Data from: Transatlantic secondary contact in Atlantic salmon, comparing microsatellites, a SNP array, and Restriction Associated DNA sequencing for the resolution of complex spatial structure
Identification of discrete and unique assemblages of individuals or populations is central to the management of exploited species. Advances in population genomics provide new opportunities for re-evaluating existing conservation units but comparisons among approaches remain rare. We compare the util...
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ftzenodo:oai:zenodo.org:4986304 2024-09-15T17:55:41+00:00 Data from: Transatlantic secondary contact in Atlantic salmon, comparing microsatellites, a SNP array, and Restriction Associated DNA sequencing for the resolution of complex spatial structure Bradbury, Ian R. Hamilton, Lorraine C. Dempson, J. Brian Robertson, Martha J. Bourret, Vincent Bernatchez, Louis Verspoor, Eric Dempson, Brian 2015-09-22 https://doi.org/10.5061/dryad.7tv21 unknown Zenodo https://doi.org/10.1111/mec.13395 https://zenodo.org/communities/dryad https://doi.org/10.5061/dryad.7tv21 oai:zenodo.org:4986304 info:eu-repo/semantics/openAccess Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode Salmo salar Wildlife Management info:eu-repo/semantics/other 2015 ftzenodo https://doi.org/10.5061/dryad.7tv2110.1111/mec.13395 2024-07-27T02:35:41Z Identification of discrete and unique assemblages of individuals or populations is central to the management of exploited species. Advances in population genomics provide new opportunities for re-evaluating existing conservation units but comparisons among approaches remain rare. We compare the utility of RAD-seq, a single nucleotide polymorphism (SNP) array and a microsatellite panel to resolve spatial structuring under a scenario of possible trans-Atlantic secondary contact in a threatened Atlantic Salmon, Salmo salar, population in southern Newfoundland. Bayesian clustering indentified two large groups subdividing the existing conservation unit and multivariate analyses indicated significant similarity in spatial structuring among the three data sets. mtDNA alleles diagnostic for European ancestry displayed increased frequency in southeastern Newfoundland and were correlated with spatial structure in all marker types. Evidence consistent with introgression among these two groups was present in both SNP data sets but not the microsatellite data. Asymmetry in the degree of introgression was also apparent in SNP data sets with evidence of gene flow towards the east or European type. This work highlights the utility of RAD-seq based approaches for the resolution of complex spatial patterns, resolves a region of trans-Atlantic secondary contact in Atlantic Salmon in Newfoundland and demonstrates the utility of multiple marker comparisons in identifying dynamics of introgression. Southern Newfoundland Atlantic Salmon microsatellite data Atlantic salmon microsatellite data, for 2439 individuals, with an average of 78.7 individuals per population Microsatellite data.csv Atlantic salmon RAD-seq data VCF format VCF file for Atlantic salmon RAD-seq data from southern Newfoundland populations 20130820_FOC_Salmon_Bradbury_std.vcf Distance matrices Genetic and geographic distance matrices SNP Array genotype data SNP array genotypes for 5,568 SNP loci collected with the V2 Atlantic salmon SNP-array developed by the Centre ... Other/Unknown Material Atlantic salmon Newfoundland Salmo salar Zenodo |
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topic |
Salmo salar Wildlife Management |
spellingShingle |
Salmo salar Wildlife Management Bradbury, Ian R. Hamilton, Lorraine C. Dempson, J. Brian Robertson, Martha J. Bourret, Vincent Bernatchez, Louis Verspoor, Eric Dempson, Brian Data from: Transatlantic secondary contact in Atlantic salmon, comparing microsatellites, a SNP array, and Restriction Associated DNA sequencing for the resolution of complex spatial structure |
topic_facet |
Salmo salar Wildlife Management |
description |
