Data from: Detecting genotypic changes associated with selective mortality at sea in Atlantic salmon: polygenic multi-locus analysis surpasses genome scan
Wild populations of Atlantic salmon have declined worldwide. While the causes for this decline may be complex and numerous, increased mortality at sea is predicted to be one of the major contributing factors. Examining the potential changes occurring in the genome-wide composition of populations dur...
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Online Access: | https://doi.org/10.5061/dryad.j86v9 |
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fttriple:oai:gotriple.eu:50|dedup_wf_001::8e21eef7c5af44cb35e1d2fa17c36961 2023-05-15T15:31:28+02:00 Data from: Detecting genotypic changes associated with selective mortality at sea in Atlantic salmon: polygenic multi-locus analysis surpasses genome scan Bourret, Vincent Dionne, Mélanie Bernatchez, Louis 2020-07-18 https://doi.org/10.5061/dryad.j86v9 en eng Dryad http://dx.doi.org/10.5061/dryad.j86v9 https://dx.doi.org/10.5061/dryad.j86v9 lic_creative-commons 10.5061/dryad.j86v9 oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:85965 oai:easy.dans.knaw.nl:easy-dataset:85965 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 re3data_____::r3d100000044 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c single nucleotide polymorphism Mortality at sea Fisheries Management Salmo salar conservation salmonids Contemporary Evolution Life sciences medicine and health care Local adaptation North America Canada Québec envir anthro-se Dataset https://vocabularies.coar-repositories.org/resource_types/c_ddb1/ 2020 fttriple https://doi.org/10.5061/dryad.j86v9 2023-01-22T17:08:26Z Wild populations of Atlantic salmon have declined worldwide. While the causes for this decline may be complex and numerous, increased mortality at sea is predicted to be one of the major contributing factors. Examining the potential changes occurring in the genome-wide composition of populations during this migration has the potential to tease apart some of the factors influencing marine mortality. Here, we genotyped 5568 SNPs in Atlantic salmon populations representing two distinct regional genetic groups and across two cohorts to test for differential allelic and genotypic frequencies between juveniles (smolts) migrating to sea and adults (grilses) returning to freshwater after one year at sea. Given the complexity of the traits potentially associated with sea mortality, we contrasted the outcomes of a single-locus FST based genome scan method with a new multi-locus framework to test for genetically-based differential mortality at sea. While numerous outliers were identified by the single-locus analysis, no evidence for parallel, temporally repeated selection was found. In contrast, the multi-locus approach detected repeated patterns of selection for a multi-locus group of 34 co-varying SNPs in one of the two populations. No significant pattern of selective mortality was detected in the other population, suggesting different causes of mortality among populations. These results first support the hypothesis that selection mainly causes small changes in allele frequencies among many co-varying loci rather than a small number of changes in loci with large effects. They also point out that moving away from the a strict “selective sweep paradigm” towards a multi-locus genetics framework may be a more useful approach for studying the genomic signatures of natural selection on complex traits in wild populations. Genotypes_PowerMarkerGenotype file for 2923 SNPs retained for analyses performed in the article.Donnees_genet SAS 2923Input file for SAS analysesSAS Discriminant AnalysisSAS analyses ... Dataset Atlantic salmon Salmo salar Unknown Canada |
institution |
Open Polar |
collection |
Unknown |
op_collection_id |
fttriple |
language |
English |
topic |
single nucleotide polymorphism Mortality at sea Fisheries Management Salmo salar conservation salmonids Contemporary Evolution Life sciences medicine and health care Local adaptation North America Canada Québec envir anthro-se |
spellingShingle |
single nucleotide polymorphism Mortality at sea Fisheries Management Salmo salar conservation salmonids Contemporary Evolution Life sciences medicine and health care Local adaptation North America Canada Québec envir anthro-se Bourret, Vincent Dionne, Mélanie Bernatchez, Louis Data from: Detecting genotypic changes associated with selective mortality at sea in Atlantic salmon: polygenic multi-locus analysis surpasses genome scan |
topic_facet |
single nucleotide polymorphism Mortality at sea Fisheries Management Salmo salar conservation salmonids Contemporary Evolution Life sciences medicine and health care Local adaptation North America Canada Québec envir anthro-se |
description |
Wild populations of Atlantic salmon have declined worldwide. While the causes for this decline may be complex and numerous, increased mortality at sea is predicted to be one of the major contributing factors. Examining the potential changes occurring in the genome-wide composition of populations during this migration has the potential to tease apart some of the factors influencing marine mortality. Here, we genotyped 5568 SNPs in Atlantic salmon populations representing two distinct regional genetic groups and across two cohorts to test for differential allelic and genotypic frequencies between juveniles (smolts) migrating to sea and adults (grilses) returning to freshwater after one year at sea. Given the complexity of the traits potentially associated with sea mortality, we contrasted the outcomes of a single-locus FST based genome scan method with a new multi-locus framework to test for genetically-based differential mortality at sea. While numerous outliers were identified by the single-locus analysis, no evidence for parallel, temporally repeated selection was found. In contrast, the multi-locus approach detected repeated patterns of selection for a multi-locus group of 34 co-varying SNPs in one of the two populations. No significant pattern of selective mortality was detected in the other population, suggesting different causes of mortality among populations. These results first support the hypothesis that selection mainly causes small changes in allele frequencies among many co-varying loci rather than a small number of changes in loci with large effects. They also point out that moving away from the a strict “selective sweep paradigm” towards a multi-locus genetics framework may be a more useful approach for studying the genomic signatures of natural selection on complex traits in wild populations. Genotypes_PowerMarkerGenotype file for 2923 SNPs retained for analyses performed in the article.Donnees_genet SAS 2923Input file for SAS analysesSAS Discriminant AnalysisSAS analyses ... |
format |
Dataset |
author |
Bourret, Vincent Dionne, Mélanie Bernatchez, Louis |
author_facet |
Bourret, Vincent Dionne, Mélanie Bernatchez, Louis |
author_sort |
Bourret, Vincent |
title |
Data from: Detecting genotypic changes associated with selective mortality at sea in Atlantic salmon: polygenic multi-locus analysis surpasses genome scan |
title_short |
Data from: Detecting genotypic changes associated with selective mortality at sea in Atlantic salmon: polygenic multi-locus analysis surpasses genome scan |
title_full |
Data from: Detecting genotypic changes associated with selective mortality at sea in Atlantic salmon: polygenic multi-locus analysis surpasses genome scan |
title_fullStr |
Data from: Detecting genotypic changes associated with selective mortality at sea in Atlantic salmon: polygenic multi-locus analysis surpasses genome scan |
title_full_unstemmed |
Data from: Detecting genotypic changes associated with selective mortality at sea in Atlantic salmon: polygenic multi-locus analysis surpasses genome scan |
title_sort |
data from: detecting genotypic changes associated with selective mortality at sea in atlantic salmon: polygenic multi-locus analysis surpasses genome scan |
publisher |
Dryad |
publishDate |
2020 |
url |
https://doi.org/10.5061/dryad.j86v9 |
geographic |
Canada |
geographic_facet |
Canada |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_source |
10.5061/dryad.j86v9 oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:85965 oai:easy.dans.knaw.nl:easy-dataset:85965 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 re3data_____::r3d100000044 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c |
op_relation |
http://dx.doi.org/10.5061/dryad.j86v9 https://dx.doi.org/10.5061/dryad.j86v9 |
op_rights |
lic_creative-commons |
op_doi |
https://doi.org/10.5061/dryad.j86v9 |
_version_ |
1766361980904407040 |