Data from: Genotyping-by-sequencing of genome-wide microsatellite loci reveals fine-scale harvest composition in a coastal Atlantic salmon fishery
Individual assignment and genetic mixture analysis are commonly utilized in contemporary wildlife and fisheries management. Although microsatellite loci provide unparalleled numbers of alleles per locus, their use in assignment applications is increasingly limited. However, next-generation sequencin...
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Online Access: | https://doi.org/10.5061/dryad.864rv |
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fttriple:oai:gotriple.eu:50|dedup_wf_001::f31175a21c6ba3fc34b3fed62df7ccff 2023-05-15T15:29:02+02:00 Data from: Genotyping-by-sequencing of genome-wide microsatellite loci reveals fine-scale harvest composition in a coastal Atlantic salmon fishery Bradbury, Ian R. Wringe, Brendan F. Watson, Beth Paterson, Ian Horne, John Beiko, Robert Lehnert, Sarah J. Clément, Marie Anderson, Eric C. Jeffery, Nicholas W. Duffy, Steven Sylvester, Emma Robertson, Martha Bentzen, Paul 2018-01-29 https://doi.org/10.5061/dryad.864rv undefined unknown http://dx.doi.org/10.5061/dryad.864rv https://dx.doi.org/10.5061/dryad.864rv lic_creative-commons oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:113962 10.5061/dryad.864rv oai:easy.dans.knaw.nl:easy-dataset:113962 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 re3data_____::r3d100000044 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c Life sciences medicine and health care conservation genetics microsatellite Mixed-stock analysis Fisheries Management Salmo salar Next-generation sequencing Genetic assignment Labrador Canada envir geo Dataset https://vocabularies.coar-repositories.org/resource_types/c_ddb1/ 2018 fttriple https://doi.org/10.5061/dryad.864rv 2023-01-22T16:52:50Z Individual assignment and genetic mixture analysis are commonly utilized in contemporary wildlife and fisheries management. Although microsatellite loci provide unparalleled numbers of alleles per locus, their use in assignment applications is increasingly limited. However, next-generation sequencing, in conjunction with novel bioinformatic tools allows large numbers of microsatellite loci to be simultaneously genotyped, presenting new opportunities for individual assignment and genetic mixture analysis. Here we scanned the published Atlantic salmon genome to identify 706 microsatellite loci, from which we developed a final panel of 101 microsatellites distributed across the genome (average 3.4 loci per chromosome). Using samples from 35 Atlantic salmon populations (n=1485 individuals) from coastal Labrador, Canada, a region characterized by low levels of differentiation in this species, this panel identified 844 alleles (average of 8.4 alleles per locus). Simulation-based evaluations of assignment and mixture identification accuracy revealed unprecedented resolution, clearly identifying 26 rivers or groups of rivers spanning 500 km of coastline. This baseline was used to examine the stock composition of 696 individuals harvested in the Labrador Atlantic salmon fishery and revealed that coastal fisheries largely targeted regional groups (<300km). This work suggests that the development and application of large sequenced microsatellite panels presents great potential for stock resolution in Atlantic salmon and more broadly in other exploited anadromous and marine species. Labrador Atlantic Salmon Sequenced Microsatellite DataGenepop file of sequenced microsatellite genotype data for 35 salmon populations in Labrador Canada. Dataset Atlantic salmon Salmo salar Unknown Canada |
institution |
Open Polar |
collection |
Unknown |
op_collection_id |
fttriple |
language |
unknown |
topic |
Life sciences medicine and health care conservation genetics microsatellite Mixed-stock analysis Fisheries Management Salmo salar Next-generation sequencing Genetic assignment Labrador Canada envir geo |
spellingShingle |
Life sciences medicine and health care conservation genetics microsatellite Mixed-stock analysis Fisheries Management Salmo salar Next-generation sequencing Genetic assignment Labrador Canada envir geo Bradbury, Ian R. Wringe, Brendan F. Watson, Beth Paterson, Ian Horne, John Beiko, Robert Lehnert, Sarah J. Clément, Marie Anderson, Eric C. Jeffery, Nicholas W. Duffy, Steven Sylvester, Emma Robertson, Martha Bentzen, Paul Data from: Genotyping-by-sequencing of genome-wide microsatellite loci reveals fine-scale harvest composition in a coastal Atlantic salmon fishery |
