Bottleneck‐associated changes in the genomic landscape of genetic diversity in wild lynx populations
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 f...
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ftpubmed:oai:pubmedcentral.nih.gov:8591332 2023-05-15T18:50:27+02:00 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. 2021-10-08 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8591332/ http://www.ncbi.nlm.nih.gov/pubmed/34815746 https://doi.org/10.1111/eva.13302 en eng John Wiley and Sons Inc. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8591332/ http://www.ncbi.nlm.nih.gov/pubmed/34815746 http://dx.doi.org/10.1111/eva.13302 © 2021 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd. https://creativecommons.org/licenses/by/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. CC-BY Evol Appl Original Articles Text 2021 ftpubmed https://doi.org/10.1111/eva.13302 2021-11-28T01:26:46Z 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. Text Lynx Lynx lynx lynx PubMed Central (PMC) Evolutionary Applications 14 11 2664 2679 |
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Original Articles |
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Original Articles 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 |
topic_facet |
Original Articles |
description |
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. |
format |
Text |
author |
Lucena‐Perez, Maria Kleinman‐Ruiz, Daniel Marmesat, Elena Saveljev, Alexander P. Schmidt, Krzysztof Godoy, José A. |
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 |
John Wiley and Sons Inc. |
publishDate |
2021 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8591332/ http://www.ncbi.nlm.nih.gov/pubmed/34815746 https://doi.org/10.1111/eva.13302 |
genre |
Lynx Lynx lynx lynx |
genre_facet |
Lynx Lynx lynx lynx |
op_source |
Evol Appl |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8591332/ http://www.ncbi.nlm.nih.gov/pubmed/34815746 http://dx.doi.org/10.1111/eva.13302 |
op_rights |
© 2021 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd. https://creativecommons.org/licenses/by/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. |
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CC-BY |
op_doi |
https://doi.org/10.1111/eva.13302 |
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Evolutionary Applications |
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14 |
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2679 |
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