Bottleneck‐associated changes in the genomic landscape of genetic diversity in wild lynx populations

Abstract Demographic bottlenecks generally reduce genetic diversity through more intense genetic drift, but their net effect may vary along the genome due to the random nature of genetic drift and to local effects of recombination, mutation, and selection. Here, we analyzed the changes in genetic di...

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Autores principales:	Maria Lucena‐Perez, Daniel Kleinman‐Ruiz, Elena Marmesat, Alexander P. Saveljev, Krzysztof Schmidt, José A. Godoy
Formato:	article
Lenguaje:	EN
Publicado:	Wiley 2021
Materias:	bottleneck endangered species genetic diversity genetic drift genetic erosion genetic load Evolution QH359-425
Acceso en línea:	https://doaj.org/article/1be0a5ec259e4709bdcac04d7e1be19d
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spelling	oai:doaj.org-article:1be0a5ec259e4709bdcac04d7e1be19d2021-11-15T07:15:49ZBottleneck‐associated changes in the genomic landscape of genetic diversity in wild lynx populations1752-457110.1111/eva.13302https://doaj.org/article/1be0a5ec259e4709bdcac04d7e1be19d2021-11-01T00:00:00Zhttps://doi.org/10.1111/eva.13302https://doaj.org/toc/1752-4571Abstract Demographic bottlenecks generally reduce genetic diversity through more intense genetic drift, but their net effect may vary along the genome due to the random nature of genetic drift and to local effects of recombination, mutation, and selection. Here, we analyzed the changes in genetic diversity following a bottleneck by comparing whole‐genome diversity patterns in populations with and without severe recent documented declines of Iberian (Lynx pardinus, n = 31) and Eurasian lynx (Lynx lynx, n = 29). As expected, overall genomic diversity correlated negatively with bottleneck intensity and/or duration. Correlations of genetic diversity with divergence, chromosome size, gene or functional site content, GC content, or recombination were observed in nonbottlenecked populations, but were weaker in bottlenecked populations. Also, functional features under intense purifying selection and the X chromosome showed an increase in the observed density of variants, even resulting in higher θW diversity than in nonbottlenecked populations. Increased diversity seems to be related to both a higher mutational input in those regions creating a large collection of low‐frequency variants, a few of which increase in frequency during the bottleneck to the point they become detectable with our limited sample, and the reduced efficacy of purifying selection, which affects not only protein structure and function but also the regulation of gene expression. The results of this study alert to the possible reduction of fitness and adaptive potential associated with the genomic erosion in regulatory elements. Further, the detection of a gain of diversity in ultra‐conserved elements can be used as a sensitive and easy‐to‐apply signature of genetic erosion in wild populations.Maria Lucena‐PerezDaniel Kleinman‐RuizElena MarmesatAlexander P. SaveljevKrzysztof SchmidtJosé A. GodoyWileyarticlebottleneckendangered speciesgenetic diversitygenetic driftgenetic erosiongenetic loadEvolutionQH359-425ENEvolutionary Applications, Vol 14, Iss 11, Pp 2664-2679 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	bottleneck endangered species genetic diversity genetic drift genetic erosion genetic load Evolution QH359-425
spellingShingle	bottleneck endangered species genetic diversity genetic drift genetic erosion genetic load Evolution QH359-425 Maria Lucena‐Perez Daniel Kleinman‐Ruiz Elena Marmesat Alexander P. Saveljev Krzysztof Schmidt José A. Godoy Bottleneck‐associated changes in the genomic landscape of genetic diversity in wild lynx populations
description	Abstract Demographic bottlenecks generally reduce genetic diversity through more intense genetic drift, but their net effect may vary along the genome due to the random nature of genetic drift and to local effects of recombination, mutation, and selection. Here, we analyzed the changes in genetic diversity following a bottleneck by comparing whole‐genome diversity patterns in populations with and without severe recent documented declines of Iberian (Lynx pardinus, n = 31) and Eurasian lynx (Lynx lynx, n = 29). As expected, overall genomic diversity correlated negatively with bottleneck intensity and/or duration. Correlations of genetic diversity with divergence, chromosome size, gene or functional site content, GC content, or recombination were observed in nonbottlenecked populations, but were weaker in bottlenecked populations. Also, functional features under intense purifying selection and the X chromosome showed an increase in the observed density of variants, even resulting in higher θW diversity than in nonbottlenecked populations. Increased diversity seems to be related to both a higher mutational input in those regions creating a large collection of low‐frequency variants, a few of which increase in frequency during the bottleneck to the point they become detectable with our limited sample, and the reduced efficacy of purifying selection, which affects not only protein structure and function but also the regulation of gene expression. The results of this study alert to the possible reduction of fitness and adaptive potential associated with the genomic erosion in regulatory elements. Further, the detection of a gain of diversity in ultra‐conserved elements can be used as a sensitive and easy‐to‐apply signature of genetic erosion in wild populations.
format	article
author	Maria Lucena‐Perez Daniel Kleinman‐Ruiz Elena Marmesat Alexander P. Saveljev Krzysztof Schmidt José A. Godoy
author_facet	Maria Lucena‐Perez Daniel Kleinman‐Ruiz Elena Marmesat Alexander P. Saveljev Krzysztof Schmidt José A. Godoy
author_sort	Maria Lucena‐Perez
title	Bottleneck‐associated changes in the genomic landscape of genetic diversity in wild lynx populations
title_short	Bottleneck‐associated changes in the genomic landscape of genetic diversity in wild lynx populations
title_full	Bottleneck‐associated changes in the genomic landscape of genetic diversity in wild lynx populations
title_fullStr	Bottleneck‐associated changes in the genomic landscape of genetic diversity in wild lynx populations
title_full_unstemmed	Bottleneck‐associated changes in the genomic landscape of genetic diversity in wild lynx populations
title_sort	bottleneck‐associated changes in the genomic landscape of genetic diversity in wild lynx populations
publisher	Wiley
publishDate	2021
url	https://doaj.org/article/1be0a5ec259e4709bdcac04d7e1be19d
work_keys_str_mv	AT marialucenaperez bottleneckassociatedchangesinthegenomiclandscapeofgeneticdiversityinwildlynxpopulations AT danielkleinmanruiz bottleneckassociatedchangesinthegenomiclandscapeofgeneticdiversityinwildlynxpopulations AT elenamarmesat bottleneckassociatedchangesinthegenomiclandscapeofgeneticdiversityinwildlynxpopulations AT alexanderpsaveljev bottleneckassociatedchangesinthegenomiclandscapeofgeneticdiversityinwildlynxpopulations AT krzysztofschmidt bottleneckassociatedchangesinthegenomiclandscapeofgeneticdiversityinwildlynxpopulations AT joseagodoy bottleneckassociatedchangesinthegenomiclandscapeofgeneticdiversityinwildlynxpopulations
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Bottleneck‐associated changes in the genomic landscape of genetic diversity in wild lynx populations

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