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 data sets. mtDNA alleles
diagnostic for European ancestry displayed increased frequency in
southeastern Newfoundland and were correlated with spatial structure in
all marker types. Evidence consistent with introgression among these two
groups was present in both SNP data sets but not the microsatellite data.
Asymmetry in the degree of introgression was also apparent in SNP data
sets 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 in Atlantic Salmon in Newfoundland and demonstrates the utility of
multiple marker comparisons in identifying dynamics of introgression.