title: Accuracy of Assignment of Atlantic Salmon (Salmo salar L.) to Rivers and Regions in Scotland and Northeast England Based on Single Nucleotide Polymorphism (SNP) Markers.
abstract: Understanding the habitat use patterns of migratory fish, such as Atlantic salmon (Salmo salar L.), and the natural and anthropogenic impacts on them, is aided by the ability to identify individuals to their stock of origin. Presented here are the results of an analysis of informative single nucleotide polymorphic (SNP) markers for detecting genetic structuring in Atlantic salmon in Scotland and NE England and their ability to allow accurate genetic stock identification. 3,787 fish from 147 sites covering 27 rivers were screened at 5,568 SNP markers. In order to identify a cost-effective subset of SNPs, they were ranked according to their ability to differentiate between fish from different rivers. A panel of 288 SNPs was used to examine both individual assignments and mixed stock fisheries and eighteen assignment units were defined. The results improved greatly on previously available methods and, for the first time, fish caught in the marine environment can be confidently assigned to geographically coherent units within Scotland and NE England, including individual rivers. As such, this SNP panel has the potential to aid understanding of the various influences acting upon Atlantic salmon on their marine migrations, be they natural environmental variations and/or anthropogenic impacts, such as mixed stock fisheries and interactions with marine power generation installations.
authors.affiliation: Marine Scotland Science, Freshwater Fisheries Laboratory, Faskally, Pitlochry, Scotland, United Kingdom, PH16 5LB.
authors.forename: John
authors.initials: J
authors.lastname: Gilbey
authors.affiliation: Marine Scotland Science, Freshwater Fisheries Laboratory, Faskally, Pitlochry, Scotland, United Kingdom, PH16 5LB.
authors.forename: Eef
authors.initials: E
authors.lastname: Cauwelier
authors.affiliation: Rivers and Fisheries Trusts of Scotland, Suite 1F40, 2 Commercial Street, Edinburgh, Scotland, United Kingdom, EH6 6JA.
authors.forename: Mark W
authors.initials: MW
authors.lastname: Coulson
authors.affiliation: Marine Scotland Science, Freshwater Fisheries Laboratory, Faskally, Pitlochry, Scotland, United Kingdom, PH16 5LB.
authors.forename: Lee
authors.initials: L
authors.lastname: Stradmeyer
authors.affiliation: Marine Scotland Science, Freshwater Fisheries Laboratory, Faskally, Pitlochry, Scotland, United Kingdom, PH16 5LB.
authors.forename: James N
authors.initials: JN
authors.lastname: Sampayo
authors.affiliation: Marine Scotland Science, Freshwater Fisheries Laboratory, Faskally, Pitlochry, Scotland, United Kingdom, PH16 5LB.
authors.forename: Anja
authors.initials: A
authors.lastname: Armstrong
authors.affiliation: Marine Scotland Science, Freshwater Fisheries Laboratory, Faskally, Pitlochry, Scotland, United Kingdom, PH16 5LB.
authors.forename: Eric
authors.initials: E
authors.lastname: Verspoor
authors.affiliation: Environment Agency, Tyneside House, Newcastle Business Park, Newcastle upon Tyne, England, United Kingdom, NE4 7AR.
authors.forename: Laura
authors.initials: L
authors.lastname: Corrigan
authors.affiliation: Environment Agency, Tyneside House, Newcastle Business Park, Newcastle upon Tyne, England, United Kingdom, NE4 7AR.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Shelley
authors.affiliation: Marine Scotland Science, Freshwater Fisheries Laboratory, Faskally, Pitlochry, Scotland, United Kingdom, PH16 5LB.
authors.forename: Stuart
authors.initials: S
authors.lastname: Middlemas
mesh_terms: D000818:Animals; D004739:England; D020641:Polymorphism, Single Nucleotide; D045483:Rivers; D020317:Salmo salar / Q000235:genetics*; D012606:Scotland