topic_facet |
Life sciences medicine and health care conservation genetics microsatellite Mixed-stock analysis Fisheries Management Salmo salar Next-generation sequencing Genetic assignment Labrador Canada envir geo |
description |
Individual assignment and genetic mixture analysis are commonly utilized in contemporary wildlife and fisheries management. Although microsatellite loci provide unparalleled numbers of alleles per locus, their use in assignment applications is increasingly limited. However, next-generation sequencing, in conjunction with novel bioinformatic tools allows large numbers of microsatellite loci to be simultaneously genotyped, presenting new opportunities for individual assignment and genetic mixture analysis. Here we scanned the published Atlantic salmon genome to identify 706 microsatellite loci, from which we developed a final panel of 101 microsatellites distributed across the genome (average 3.4 loci per chromosome). Using samples from 35 Atlantic salmon populations (n=1485 individuals) from coastal Labrador, Canada, a region characterized by low levels of differentiation in this species, this panel identified 844 alleles (average of 8.4 alleles per locus). Simulation-based evaluations of assignment and mixture identification accuracy revealed unprecedented resolution, clearly identifying 26 rivers or groups of rivers spanning 500 km of coastline. This baseline was used to examine the stock composition of 696 individuals harvested in the Labrador Atlantic salmon fishery and revealed that coastal fisheries largely targeted regional groups (<300km). This work suggests that the development and application of large sequenced microsatellite panels presents great potential for stock resolution in Atlantic salmon and more broadly in other exploited anadromous and marine species. Labrador Atlantic Salmon Sequenced Microsatellite DataGenepop file of sequenced microsatellite genotype data for 35 salmon populations in Labrador Canada. |
format |
Dataset |
author |
Bradbury, Ian R. Wringe, Brendan F. Watson, Beth Paterson, Ian Horne, John Beiko, Robert Lehnert, Sarah J. Clément, Marie Anderson, Eric C. Jeffery, Nicholas W. Duffy, Steven Sylvester, Emma Robertson, Martha Bentzen, Paul |
author_facet |
Bradbury, Ian R. Wringe, Brendan F. Watson, Beth Paterson, Ian Horne, John Beiko, Robert Lehnert, Sarah J. Clément, Marie Anderson, Eric C. Jeffery, Nicholas W. Duffy, Steven Sylvester, Emma Robertson, Martha Bentzen, Paul |
author_sort |
Bradbury, Ian R. |
title |
Data from: Genotyping-by-sequencing of genome-wide microsatellite loci reveals fine-scale harvest composition in a coastal Atlantic salmon fishery |
title_short |
Data from: Genotyping-by-sequencing of genome-wide microsatellite loci reveals fine-scale harvest composition in a coastal Atlantic salmon fishery |
title_full |
Data from: Genotyping-by-sequencing of genome-wide microsatellite loci reveals fine-scale harvest composition in a coastal Atlantic salmon fishery |
title_fullStr |
Data from: Genotyping-by-sequencing of genome-wide microsatellite loci reveals fine-scale harvest composition in a coastal Atlantic salmon fishery |
title_full_unstemmed |
Data from: Genotyping-by-sequencing of genome-wide microsatellite loci reveals fine-scale harvest composition in a coastal Atlantic salmon fishery |
title_sort |
data from: genotyping-by-sequencing of genome-wide microsatellite loci reveals fine-scale harvest composition in a coastal atlantic salmon fishery |
publishDate |
2018 |
url |
https://doi.org/10.5061/dryad.864rv |
geographic |
Canada |
geographic_facet |
Canada |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_source |
oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:113962 10.5061/dryad.864rv oai:easy.dans.knaw.nl:easy-dataset:113962 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 re3data_____::r3d100000044 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c |
op_relation |
http://dx.doi.org/10.5061/dryad.864rv https://dx.doi.org/10.5061/dryad.864rv |
op_rights |
lic_creative-commons |
op_doi |
https://doi.org/10.5061/dryad.864rv |
_version_ |
1766359397041176576 |