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.

John Gilbey,Anja Armstrong,Eric Verspoor,Stuart Middlemas,Lee Stradmeyer,Eef Cauwelier,James N Sampayo,Laura Corrigan,Mark W Coulson,Jonathan Shelley,Timothy Darren Clark

doi:10.1371/journal.pone.0164327

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.

Highlights

Stock identification in fish species has become an integral component of modern fisheries management and for studying adaptation in wild populations [1, 2]
Reliable and cost-effective techniques of performing genetic stock identification are important in helping to provide an understanding into the migratory patterns of the various components making up the total salmon stock [85]
Such information is useful in understanding the impacts of natural or anthropogenic changes in the marine environment through mechanisms such as climate change, mixed stock fisheries and offshore developments associated with energy generation

Summary

Introduction

Stock identification in fish species has become an integral component of modern fisheries management and for studying adaptation in wild populations [1, 2]. To manage a species successfully, it is important to understand the underlying structure of the various populations making up the total stock and how exploitation, natural and anthropogenic influences are distributed between the different components [1] Disregarding this structure has the potential to give rise to misleading conclusions when examining a species’ biological characteristics which, in turn, may lead to differential exploitation of parts of a stock and associated selective changes in phenotypic characters s [3,4,5,6]. Techniques to identify the origin of salmonids captured away from their natal rivers were based around physical tagging of fish [8, 9] While such techniques provided invaluable and unambiguous information on the origin of the tagged fish, only relatively small numbers of fish could be studied in this way. Other techniques, such as stable isotope analysis [10], otolith morphology and microchemistry [11], and parasite tracking [12] have been used to identify stock origins, with varying levels of success

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