Data from: SNP-array reveals genome wide patterns of geographical and potential adaptive divergence across the natural range of Atlantic salmon (Salmo salar)
Atlantic salmon (Salmo salar) is one of the most extensively studied fish species in the world due to its significance in aquaculture, fisheries and ongoing conservation efforts to protect declining populations. Yet, limited genomic resources have hampered our understanding of genetic architecture i...
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ftzenodo:oai:zenodo.org:4986095 2023-05-15T15:31:16+02:00 Data from: SNP-array reveals genome wide patterns of geographical and potential adaptive divergence across the natural range of Atlantic salmon (Salmo salar) Bourret, Vincent Kent, Matthew P. Primmer, Craig R. Vasemägi, Anti Karlsson, Sten Hindar, Kjetil McGinnity, Philip Verspoor, Eric Bernatchez, Louis Lien, Sigbjørn 2018-02-15 https://zenodo.org/record/4986095 https://doi.org/10.5061/dryad.gm367 unknown doi:10.1111/mec.12003 https://zenodo.org/communities/dryad https://zenodo.org/record/4986095 https://doi.org/10.5061/dryad.gm367 oai:zenodo.org:4986095 info:eu-repo/semantics/openAccess https://creativecommons.org/publicdomain/zero/1.0/legalcode single nucleotide polymorphism Salmo salar Aquaculture info:eu-repo/semantics/other dataset 2018 ftzenodo https://doi.org/10.5061/dryad.gm36710.1111/mec.12003 2023-03-10T17:38:48Z Atlantic salmon (Salmo salar) is one of the most extensively studied fish species in the world due to its significance in aquaculture, fisheries and ongoing conservation efforts to protect declining populations. Yet, limited genomic resources have hampered our understanding of genetic architecture in the species and the genetic basis of adaptation to the wide range of natural and artificial environments it occupies. In this paper, we describe the development of a medium density Atlantic salmon SNP-array based on Expressed Sequence Tags (ESTs) and genomic sequencing. The array was used in the most extensive assessment of population genetic structure performed to date in this species. A total of 6176 informative SNPs were successfully genotyped in 38 anadromous and freshwater wild populations distributed across the species natural range. Principal component analysis clearly differentiated European and North American populations, and within Europe, three major regional genetic groups were identified for the first time in a single analysis. We assessed the potential for the array to disentangle neutral and putative adaptive divergence of SNP allele frequencies across populations and among regional groups. In Europe, secondary contact zones were identified between major clusters where endogenous and exogenous barriers could be associated, rendering the interpretation of environmental influence on potentially adaptive divergence equivocal. A small number of markers highly divergent in allele frequencies (outliers) were observed between (multiple) freshwater and anadromous populations, between northern and southern latitudes, and when comparing Baltic populations to all others. We also discuss the potential future applications of the SNP-array for conservation, management and aquaculture. Genotypes_Dryad6176 SNP genotypes for 1295 samples used in submitted analysis (all but Foyle River population). For access to genotypes from Foyle River samples, please contact Dr. Dennis Ensing at Agri-Food & Biosciences ... Dataset Atlantic salmon Salmo salar Zenodo |
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unknown |
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single nucleotide polymorphism Salmo salar Aquaculture |
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single nucleotide polymorphism Salmo salar Aquaculture Bourret, Vincent Kent, Matthew P. Primmer, Craig R. Vasemägi, Anti Karlsson, Sten Hindar, Kjetil McGinnity, Philip Verspoor, Eric Bernatchez, Louis Lien, Sigbjørn Data from: SNP-array reveals genome wide patterns of geographical and potential adaptive divergence across the natural range of Atlantic salmon (Salmo salar) |
topic_facet |
single nucleotide polymorphism Salmo salar Aquaculture |
description |
Atlantic salmon (Salmo salar) is one of the most extensively studied fish species in the world due to its significance in aquaculture, fisheries and ongoing conservation efforts to protect declining populations. Yet, limited genomic resources have hampered our understanding of genetic architecture in the species and the genetic basis of adaptation to the wide range of natural and artificial environments it occupies. In this paper, we describe the development of a medium density Atlantic salmon SNP-array based on Expressed Sequence Tags (ESTs) and genomic sequencing. The array was used in the most extensive assessment of population genetic structure performed to date in this species. A total of 6176 informative SNPs were successfully genotyped in 38 anadromous and freshwater wild populations distributed across the species natural range. Principal component analysis clearly differentiated European and North American populations, and within Europe, three major regional genetic groups were identified for the first time in a single analysis. We assessed the potential for the array to disentangle neutral and putative adaptive divergence of SNP allele frequencies across populations and among regional groups. In Europe, secondary contact zones were identified between major clusters where endogenous and exogenous barriers could be associated, rendering the interpretation of environmental influence on potentially adaptive divergence equivocal. A small number of markers highly divergent in allele frequencies (outliers) were observed between (multiple) freshwater and anadromous populations, between northern and southern latitudes, and when comparing Baltic populations to all others. We also discuss the potential future applications of the SNP-array for conservation, management and aquaculture. Genotypes_Dryad6176 SNP genotypes for 1295 samples used in submitted analysis (all but Foyle River population). For access to genotypes from Foyle River samples, please contact Dr. Dennis Ensing at Agri-Food & Biosciences ... |
format |
Dataset |
author |
Bourret, Vincent Kent, Matthew P. Primmer, Craig R. Vasemägi, Anti Karlsson, Sten Hindar, Kjetil McGinnity, Philip Verspoor, Eric Bernatchez, Louis Lien, Sigbjørn |
author_facet |
Bourret, Vincent Kent, Matthew P. Primmer, Craig R. Vasemägi, Anti Karlsson, Sten Hindar, Kjetil McGinnity, Philip Verspoor, Eric Bernatchez, Louis Lien, Sigbjørn |
author_sort |
Bourret, Vincent |
title |
Data from: SNP-array reveals genome wide patterns of geographical and potential adaptive divergence across the natural range of Atlantic salmon (Salmo salar) |
title_short |
Data from: SNP-array reveals genome wide patterns of geographical and potential adaptive divergence across the natural range of Atlantic salmon (Salmo salar) |
title_full |
Data from: SNP-array reveals genome wide patterns of geographical and potential adaptive divergence across the natural range of Atlantic salmon (Salmo salar) |
title_fullStr |
Data from: SNP-array reveals genome wide patterns of geographical and potential adaptive divergence across the natural range of Atlantic salmon (Salmo salar) |
title_full_unstemmed |
Data from: SNP-array reveals genome wide patterns of geographical and potential adaptive divergence across the natural range of Atlantic salmon (Salmo salar) |
title_sort |
data from: snp-array reveals genome wide patterns of geographical and potential adaptive divergence across the natural range of atlantic salmon (salmo salar) |
publishDate |
2018 |
url |
https://zenodo.org/record/4986095 https://doi.org/10.5061/dryad.gm367 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_relation |
doi:10.1111/mec.12003 https://zenodo.org/communities/dryad https://zenodo.org/record/4986095 https://doi.org/10.5061/dryad.gm367 oai:zenodo.org:4986095 |
op_rights |
info:eu-repo/semantics/openAccess https://creativecommons.org/publicdomain/zero/1.0/legalcode |
op_doi |
https://doi.org/10.5061/dryad.gm36710.1111/mec.12003 |
_version_ |
1766361761023262720 |