Regional mtDNA SNP differentiation in European Atlantic salmon (Salmo salar): an assessment of potential utility for determination of natal origin

Abstract

Verspoor, E., Consuegra, S., Fridjonsson, O., Hjorleifsdottir, S., Knox, D., Olafsson, K., Tompsett, S., Wennevik, V., and Garciá de Leániz, C. 2012. Regional mtDNA SNP differentiation in European Atlantic salmon (Salmo salar): an assessment of potential utility for determination of natal origin. – ICES Journal of Marine Science, 69: 1625–1636. The Atlantic salmon, Salmo salar, shows geographically structured differentiation at various classes of molecular genetic variation, among and within river stocks. Nuclear microsatellite locus variation at multiple loci has been exploited for more than a decade as a marker for the continental origin of fish caught at sea in distant-water fisheries. However, a simpler, more cost-effective, but still accurate, assignment can be obtained using a single microsatellite locus in combination with a mitochondrial DNA (mtDNA) single-nucleotide polymorphism (SNP) detected by restriction enzyme digestion. Following on from this, a preliminary study was made of the potential for using mtDNA SNP variation to enhance the resolving power and cost-effectiveness of within-continent assignment of European salmon as determined using microsatellites. Variation in 20 mtDNA regions, encompassing ∼43% of this genome, in 330 salmon from 29 rivers across Europe, was analysed. High levels of inter-individual and inter-river variation were found, as well as evidence of regional differentiation paralleling observed microsatellite differentiation. The observations indicate scope for using mtDNA SNPs along with microsatellites for genetically based assignment of European salmon to region and river of natal origin, but further study is needed.

Ice sheets and genetics: Insights into the phylogeography of Scottish Atlantic salmon, Salmo salar L.

“…These can be particularly informative for species such as the Atlantic salmon for which there exist both a robust knowledge of their relevant biology as well as large genetic data sets from across the species’ range (e.g. mtDNA—Nilsson et al., ; Verspoor et al., ; nuclear SNPs—Bourret et al., ; Bradbury et al., ; Gilbey et al., ; microsatellites—Ellis et al., ; Bradbury et al., ). This makes the Atlantic salmon an ideal model species for exploring the IPH approach and advancing general understanding of how post‐glacial landscape and climate change has specifically conditioned contemporary patterns of phylogenetic diversity.…”

Genetic population structure ofGyrodactylus thymalli(Monogenea) in a large Norwegian river system

“…Furthermore, the rising of the landmass following the glaciation strongly affected how different groups of fish species colonized Norway from various geographic areas and water systems (Huitfeldt-Kaas, 1918). Here, the anadromous Atlantic salmon colonized Norway along its entire coastline likely from a southern and northeastern glacial refugium (Verspoor et al, 2012). The European grayling and the minnow colonized Norway from a southern and a northern glacial refugium (Holmen, 2013;Koskinen et al, 2002a).…”

Genetic evidence of local exploitation of Atlantic salmon in a coastal subsistence fishery in the Northwest Atlantic

“…In Pacific salmonids and to a lesser extent Atlantic salmonids, genetic stock identification (GSI) has been used extensively to disentangle mixtures of individuals (e.g., Koljonen et al 2007;Larson et al 2013;Shaklee et al 1998). Previous GSI studies in Atlantic salmon have largely been limited to the eastern Atlantic (but see Gauthier-Ouellet et al 2009;Sheehan et al 2010) and have utilized a variety of genetic markers, including allozymes (e.g., Koljonen and Pella 1997;Verspoor 2005), mtDNA (Verspoor et al 2012), microsatellites (e.g., Ensing et al 2013;Griffiths et al 2010;Vähä et al 2011), and single nucleotide polymorphisms (e.g., Jensen et al 2013). The ultimate power of genetic approaches to resolve western Atlantic salmon populations contributing to mixed harvests depends on the degree of isolation among the contributing populations, the diversity of the markers used (Kalinowski 2004), and an adequate representation of spatial molecular diversity in a genetic baseline.…”