Identification of discrete and unique assemblages of individuals or populations is central to the management of exploited species. Advances in population genomics provide new opportunities for re-evaluating existing conservation units but comparisons among approaches remain rare. We compare the utility of RAD-seq, a single nucleotide polymorphism (SNP) array and a microsatellite panel to resolve spatial structuring under a scenario of possible trans-Atlantic secondary contact in a threatened Atlantic Salmon, Salmo salar, population in southern Newfoundland. Bayesian clustering indentified two large groups subdividing the existing conservation unit and multivariate analyses indicated significant similarity in spatial structuring among the three data sets. mtDNA alleles diagnostic for European ancestry displayed increased frequency in southeastern Newfoundland and were correlated with spatial structure in all marker types. Evidence consistent with introgression among these two groups was present in both SNP data sets but not the microsatellite data. Asymmetry in the degree of introgression was also apparent in SNP data sets with evidence of gene flow towards the east or European type. This work highlights the utility of RAD-seq based approaches for the resolution of complex spatial patterns, resolves a region of trans-Atlantic secondary contact in Atlantic Salmon in Newfoundland and demonstrates the utility of multiple marker comparisons in identifying dynamics of introgression. Southern Newfoundland Atlantic Salmon microsatellite data Atlantic salmon microsatellite data, for 2439 individuals, with an average of 78.7 individuals per population Microsatellite data.csv Atlantic salmon RAD-seq data VCF format VCF file for Atlantic salmon RAD-seq data from southern Newfoundland populations 20130820_FOC_Salmon_Bradbury_std.vcf Distance matrices Genetic and geographic distance matrices SNP Array genotype data SNP array genotypes for 5,568 SNP loci collected with the V2 Atlantic salmon SNP-array developed by the Centre ... |
format |
Other/Unknown Material |
author |
Bradbury, Ian R. Hamilton, Lorraine C. Dempson, J. Brian Robertson, Martha J. Bourret, Vincent Bernatchez, Louis Verspoor, Eric Dempson, Brian |
author_facet |
Bradbury, Ian R. Hamilton, Lorraine C. Dempson, J. Brian Robertson, Martha J. Bourret, Vincent Bernatchez, Louis Verspoor, Eric Dempson, Brian |
author_sort |
Bradbury, Ian R. |
title |
Data from: Transatlantic secondary contact in Atlantic salmon, comparing microsatellites, a SNP array, and Restriction Associated DNA sequencing for the resolution of complex spatial structure |
title_short |
Data from: Transatlantic secondary contact in Atlantic salmon, comparing microsatellites, a SNP array, and Restriction Associated DNA sequencing for the resolution of complex spatial structure |
title_full |
Data from: Transatlantic secondary contact in Atlantic salmon, comparing microsatellites, a SNP array, and Restriction Associated DNA sequencing for the resolution of complex spatial structure |
title_fullStr |
Data from: Transatlantic secondary contact in Atlantic salmon, comparing microsatellites, a SNP array, and Restriction Associated DNA sequencing for the resolution of complex spatial structure |
title_full_unstemmed |
Data from: Transatlantic secondary contact in Atlantic salmon, comparing microsatellites, a SNP array, and Restriction Associated DNA sequencing for the resolution of complex spatial structure |
title_sort |
data from: transatlantic secondary contact in atlantic salmon, comparing microsatellites, a snp array, and restriction associated dna sequencing for the resolution of complex spatial structure |
publisher |
Zenodo |
publishDate |
2015 |
url |
https://doi.org/10.5061/dryad.7tv21 |
genre |
Atlantic salmon Newfoundland Salmo salar |
genre_facet |
Atlantic salmon Newfoundland Salmo salar |
op_relation |
https://doi.org/10.1111/mec.13395 https://zenodo.org/communities/dryad https://doi.org/10.5061/dryad.7tv21 oai:zenodo.org:4986304 |
op_rights |
info:eu-repo/semantics/openAccess Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode |
op_doi |
https://doi.org/10.5061/dryad.7tv2110.1111/mec.13395 |
_version_ |
1810431928465096704 |