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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Online Access: | http://hdl.handle.net/10261/252552 https://doi.org/10.1111/eva.13302 https://doi.org/10.13039/501100004837 |
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ftcsic:oai:digital.csic.es:10261/252552 2024-02-11T10:09:32+01:00 Bottleneck-associated changes in the genomic landscape of genetic diversity in wild lynx populations Lucena-Pérez, María Kleinman-Ruiz, Daniel Marmesat, Elena Saveljev,Alexander P. Schmidt, Krzysztof Godoy, José A. Ministerio de Ciencia e Innovación (España) 2021 http://hdl.handle.net/10261/252552 https://doi.org/10.1111/eva.13302 https://doi.org/10.13039/501100004837 en eng John Wiley & Sons #PLACEHOLDER_PARENT_METADATA_VALUE# info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PGC2018-095810-B-I00 Publisher's version https://doi.org/10.1111/eva.13302 Sí Evolutionary Applications, (2021) http://hdl.handle.net/10261/252552 doi:10.1111/eva.13302 http://dx.doi.org/10.13039/501100004837 open artículo http://purl.org/coar/resource_type/c_6501 2021 ftcsic https://doi.org/10.1111/eva.1330210.13039/501100004837 2024-01-16T11:14:37Z 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. Peer reviewed Article in Journal/Newspaper Lynx Lynx lynx lynx Digital.CSIC (Spanish National Research Council) Evolutionary Applications |
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Open Polar |
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Digital.CSIC (Spanish National Research Council) |
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ftcsic |
language |
English |
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 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. Peer reviewed |
author2 |
Ministerio de Ciencia e Innovación (España) |
format |
Article in Journal/Newspaper |
author |
Lucena-Pérez, María Kleinman-Ruiz, Daniel Marmesat, Elena Saveljev,Alexander P. Schmidt, Krzysztof Godoy, José A. |
spellingShingle |
Lucena-Pérez, María 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-Pérez, María Kleinman-Ruiz, Daniel Marmesat, Elena Saveljev,Alexander P. Schmidt, Krzysztof Godoy, José A. |
author_sort |
Lucena-Pérez, María |
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 & Sons |
publishDate |
2021 |
url |
http://hdl.handle.net/10261/252552 https://doi.org/10.1111/eva.13302 https://doi.org/10.13039/501100004837 |
genre |
Lynx Lynx lynx lynx |
genre_facet |
Lynx Lynx lynx lynx |
op_relation |
#PLACEHOLDER_PARENT_METADATA_VALUE# info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PGC2018-095810-B-I00 Publisher's version https://doi.org/10.1111/eva.13302 Sí Evolutionary Applications, (2021) http://hdl.handle.net/10261/252552 doi:10.1111/eva.13302 http://dx.doi.org/10.13039/501100004837 |
op_rights |
open |
op_doi |
https://doi.org/10.1111/eva.1330210.13039/501100004837 |
container_title |
Evolutionary Applications |
_version_ |
1790609461716451328 |