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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Online Access: | https://doi.org/10.5061/dryad.gm367.2 https://doi.org/10.5061/dryad.gm367.1 https://doi.org/10.5061/dryad.gm367 |
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fttriple:oai:gotriple.eu:50|dedup_wf_001::158cd24e76d5b1b7f7118131ec5947f3 2023-05-15T15:31:13+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 2022-07-05 https://doi.org/10.5061/dryad.gm367.2 https://doi.org/10.5061/dryad.gm367.1 https://doi.org/10.5061/dryad.gm367 undefined unknown http://dx.doi.org/10.5061/dryad.gm367.2 https://dx.doi.org/10.5061/dryad.gm367.2 http://dx.doi.org/10.5061/dryad.gm367.1 https://dx.doi.org/10.5061/dryad.gm367 https://dx.doi.org/10.5061/dryad.gm367.1 http://dx.doi.org/10.5061/dryad.gm367 lic_creative-commons oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:102922 10.5061/dryad.gm367.2 oai:easy.dans.knaw.nl:easy-dataset:102922 oai:easy.dans.knaw.nl:easy-dataset:118383 10.5061/dryad.gm367 10.5061/dryad.gm367.1 oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:118383 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 re3data_____::r3d100000044 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c Life sciences medicine and health care Salmonids Single Nucleotide Polymorphism Population Genetics Conservation Aquaculture Selection Europe North America Salmo salar envir geo Dataset https://vocabularies.coar-repositories.org/resource_types/c_ddb1/ 2022 fttriple https://doi.org/10.5061/dryad.gm367.2 https://doi.org/10.5061/dryad.gm367.1 https://doi.org/10.5061/dryad.gm367 https://doi.org/10.5061/DRYAD.GM367.2 2023-01-22T17:23:31Z 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 Unknown |
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Open Polar |
collection |
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op_collection_id |
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language |
unknown |
topic |
Life sciences medicine and health care Salmonids Single Nucleotide Polymorphism Population Genetics Conservation Aquaculture Selection Europe North America Salmo salar envir geo |
spellingShingle |
Life sciences medicine and health care Salmonids Single Nucleotide Polymorphism Population Genetics Conservation Aquaculture Selection Europe North America Salmo salar envir geo 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 |
Life sciences medicine and health care Salmonids Single Nucleotide Polymorphism Population Genetics Conservation Aquaculture Selection Europe North America Salmo salar envir geo |
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 |
2022 |
url |
https://doi.org/10.5061/dryad.gm367.2 https://doi.org/10.5061/dryad.gm367.1 https://doi.org/10.5061/dryad.gm367 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_source |
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op_relation |
http://dx.doi.org/10.5061/dryad.gm367.2 https://dx.doi.org/10.5061/dryad.gm367.2 http://dx.doi.org/10.5061/dryad.gm367.1 https://dx.doi.org/10.5061/dryad.gm367 https://dx.doi.org/10.5061/dryad.gm367.1 http://dx.doi.org/10.5061/dryad.gm367 |
op_rights |
lic_creative-commons |
op_doi |
https://doi.org/10.5061/dryad.gm367.2 https://doi.org/10.5061/dryad.gm367.1 https://doi.org/10.5061/dryad.gm367 https://doi.org/10.5061/DRYAD.GM367.2 |
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