Conservation genomics of anadromous Atlantic salmon across its North American range: outlier loci identify the same patterns of population structure as neutral loci
Abstract Anadromous Atlantic salmon ( Salmo salar ) is a species of major conservation and management concern in North America, where population abundance has been declining over the past 30 years. Effective conservation actions require the delineation of conservation units to appropriately reflect...
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crwiley:10.1111/mec.12972 2024-09-15T17:55:58+00:00 Conservation genomics of anadromous Atlantic salmon across its North American range: outlier loci identify the same patterns of population structure as neutral loci Moore, Jean‐Sébastien Bourret, Vincent Dionne, Mélanie Bradbury, Ian O'Reilly, Patrick Kent, Matthew Chaput, Gérald Bernatchez, Louis Natural Sciences and Engineering Research Council of Canada 2014 http://dx.doi.org/10.1111/mec.12972 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Fmec.12972 https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.12972 en eng Wiley http://onlinelibrary.wiley.com/termsAndConditions#vor http://doi.wiley.com/10.1002/tdm_license_1.1 Molecular Ecology volume 23, issue 23, page 5680-5697 ISSN 0962-1083 1365-294X journal-article 2014 crwiley https://doi.org/10.1111/mec.12972 2024-08-27T04:26:47Z Abstract Anadromous Atlantic salmon ( Salmo salar ) is a species of major conservation and management concern in North America, where population abundance has been declining over the past 30 years. Effective conservation actions require the delineation of conservation units to appropriately reflect the spatial scale of intraspecific variation and local adaptation. Towards this goal, we used the most comprehensive genetic and genomic database for Atlantic salmon to date, covering the entire North American range of the species. The database included microsatellite data from 9142 individuals from 149 sampling locations and data from a medium‐density SNP array providing genotypes for >3000 SNP s for 50 sampling locations. We used neutral and putatively selected loci to integrate adaptive information in the definition of conservation units. Bayesian clustering with the microsatellite data set and with neutral SNP s identified regional groupings largely consistent with previously published regional assessments. The use of outlier SNP s did not result in major differences in the regional groupings, suggesting that neutral markers can reflect the geographic scale of local adaptation despite not being under selection. We also performed assignment tests to compare power obtained from microsatellites, neutral SNP s and outlier SNP s. Using SNP data substantially improved power compared to microsatellites, and an assignment success of 97% to the population of origin and of 100% to the region of origin was achieved when all SNP loci were used. Using outlier SNP s only resulted in minor improvements to assignment success to the population of origin but improved regional assignment. We discuss the implications of these new genetic resources for the conservation and management of Atlantic salmon in North America. Article in Journal/Newspaper Atlantic salmon Salmo salar Wiley Online Library Molecular Ecology 23 23 5680 5697 |
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Open Polar |
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Wiley Online Library |
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crwiley |
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English |
description |
Abstract Anadromous Atlantic salmon ( Salmo salar ) is a species of major conservation and management concern in North America, where population abundance has been declining over the past 30 years. Effective conservation actions require the delineation of conservation units to appropriately reflect the spatial scale of intraspecific variation and local adaptation. Towards this goal, we used the most comprehensive genetic and genomic database for Atlantic salmon to date, covering the entire North American range of the species. The database included microsatellite data from 9142 individuals from 149 sampling locations and data from a medium‐density SNP array providing genotypes for >3000 SNP s for 50 sampling locations. We used neutral and putatively selected loci to integrate adaptive information in the definition of conservation units. Bayesian clustering with the microsatellite data set and with neutral SNP s identified regional groupings largely consistent with previously published regional assessments. The use of outlier SNP s did not result in major differences in the regional groupings, suggesting that neutral markers can reflect the geographic scale of local adaptation despite not being under selection. We also performed assignment tests to compare power obtained from microsatellites, neutral SNP s and outlier SNP s. Using SNP data substantially improved power compared to microsatellites, and an assignment success of 97% to the population of origin and of 100% to the region of origin was achieved when all SNP loci were used. Using outlier SNP s only resulted in minor improvements to assignment success to the population of origin but improved regional assignment. We discuss the implications of these new genetic resources for the conservation and management of Atlantic salmon in North America. |
author2 |
Natural Sciences and Engineering Research Council of Canada |
format |
Article in Journal/Newspaper |
author |
Moore, Jean‐Sébastien Bourret, Vincent Dionne, Mélanie Bradbury, Ian O'Reilly, Patrick Kent, Matthew Chaput, Gérald Bernatchez, Louis |
spellingShingle |
Moore, Jean‐Sébastien Bourret, Vincent Dionne, Mélanie Bradbury, Ian O'Reilly, Patrick Kent, Matthew Chaput, Gérald Bernatchez, Louis Conservation genomics of anadromous Atlantic salmon across its North American range: outlier loci identify the same patterns of population structure as neutral loci |
author_facet |
Moore, Jean‐Sébastien Bourret, Vincent Dionne, Mélanie Bradbury, Ian O'Reilly, Patrick Kent, Matthew Chaput, Gérald Bernatchez, Louis |
author_sort |
Moore, Jean‐Sébastien |
title |
Conservation genomics of anadromous Atlantic salmon across its North American range: outlier loci identify the same patterns of population structure as neutral loci |
title_short |
Conservation genomics of anadromous Atlantic salmon across its North American range: outlier loci identify the same patterns of population structure as neutral loci |
title_full |
Conservation genomics of anadromous Atlantic salmon across its North American range: outlier loci identify the same patterns of population structure as neutral loci |
title_fullStr |
Conservation genomics of anadromous Atlantic salmon across its North American range: outlier loci identify the same patterns of population structure as neutral loci |
title_full_unstemmed |
Conservation genomics of anadromous Atlantic salmon across its North American range: outlier loci identify the same patterns of population structure as neutral loci |
title_sort |
conservation genomics of anadromous atlantic salmon across its north american range: outlier loci identify the same patterns of population structure as neutral loci |
publisher |
Wiley |
publishDate |
2014 |
url |
http://dx.doi.org/10.1111/mec.12972 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Fmec.12972 https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.12972 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_source |
Molecular Ecology volume 23, issue 23, page 5680-5697 ISSN 0962-1083 1365-294X |
op_rights |
http://onlinelibrary.wiley.com/termsAndConditions#vor http://doi.wiley.com/10.1002/tdm_license_1.1 |
op_doi |
https://doi.org/10.1111/mec.12972 |
container_title |
Molecular Ecology |
container_volume |
23 |
container_issue |
23 |
container_start_page |
5680 |
op_container_end_page |
5697 |
_version_ |
1810432181248458752 |