Data from: Transatlantic secondary contact in Atlantic salmon, comparing microsatellites, a SNP array, and Restriction Associated DNA sequencing for the resolution of complex spatial structure

Identification of discrete and unique assemblages of individuals or populations is central to the management of exploited species. Advances in population genomics provide new opportunities for re-evaluating existing conservation units but comparisons among approaches remain rare. We compare the utility of RAD-seq, a single nucleotide polymorphism (SNP) array, and a microsatellite panel, to resolve spatial structuring under a scenario of possible trans-Atlantic secondary contact in a threatened Atlantic salmon, Salmo salar, population in southern Newfoundland. Bayesian clustering indentified two large groups subdividing the existing conservation unit and multivariate analyses indicated significant similarity in spatial structuring among the three datasets. mtDNA alleles diagnostic for European ancestry displayed increased frequency in eastern Newfoundland, and were correlated with spatial structure in all marker types. Evidence consistent with introgression among these two groups was evident in both SNP datasets but not the microsatellite data. Asymmetry in the degree of introgression was also apparent in SNP datasets with evidence of gene flow towards the east or European type. This work highlights the utility of RAD-seq based approaches for the resolution of complex spatial patterns, resolves a region of trans-Atlantic secondary contact Atlantic salmon in Newfoundland, and demonstrates the utility of multiple marker comparisons in identifying dynamics of introgression. --