Thermal adaptation rather than demographic history drives genetic structure inferred by copy number variants in a marine fish

Details

Serval ID
serval:BIB_8D67B8B76E4B
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Thermal adaptation rather than demographic history drives genetic structure inferred by copy number variants in a marine fish
Journal
Molecular Ecology
Author(s)
Cayuela H., Dorant Y., Mérot C., Laporte M., Normandeau E., Gagnon-Harvey S., Clément M., Sirois P., Bernatchez L.
ISSN
1365-294X (Electronic)
ISSN-L
0962-1083
Publication state
Published
Issued date
10/02/2021
Peer-reviewed
Oui
Volume
30
Pages
1624-1641
Language
english
Notes
Publication types: Journal Article
Publication Status: aheadofprint
Abstract
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 region 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, mtDNA, and AFLP markers in the past and more recently the use of 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 with that inferred based on SNPs in a previous study. Our findings underscore the complementarity of those two types of genomic variation in population genomics studies.
Keywords
copy number variants, fish, local adaptation, population genetic structure, reproductive isolation, structural variants, transposable elements
Pubmed
Funding(s)
Swiss National Science Foundation / Projects / 31003A_182265
Create date
15/02/2021 10:24
Last modification date
01/06/2021 6:37
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