Thermal adaptation rather than demographic history drives genetic structure inferred by copy number variants in a marine fish.
Increasing evidence shows that structural variants represent an overlooked aspect of genetic variation with consequential evolutionary roles. Among those, copy number variants (CNVs), including duplicated genomic regions and transposable elements (TEs), may contribute to local adaptation and/or repr...
Published in: | Molecular Ecology |
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2021
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Online Access: | https://serval.unil.ch/notice/serval:BIB_8D67B8B76E4B https://doi.org/10.1111/mec.15835 |
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ftunivlausanne:oai:serval.unil.ch:BIB_8D67B8B76E4B 2024-02-11T10:06:42+01:00 Thermal adaptation rather than demographic history drives genetic structure inferred by copy number variants in a marine fish. Cayuela, H. Dorant, Y. Mérot, C. Laporte, M. Normandeau, E. Gagnon-Harvey, S. Clément, M. Sirois, P. Bernatchez, L. 2021-04 https://serval.unil.ch/notice/serval:BIB_8D67B8B76E4B https://doi.org/10.1111/mec.15835 eng eng info:eu-repo/semantics/altIdentifier/doi/10.1111/mec.15835 info:eu-repo/semantics/altIdentifier/pmid/33565147 info:eu-repo/semantics/altIdentifier/eissn/1365-294X info:eu-repo/grantAgreement/SNF/Projects/31003A_182265/// https://serval.unil.ch/notice/serval:BIB_8D67B8B76E4B doi:10.1111/mec.15835 urn:issn:0962-1083 Molecular ecology, vol. 30, no. 7, pp. 1624-1641 Amplified Fragment Length Polymorphism Analysis Animals Atlantic Ocean DNA Copy Number Variations/genetics Demography Female Genome Polymorphism Single Nucleotide copy number variants fish local adaptation population genetic structure reproductive isolation structural variants transposable elements info:eu-repo/semantics/article article 2021 ftunivlausanne https://doi.org/10.1111/mec.15835 2024-01-22T01:04:10Z Increasing evidence shows that structural variants represent an overlooked aspect of genetic variation with consequential evolutionary roles. Among those, copy number variants (CNVs), including duplicated genomic regions and transposable elements (TEs), may contribute to local adaptation and/or reproductive isolation among divergent populations. Those mechanisms suppose that CNVs could be used to infer neutral and/or adaptive population genetic structure, whose study has been restricted to microsatellites, mitochondrial DNA and Amplified fragment length polymorphism markers in the past and more recently the use of single nucleotide polymorphisms (SNPs). Taking advantage of recent developments allowing CNV analysis from RAD-seq data, we investigated how variation in fitness-related traits, local environmental conditions and demographic history are associated with CNVs, and how subsequent copy number variation drives population genetic structure in a marine fish, the capelin (Mallotus villosus). We collected 1538 DNA samples from 35 sampling sites in the north Atlantic Ocean and identified 6620 putative CNVs. We found associations between CNVs and the gonadosomatic index, suggesting that six duplicated regions could affect female fitness by modulating oocyte production. We also detected 105 CNV candidates associated with water temperature, among which 20% corresponded to genomic regions located within the sequence of protein-coding genes, suggesting local adaptation to cold water by means of gene sequence amplification. We also identified 175 CNVs associated with the divergence of three previously defined parapatric glacial lineages, of which 24% were located within protein-coding genes, making those loci potential candidates for reproductive isolation. Lastly, our analyses unveiled a hierarchical, complex CNV population structure determined by temperature and local geography, which was in stark contrast to that inferred based on SNPs in a previous study. Our findings underline the complementarity of those two ... Article in Journal/Newspaper North Atlantic Université de Lausanne (UNIL): Serval - Serveur académique lausannois Molecular Ecology 30 7 1624 1641 |
institution |
Open Polar |
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Université de Lausanne (UNIL): Serval - Serveur académique lausannois |
op_collection_id |
ftunivlausanne |
language |
English |
topic |
Amplified Fragment Length Polymorphism Analysis Animals Atlantic Ocean DNA Copy Number Variations/genetics Demography Female Genome Polymorphism Single Nucleotide copy number variants fish local adaptation population genetic structure reproductive isolation structural variants transposable elements |
spellingShingle |
