic histories of the species.ResultsAll three nuclear regions supported the presence of an Atlantic and Non-Atlantic clade of S. fimbriatum suggesting glacial survival of the species along the Atlantic coast of Europe. Contrarily, S. squarrosum haplotypes showed three clades but no geographic structure at all. Maximum likelihood, mismatch and Bayesian analyses supported a severe historical bottleneck and a relatively recent demographic expansion of the Non-Atlantic clade of S. fimbriatum, whereas size of S. squarrosum populations has probably decreased in the past. Species wide molecular diversity of the two species was nearly the same with an excess of replacement mutations in S. fimbriatum. Similar levels of molecular diversity, contrasting phylogeographic patterns and excess of replacement mutations in S. fimbriatum compared to S. squarrosum mirror unexpected differences in the demography and population history of the species.ConclusionThis study represents the first detailed European wide phylodemographic investigation on bryophytes and shows how pattern of nucleotide polymorphism can reveal unexpected differences in the population history of haploid plants with seemingly similar characteristics.

Dataset Information

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

Publications

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

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