A microsatellite baseline for genetic stock identification of European Atlantic salmon (Salmo salar L.)

Atlantic salmon (Salmo salar L.) populations from different river origins mix in the North Atlantic during the marine life stage. To facilitate marine stock identification, we developed a genetic baseline covering the European component of the species’ range excluding the Baltic Sea, from the Russian River Megra in the north-east, the Icelandic Ellidaar in the west, and the Spanish Ulla in the south, spanning 3737 km North to South and 2717 km East to West. The baseline encompasses data for 14 microsatellites for 26 822 individual fish from 13 countries, 282 rivers, and 467 sampling sites. A hierarchy of regional genetic assignment units was defined using a combination of distance-based and Bayesian clustering. At the top level, three assignment units were identified comprising northern, southern, and Icelandic regions. A second assignment level was also defined, comprising eighteen and twenty-nine regional units for accurate individual assignment and mixed stock estimates respectively. The baseline provides the most comprehensive geographical coverage for an Atlantic salmon genetic data-set, and a unique resource for the conservation and management of the species in Europe. It is freely available to researchers to facilitate identification of the natal origin of European salmon

Identification of a single genomic region associated with seasonal river return timing in adult Scottish Atlantic salmon (Salmo salar L.) identified using a genome-wide association study.

Examination of the genetic basis of the timing of the return migration of Atlantic salmon (Salmo salar L.) to freshwater from the sea, a trait of economic and conservation interest, was carried out using a genome-wide association study. Genotype data from 52,731 single nucleotide polymorphic (SNP) markers from 73 early and 49 late running two sea-winter salmon from five rivers in eastern Scotland was examined. A single region of the Atlantic salmon chromosome Ssa09 was identified, containing nine SNP markers significantly associated with run timing, a region previously linked to variation in sea age at maturity. Validation of the markers in a group of 233 one and two sea-winter fish, including adults from a novel river, again showed significant associations between the trait and the Ssa09 region, explaining ~24% of the trait variance. The SNP loci identified provide the ability to examine trait variation in populations of Atlantic salmon and so help facilitate conservation management of the differing run timing phenotypes.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Scottish Baseline SNP Panel

Raw genotypes for the baseline SNP panel developed for Scotland and NE England

Data from: 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.

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

Assignment accuracy to river of hold-out set fish to training set reference sites using the top ranked 288 SNPs.

<p>Assignment accuracy to river of hold-out set fish to training set reference sites using the top ranked 288 SNPs.</p

Rivers (numbers) and associated sample collection sites (black circles).

<p>Rivers (numbers) and associated sample collection sites (black circles).</p

Results of the fishery simulations of the assignment units identified using the top ranked 288 SNPs.

<p>A) 100% simulations, B) Mixed Stock Fishery simulation with equal proportions in each assignment unit, C) Mixed Stock Fishery simulation with proportions in each assignment unit based on productivity of that unit. In A and B, horizontal grey lines represent actual simulated proportions and points represent mean simulation proportion estimates. In C, black bars represent simulated proportions and light bars mean simulation proportion estimates. In all plots, bars represent 95% confidence intervals calculated over 1000 replicate simulations.</p

Multidimensional plot of pairwise D_A based on all SNPs.

<p>Red points are sites identified as outliers; green points are sites south of the Tweed on the East coast; orange points are Kyle of Sutherland sites (i.e. around sites 12 and 13 on <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0164327#pone.0164327.g001" target="_blank">Fig 1</a>) and blue points represent the remaining Scottish samples.</p

Steps taken in defining assignment units and accuracy of assignment to the units identified.

<p>Steps taken in defining assignment units and accuracy of assignment to the units identified.</p

Assignment units as defined by <i>k</i>-means clustering.

<p>A) Results of <i>k</i>-means clustering (insert) showing <i>k</i> = 7 as best cluster number, shown by differently coloured symbols. B) Final assignment units after combining rivers with reciprocal misassignments.</p