Amplified Fragment Length Polymorphism Analysis Animals Atlantic Ocean DNA Copy Number Variations/genetics Demography Female Genome Polymorphism Single Nucleotide copy number variants fish local adaptation population genetic structure reproductive isolation structural variants transposable elements Cayuela, H. Dorant, Y. Mérot, C. Laporte, M. Normandeau, E. Gagnon-Harvey, S. Clément, M. Sirois, P. Bernatchez, L. Thermal adaptation rather than demographic history drives genetic structure inferred by copy number variants in a marine fish. |
topic_facet |
Amplified Fragment Length Polymorphism Analysis Animals Atlantic Ocean DNA Copy Number Variations/genetics Demography Female Genome Polymorphism Single Nucleotide copy number variants fish local adaptation population genetic structure reproductive isolation structural variants transposable elements |
description |
Increasing evidence shows that structural variants represent an overlooked aspect of genetic variation with consequential evolutionary roles. Among those, copy number variants (CNVs), including duplicated genomic regions and transposable elements (TEs), may contribute to local adaptation and/or reproductive isolation among divergent populations. Those mechanisms suppose that CNVs could be used to infer neutral and/or adaptive population genetic structure, whose study has been restricted to microsatellites, mitochondrial DNA and Amplified fragment length polymorphism markers in the past and more recently the use of single nucleotide polymorphisms (SNPs). Taking advantage of recent developments allowing CNV analysis from RAD-seq data, we investigated how variation in fitness-related traits, local environmental conditions and demographic history are associated with CNVs, and how subsequent copy number variation drives population genetic structure in a marine fish, the capelin (Mallotus villosus). We collected 1538 DNA samples from 35 sampling sites in the north Atlantic Ocean and identified 6620 putative CNVs. We found associations between CNVs and the gonadosomatic index, suggesting that six duplicated regions could affect female fitness by modulating oocyte production. We also detected 105 CNV candidates associated with water temperature, among which 20% corresponded to genomic regions located within the sequence of protein-coding genes, suggesting local adaptation to cold water by means of gene sequence amplification. We also identified 175 CNVs associated with the divergence of three previously defined parapatric glacial lineages, of which 24% were located within protein-coding genes, making those loci potential candidates for reproductive isolation. Lastly, our analyses unveiled a hierarchical, complex CNV population structure determined by temperature and local geography, which was in stark contrast to that inferred based on SNPs in a previous study. Our findings underline the complementarity of those two ... |
format |
Article in Journal/Newspaper |
author |
Cayuela, H. Dorant, Y. Mérot, C. Laporte, M. Normandeau, E. Gagnon-Harvey, S. Clément, M. Sirois, P. Bernatchez, L. |
author_facet |
Cayuela, H. Dorant, Y. Mérot, C. Laporte, M. Normandeau, E. Gagnon-Harvey, S. Clément, M. Sirois, P. Bernatchez, L. |
author_sort |
Cayuela, H. |
title |
Thermal adaptation rather than demographic history drives genetic structure inferred by copy number variants in a marine fish. |
title_short |
Thermal adaptation rather than demographic history drives genetic structure inferred by copy number variants in a marine fish. |
title_full |
Thermal adaptation rather than demographic history drives genetic structure inferred by copy number variants in a marine fish. |
title_fullStr |
Thermal adaptation rather than demographic history drives genetic structure inferred by copy number variants in a marine fish. |
title_full_unstemmed |
Thermal adaptation rather than demographic history drives genetic structure inferred by copy number variants in a marine fish. |
title_sort |
thermal adaptation rather than demographic history drives genetic structure inferred by copy number variants in a marine fish. |
publishDate |
2021 |
url |
https://serval.unil.ch/notice/serval:BIB_8D67B8B76E4B https://doi.org/10.1111/mec.15835 |
genre |
North Atlantic |
genre_facet |
North Atlantic |
op_source |
Molecular ecology, vol. 30, no. 7, pp. 1624-1641 |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1111/mec.15835 info:eu-repo/semantics/altIdentifier/pmid/33565147 info:eu-repo/semantics/altIdentifier/eissn/1365-294X info:eu-repo/grantAgreement/SNF/Projects/31003A_182265/// https://serval.unil.ch/notice/serval:BIB_8D67B8B76E4B doi:10.1111/mec.15835 urn:issn:0962-1083 |
op_doi |
https://doi.org/10.1111/mec.15835 |
container_title |
Molecular Ecology |
container_volume |
30 |
container_issue |
7 |
container_start_page |
1624 |
op_container_end_page |
1641 |
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1790604604414623744 |