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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ftdoajarticles:oai:doaj.org/article:1be0a5ec259e4709bdcac04d7e1be19d 2023-05-15T18:50:27+02:00 Bottleneck‐associated changes in the genomic landscape of genetic diversity in wild lynx populations Maria Lucena‐Perez Daniel Kleinman‐Ruiz Elena Marmesat Alexander P. Saveljev Krzysztof Schmidt José A. Godoy 2021-11-01T00:00:00Z https://doi.org/10.1111/eva.13302 https://doaj.org/article/1be0a5ec259e4709bdcac04d7e1be19d EN eng Wiley https://doi.org/10.1111/eva.13302 https://doaj.org/toc/1752-4571 1752-4571 doi:10.1111/eva.13302 https://doaj.org/article/1be0a5ec259e4709bdcac04d7e1be19d Evolutionary Applications, Vol 14, Iss 11, Pp 2664-2679 (2021) bottleneck endangered species genetic diversity genetic drift genetic erosion genetic load Evolution QH359-425 article 2021 ftdoajarticles https://doi.org/10.1111/eva.13302 2022-12-31T10:36:25Z 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. Article in Journal/Newspaper Lynx Lynx lynx lynx Directory of Open Access Journals: DOAJ Articles Evolutionary Applications 14 11 2664 2679 |
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Open Polar |
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Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
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 |
topic_facet |
bottleneck endangered species genetic diversity genetic drift genetic erosion genetic load Evolution QH359-425 |
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 in Journal/Newspaper |
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://doi.org/10.1111/eva.13302 https://doaj.org/article/1be0a5ec259e4709bdcac04d7e1be19d |
genre |
Lynx Lynx lynx lynx |
genre_facet |
Lynx Lynx lynx lynx |
op_source |
Evolutionary Applications, Vol 14, Iss 11, Pp 2664-2679 (2021) |
op_relation |
https://doi.org/10.1111/eva.13302 https://doaj.org/toc/1752-4571 1752-4571 doi:10.1111/eva.13302 https://doaj.org/article/1be0a5ec259e4709bdcac04d7e1be19d |
op_doi |
https://doi.org/10.1111/eva.13302 |
container_title |
Evolutionary Applications |
container_volume |
14 |
container_issue |
11 |
container_start_page |
2664 |
op_container_end_page |
2679 |
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1766244188793339904 |