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A comparison of stock and individual identification for sockeye salmon (Oncorhynchus nerka) in British Columbia provided by microsatellites and single nucleotide polymorphisms

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Abstract:

Variation at 14 microsatellite loci, one major histocompatibility complex (MHC) locus, and 49 single nucleotide polymorphism (SNPs) loci was surveyed in 44 populations of sockeye salmon (Oncorhynchus nerka) over 16 regions from southern and central British Columbia, Canada. Sequential addition of the five highest rated SNPs to the suite of 14 microsatellites provided the equivalent average accuracy when compared with the current suite of microsatellites and MHC. Six microsatellites provided the equivalent average stock identification resolution and individual assignment accuracy compared with 46 SNPs. For regional stock compositions, 53–104 SNPs were projected to be required to provide accuracy and precision equivalent to the microsatellites. For population-specific stock compositions, 75–79 SNPs were projected to be required to provide accuracy and precision equivalent to the microsatellites. Equivalency in individual assignment accuracy to region was estimated to require 100 SNPs of the quality evaluated in the study, whereas equivalent accuracy in assignment to specific populations was estimated to require 124 SNPs. Applications that incorporate the existing power of a combined microsatellite–SNP approach are the best current technique available for sockeye salmon stock identification applications in southern British Columbia.

Nous avons inventorié la variation à 14 locus microsatellites, un locus d’un complexe majeur d’histocompatibilité (MHC) et 49 locus de polymorphismes mononucléotidiques (SNP) dans 44 populations de saumons rouges (Oncorhynchus nerka) réparties dans 16 régions du sud et du centre de la Colombie-Britannique, Canada. L’addition séquentielle des cinq SNP ayant la plus forte cote à la suite des 14 microsatellites procure une exactitude moyenne équivalente à celle de la suite courante des microsatellites et du MHC. Six microsatellites fournissent une résolution moyenne d’identification des stocks et une exactitude des assignations individuelles équivalentes à 46 SNP. Pour ce qui est de la composition régionale des stocks, nous extrapolons qu’il faudrait 53–104 SNP pour obtenir une exactitude et une précision équivalentes à celles des microsatellites. Dans le cas des compositions de stocks spécifiques aux populations, 75–79 SNP seraient nécessaires pour obtenir l’exactitude et la précision équivalentes à celles des microsatellites. Nous estimons que, pour obtenir une équivalence dans l’exactitude des assignations individuelles à la région, il faudrait 100 SNP de même qualité que ceux évalués dans notre étude; pour une exactitude équivalente dans l’assignation à une population spécifique, il faudrait 124 SNP. Les applications qui incorporent la puissance connue de l’utilisation combinée des microsatellites et des SNP constituent la meilleure méthodologie couramment disponible pour l’identification des stocks de saumons rouges dans le sud de la Colombie-Britannique.

Document Type: Research Article

Publication date: August 1, 2010

More about this publication?
  • Published continuously since 1901 (under various titles), this monthly journal is the primary publishing vehicle for the multidisciplinary field of aquatic sciences. It publishes perspectives (syntheses, critiques, and re-evaluations), discussions (comments and replies), articles, and rapid communications, relating to current research on cells, organisms, populations, ecosystems, or processes that affect aquatic systems. The journal seeks to amplify, modify, question, or redirect accumulated knowledge in the field of fisheries and aquatic science. Occasional supplements are dedicated to single topics or to proceedings of international symposia.
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