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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crwiley:10.1111/eva.13302 2024-09-09T20:14:28+00:00 Bottleneck‐associated changes in the genomic landscape of genetic diversity in wild lynx populations Lucena‐Perez, Maria Kleinman‐Ruiz, Daniel Marmesat, Elena Saveljev, Alexander P. Schmidt, Krzysztof Godoy, José A. Dirección General de Investigación Científica y Técnica Russian Science Foundation “la Caixa” Foundation Narodowe Centrum Nauki FP7 People: Marie-Curie Actions 2021 http://dx.doi.org/10.1111/eva.13302 https://onlinelibrary.wiley.com/doi/pdf/10.1111/eva.13302 https://onlinelibrary.wiley.com/doi/full-xml/10.1111/eva.13302 en eng Wiley http://creativecommons.org/licenses/by/4.0/ Evolutionary Applications volume 14, issue 11, page 2664-2679 ISSN 1752-4571 1752-4571 journal-article 2021 crwiley https://doi.org/10.1111/eva.13302 2024-06-20T04:23:34Z 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 θ W 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 Wiley Online Library Evolutionary Applications 14 11 2664 2679 |
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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 θ W 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. |
author2 |
Dirección General de Investigación Científica y Técnica Russian Science Foundation “la Caixa” Foundation Narodowe Centrum Nauki FP7 People: Marie-Curie Actions |
format |
Article in Journal/Newspaper |
author |
Lucena‐Perez, Maria Kleinman‐Ruiz, Daniel Marmesat, Elena Saveljev, Alexander P. Schmidt, Krzysztof Godoy, José A. |
spellingShingle |
Lucena‐Perez, Maria Kleinman‐Ruiz, Daniel Marmesat, Elena Saveljev, Alexander P. Schmidt, Krzysztof Godoy, José A. Bottleneck‐associated changes in the genomic landscape of genetic diversity in wild lynx populations |
author_facet |
Lucena‐Perez, Maria Kleinman‐Ruiz, Daniel Marmesat, Elena Saveljev, Alexander P. Schmidt, Krzysztof Godoy, José A. |
author_sort |
Lucena‐Perez, Maria |
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 |
http://dx.doi.org/10.1111/eva.13302 https://onlinelibrary.wiley.com/doi/pdf/10.1111/eva.13302 https://onlinelibrary.wiley.com/doi/full-xml/10.1111/eva.13302 |
genre |
Lynx Lynx lynx lynx |
genre_facet |
Lynx Lynx lynx lynx |
op_source |
Evolutionary Applications volume 14, issue 11, page 2664-2679 ISSN 1752-4571 1752-4571 |
op_rights |
http://creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/10.1111/eva.13302 |
container_title |
Evolutionary Applications |
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14 |
container_issue |
11 |
container_start_page |
2664 |
op_container_end_page |
2679 |
_version_ |
1809816129595506688 |