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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Online Access: | https://doi.org/10.5061/dryad.7tv21 |
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fttriple:oai:gotriple.eu:50|dedup_wf_001::0f3dd5108171e2bb0c87956671fd99a1 2023-05-15T15:28:42+02:00 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 undefined unknown http://dx.doi.org/10.5061/dryad.7tv21 https://dx.doi.org/10.5061/dryad.7tv21 lic_creative-commons oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:90287 oai:easy.dans.knaw.nl:easy-dataset:90287 10.5061/dryad.7tv21 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 re3data_____::r3d100000044 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 Life sciences medicine and health care conservation genetics Fisheries Management Salmo salar Atlantic salmon hybridization Wildlife Management Population Genetics - Empirical Newfoundland geo envir Dataset https://vocabularies.coar-repositories.org/resource_types/c_ddb1/ 2015 fttriple https://doi.org/10.5061/dryad.7tv21 2023-01-22T17:22:25Z 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 dataAtlantic salmon microsatellite data, for 2439 individuals, with an average of 78.7 individuals per populationMicrosatellite data.csvAtlantic salmon RAD-seq data VCF formatVCF file for Atlantic salmon RAD-seq data from southern Newfoundland populations20130820_FOC_Salmon_Bradbury_std.vcfDistance matricesGenetic and geographic distance matricesSNP Array genotype dataSNP array genotypes for 5,568 SNP loci collected with the V2 Atlantic salmon SNP-array developed by the Centre for ... Dataset Atlantic salmon Newfoundland Salmo salar Unknown |
institution |
Open Polar |
collection |
Unknown |
op_collection_id |
fttriple |
language |
unknown |
topic |
Life sciences medicine and health care conservation genetics Fisheries Management Salmo salar Atlantic salmon hybridization Wildlife Management Population Genetics - Empirical Newfoundland geo envir |
spellingShingle |
Life sciences medicine and health care conservation genetics Fisheries Management Salmo salar Atlantic salmon hybridization Wildlife Management Population Genetics - Empirical Newfoundland geo envir 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 |
Life sciences medicine and health care conservation genetics Fisheries Management Salmo salar Atlantic salmon hybridization Wildlife Management Population Genetics - Empirical Newfoundland geo envir |
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 dataAtlantic salmon microsatellite data, for 2439 individuals, with an average of 78.7 individuals per populationMicrosatellite data.csvAtlantic salmon RAD-seq data VCF formatVCF file for Atlantic salmon RAD-seq data from southern Newfoundland populations20130820_FOC_Salmon_Bradbury_std.vcfDistance matricesGenetic and geographic distance matricesSNP Array genotype dataSNP array genotypes for 5,568 SNP loci collected with the V2 Atlantic salmon SNP-array developed by the Centre for ... |
format |
Dataset |
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 |
publishDate |
2015 |
url |
https://doi.org/10.5061/dryad.7tv21 |
genre |
Atlantic salmon Newfoundland Salmo salar |
genre_facet |
Atlantic salmon Newfoundland Salmo salar |
op_source |
oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:90287 oai:easy.dans.knaw.nl:easy-dataset:90287 10.5061/dryad.7tv21 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 re3data_____::r3d100000044 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 |
op_relation |
http://dx.doi.org/10.5061/dryad.7tv21 https://dx.doi.org/10.5061/dryad.7tv21 |
op_rights |
lic_creative-commons |
op_doi |
https://doi.org/10.5061/dryad.7tv21 |
_version_ |
1766359048127512576 |