DOI: 10.5061/dryad.sb601
title: Data from: Conservation genomics of anadromous Atlantic salmon across its North American range: outlier loci identify the same patterns of population structure as neutral loci

description: 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 9,142 individuals from 149 sampling locations and
 data from a medium-density SNP array providing genotypes for &gt;3,000
 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 dataset 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.
description: Microsatellite
 genotypesGenotypes for the 15
 microsatellite loci for all 153 sampling locations listed in table
 S1.Ssalar_usat_genepop_23Sep2014.txtSNP genotypesGenotype data for all 3,192 SNP loci (i.e., SNPs after filters, see manuscript for details) and all 50 sampling locations listed in table S2 in Genepop format.Ssalar_SNPall_genepop_28Apr2014.txtGenotypes for loci under balancing selection inferred from BayescanIn genepop format with loci namesSsalar_SNP_Bayescan_Regions_neutral_genepop_15Apr2014.txtGenotypes for loci under positive selection inferred from BayescanIn genepop format with loci namesSsalar_SNP_Bayescan_Regions_positive_genepop_15Apr2014.txtGenotypes for outlier loci inferred from Hierarchical FDistIn genepop formal with loci namesSsalar_SNP_ArlequinHier_Fct0.01_genepop_28Apr2014.txtGenotypes for outlier loci inferred using the nested FDist approachIn genepop format with loci namesSsalar_SNP_nested_hierFdist_29Apr2014.txtExample mainparam STRUCTURE fileThese are the specs for performing the hierarchical population structure analyses on the regional groupings. Identical analyses were performed independently for each regional groupings as detailed in the manuscript.mainparamsDetails of the Bayescan runThe .verif file from the Bayescan analysis provides details of the parameters used for the run identifying outlier loci and putatively neutral loci in Bayescan. Note that the analysis was performed on regional groups, not on populations and that the genepop file would need to be modified accordingly.Ssalar_SNP_bayescan_REGIONS_8Apr2014_Verif.txtGenetic map dataPosition of all loci used in the present study on the (female) genetic map of Atlantic salmon. Distance units for the locations are in centimorgan, 'lg' refers to linkage groups and the 'totalPos' column refers to distance from the beginning of lg 1. Other distances are for each linkage group separately.MapData_JSM_9May2014.csvR code to generate random lociThis R code was used to generate the random loci in figure 6.Generate_random_loci.RNeighbour-joining tree outfileOutput from Phylip program 'Neighbour' for the neighbour-joining of Cavalli-Sforza genetic distances in figure 2ssalar_outtree.trePHYLIP infile for NJ treePHYLIP infile associated with the NJ tree in fig 2. Note that the Moisie River is removed from this analysis because it is missing all data at one loci.Ssalar_usat_PHYLIP_MOIrem_17Mar2014.inf