Conservation genomics of anadromous Atlantic salmon across its North American range: outlier loci identify the same patterns of population structure as neutral loci

Abstract

Anadromous Atlantic salmon (Salmo salar) is a species of major conservation and management concern in North America, where population abundance has been declining over the past 30 years. Effective conservation actions require the delineation of conservation units to appropriately reflect the spatial scale of intraspecific variation and local adaptation. Towards this goal, we used the most comprehensive genetic and genomic database for Atlantic salmon to date, covering the entire North American range of the species. The database included microsatellite data from 9142 individuals from 149 sampling locations and data from a medium-density SNP array providing genotypes for >3000 SNPs for 50 sampling locations. We used neutral and putatively selected loci to integrate adaptive information in the definition of conservation units. Bayesian clustering with the microsatellite data set and with neutral SNPs identified regional groupings largely consistent with previously published regional assessments. The use of outlier SNPs did not result in major differences in the regional groupings, suggesting that neutral markers can reflect the geographic scale of local adaptation despite not being under selection. We also performed assignment tests to compare power obtained from microsatellites, neutral SNPs and outlier SNPs. Using SNP data substantially improved power compared to microsatellites, and an assignment success of 97% to the population of origin and of 100% to the region of origin was achieved when all SNP loci were used. Using outlier SNPs only resulted in minor improvements to assignment success to the population of origin but improved regional assignment. We discuss the implications of these new genetic resources for the conservation and management of Atlantic salmon in North America.

RAD sequencing reveals genomewide divergence between independent invasions of the European green crab (Carcinus maenas) in the Northwest Atlantic

“…Similar conclusions were reached by Moore et al. (2014) and Candy et al. (2015) for Atlantic salmon and Pacific eulachon ( Thaleichthys pacificus ), respectively, where outlier SNPs showed the same population structure as neutral SNPs.…”

“…For instance, both Moore et al. (2014) and Candy et al. (2015) focus on anadromous fish species where gene flow may be low and genomewide divergence likely.…”

“…We observed strong evidence for two genetically and geographically distinct populations of green crab spatially segregated in eastern North America corresponding to two independent invasions (Darling et al., 2008, 2014), which show clear latitudinal clines in RAD‐seq‐derived SNP allele frequency. As observed in other species (e.g., Atlantic salmon ( Salmo salar ), Freamo, O'Reilly, Berg, Lien, & Boulding, 2011; Moore et al., 2014; sea scallop ( Placopecten magellanicus ), Van Wyngaarden et al., 2017), our most divergent SNPs (i.e., outliers) explained more of the spatial variance in allele frequency than either background (neutral) SNPs or COI data. Interestingly, genomewide divergence was so prominent that background genomic variation (i.e., neutral SNPs) explained an order of magnitude more of the variation between northern and southern groups than observed in native species in the region (e.g., sea scallop, Van Wyngaarden et al., 2017), and locus‐specific F ST values were an order of magnitude larger across the genome than observed in native species [e.g., American lobster, Homarus americanus , Benestan et al.…”

Genetic mixed stock analysis of an interceptory Atlantic salmon fishery in the Northwest Atlantic

“…However, as genetic baselines are established in more species, such as Atlantic salmon, Salmo salar (e.g., Bradbury et al, 2015;Ensing et al, 2013;Griffiths et al, 2010;Moore et al, 2014), new opportunities exist for broader application. Atlantic salmon, have traditionally been subject to mixed stock harvests during the marine phase of their life history, commonly associated with marine feeding areas or migratory routes (e.g., Chase, 2003;Saunders, 1981).…”

Pollinizer Efficacy of Several ‘Ingeborg’ Pear Pollinizers in Hardanger, Norway, Examined Using Microsatellite Markers

“…Although a comparative study has shown that the identification of a highly informative set of single-nucleotide polymorphism (SNP) from a large panel showed significantly more accurate individual genetic assignment compared with the combination of SSR loci (Glover et al, 2010), Moore et al (2014) found that microsatellite markers are accurate genetic markers for genetic assignment, especially in combination with informative SNPs. In the case of plant parentage, pollination and dispersal analyses, and microsatellites with their various limitations remain an important genetic marker (Ashley, 2010).…”