Transatlantic secondary contact in Atlantic Salmon, comparing microsatellites, a single nucleotide polymorphism array and restriction‐site associated DNA sequencing for the resolution of complex spatial structure

Abstract

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.

Genetic population structure in Greenland halibut (Reinhardtius hippoglossoides) and its relevance to fishery management

“…Although low genetic differentiation was observed, subdivision of the species into eastern and western Atlantic populations was evident. Transatlantic patterns of genetic differentiation have been reported in other migratory species of the North Atlantic, such as Atlantic cod (Gadus morhua) (Carr and Marshall 2008;Bradbury et al 2013), Atlantic salmon (Salmo salar) (Bradbury et al 2015), Atlantic mackerel (Scomber scombrus) (Nesbø et al 2000), and Atlantic wolfish (Anarhichas lupus) (McCusker and Bentzen 2010). One explanation may be that the observed genetic structure reflects the historical population expansion of the species from glacial refugia on either side of the Atlantic.…”

Population genomics of an endemic Mediterranean fish: differentiation by fine scale dispersal and adaptation

“…The differences with our study could be due to the different resolution of the molecular markers used or to real differences in connectivity mediated by a longer larval duration among others. Therefore, genome-wide SNP genotyping could provide much greater power than traditional markers to detect genetic differentiation and thus, to define barriers to the dispersion of studied organisms5152.…”

Extensive hybridization following a large escape of domesticated Atlantic salmon in the Northwest Atlantic

“…No effort was made to screen for or remove potential sibs from these baseline groups 41 . These baseline individuals were first screened using a 5568 SNP-locus panel developed by the Centre for Integrative Genomics (CIGENE, Norway 42,43 ) as per Bradbury et al 44 . Locus calls were visually confirmed and loci were retained if call rates were >0.85 and with overall minor allele frequencies >0.01 or a minor allele frequency >0.05 in either population 44 .…”

“…These baseline individuals were first screened using a 5568 SNP-locus panel developed by the Centre for Integrative Genomics (CIGENE, Norway 42,43 ) as per Bradbury et al 44 . Locus calls were visually confirmed and loci were retained if call rates were >0.85 and with overall minor allele frequencies >0.01 or a minor allele frequency >0.05 in either population 44 . The loci retained after quality control filtering were ranked by Weir and Cockerham’s 45 F ST between the two pooled reference groups (wild and domestic salmon), and the 95 most informative loci for which suitable assays could be developed were incorporated into the custom Fluidigm EPI array (see below).…”