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...
Main Authors: | , , , , , , , , , |
---|---|
Format: | Article in Journal/Newspaper |
Language: | unknown |
Published: |
2018
|
Subjects: | |
Online Access: | http://hdl.handle.net/10255/dryad.41016 http://hdl.handle.net/10255/dryad.172039 https://doi.org/10.5061/dryad.gm367.2 |
id |
ftdryad:oai:v1.datadryad.org:10255/dryad.172039 |
---|---|
record_format |
openpolar |
spelling |
ftdryad:oai:v1.datadryad.org:10255/dryad.172039 2023-05-15T15:31:04+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 Europe North America 2018-02-15T21:24:31Z http://hdl.handle.net/10255/dryad.41016 http://hdl.handle.net/10255/dryad.172039 https://doi.org/10.5061/dryad.gm367.2 unknown doi:10.5061/dryad.gm367.2/1.2 doi:10.5061/dryad.gm367.2/2.2 doi:10.5061/dryad.gm367.2/3.2 doi:10.1111/mec.12003 PMID:22967111 doi:10.5061/dryad.gm367.2 Bourret V, Kent MP, Primmer CR, Vasemägi A, Karlsson S, Hindar K, McGinnity P, Verspoor E, Bernatchez L, Lien S (2012) SNP-array reveals genome wide patterns of geographical and potential adaptive divergence across the natural range of Atlantic salmon (Salmo salar). Molecular Ecology 22(3): 532–551. http://hdl.handle.net/10255/dryad.41016 http://hdl.handle.net/10255/dryad.172039 Salmonids Single Nucleotide Polymorphism Population Genetics Conservation Aquaculture Selection Article 2018 ftdryad https://doi.org/10.5061/dryad.gm367.2 https://doi.org/10.5061/dryad.gm367.2/1.2 https://doi.org/10.5061/dryad.gm367.2/2.2 https://doi.org/10.5061/dryad.gm367.2/3.2 https://doi.org/10.1111/mec.12003 2020-01-01T16:05:02Z 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. Article in Journal/Newspaper Atlantic salmon Salmo salar Dryad Digital Repository (Duke University) |
institution |
Open Polar |
collection |
Dryad Digital Repository (Duke University) |
op_collection_id |
ftdryad |
language |
unknown |
topic |
Salmonids Single Nucleotide Polymorphism Population Genetics Conservation Aquaculture Selection |
spellingShingle |
Salmonids Single Nucleotide Polymorphism Population Genetics Conservation Aquaculture Selection 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 |
Salmonids Single Nucleotide Polymorphism Population Genetics Conservation Aquaculture Selection |
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. |
format |
Article in Journal/Newspaper |
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 |
http://hdl.handle.net/10255/dryad.41016 http://hdl.handle.net/10255/dryad.172039 https://doi.org/10.5061/dryad.gm367.2 |
op_coverage |
Europe North America |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_relation |
doi:10.5061/dryad.gm367.2/1.2 doi:10.5061/dryad.gm367.2/2.2 doi:10.5061/dryad.gm367.2/3.2 doi:10.1111/mec.12003 PMID:22967111 doi:10.5061/dryad.gm367.2 Bourret V, Kent MP, Primmer CR, Vasemägi A, Karlsson S, Hindar K, McGinnity P, Verspoor E, Bernatchez L, Lien S (2012) SNP-array reveals genome wide patterns of geographical and potential adaptive divergence across the natural range of Atlantic salmon (Salmo salar). Molecular Ecology 22(3): 532–551. http://hdl.handle.net/10255/dryad.41016 http://hdl.handle.net/10255/dryad.172039 |
op_doi |
https://doi.org/10.5061/dryad.gm367.2 https://doi.org/10.5061/dryad.gm367.2/1.2 https://doi.org/10.5061/dryad.gm367.2/2.2 https://doi.org/10.5061/dryad.gm367.2/3.2 https://doi.org/10.1111/mec.12003 |
_version_ |
1766361554064769024 |