DOI: 10.5061/dryad.0g6hq
title: Data from: Environmental adaptation in Chinook salmon (Oncorhynchus tshawytscha) throughout their North American range

description: Landscape genomics is a rapidly growing field with recent advances in both
 genotyping efficiency and statistical analyses that provide insight
 towards local adaptation of populations under varying environmental and
 selective pressure. Chinook salmon (Oncorhynchus tshawytscha) are a
 broadly distributed Pacific salmon species, occupying a diversity of
 habitats throughout the northeastern Pacific with pronounced variation in
 environmental and climate features but little is understood regarding
 local adaptation in this species. We used a multivariate method,
 redundancy analysis (RDA), to identify polygenic correlations between 19
 703 SNP loci and a suite of environmental variables in 46 collections of
 Chinook salmon (1956 total individuals) distributed throughout much of its
 North American range. Models in RDA were conducted on both rangewide and
 regional scales by hierarchical partitioning of the populations into three
 distinct genetic lineages. Our results indicate that between 5.8 and 21.8%
 of genomic variation can be accounted for by environmental features, and
 566 putatively adaptive loci were identified as targets of environmental
 adaptation. The most influential drivers of adaptive divergence included
 precipitation in the driest quarter of the year (Rangewide and North
 Coastal Lineage, anova P = 0.002 and 0.01, respectively), precipitation in
 the wettest quarter of the year (Interior Columbia River Stream-Type
 Lineage, anova P = 0.03), variation in mean diurnal range in temperature
 (South Coastal Lineage, anova P = 0.005), and migration distance
 (Rangewide, anova P = 0.001). Our results indicate that environmental
 features are strong drivers of adaptive genomic divergence in this
 species, and provide a foundation to investigate how Chinook salmon might
 respond to global environmental change.
description: Allele
 FrequenciesAllele Frequencies - The
 frequency of the major allele (P) is indicated for each of 19,703 SNP loci
 for each population (indicated by abbreviation as described in Table 1),
 including the global average MAF, and the global average genotype success
 rate (GSR).Hecht_OtsLandscapeGenomics_Dryad-AlleleFreq_061915.xlsxGenotypesGenotypes: Individual genotypes for each sample at each of the 19,703 loci. Sample ID is population abbreviation (see Table 1) followed by "xXXX", where XXX is a three digit numerical identifier.Hecht_OtsLandscapeGenomics_Dryad-Genotypes_061915.xlsxHardy Weinberg equilibriumHardy Weinberg equilibrium: Locus summary by population including estimates of the genotyping success rate (GSR), the P-value from a chi-square test of the deviation from Hardy-Weinberg Equilibrium (HWE, * reported is the raw uncorrected p-value, the Bonferroni threshold p-value for 19,703 comparisons at α=0.05 level is 0.05/19703 = 0.00000254), the observed heterozygosity (Ho), the expected heterozygosity based on HWE (He), and the minor allele (Q) frequency (MAF). Populations are numbered according to Table 1, and the colored font corresponds to the lineage of the population (blue, North Coastal Lineage; red, South Coastal Lineage; green, Interior Columbia River Stream-Type Lineage).Hecht_OtsLandscapeGenomics_Dryad-HWE_061915.xlsxGENEPOP-Rangewide_NeutralSNPsInput file for GENEPOPLOSITAN-RangewideInput file for Lositan for all populations, 19,703 SNPsOts_RADcatalog_21504SNPsPre-filtered RAD catalog of 21,504 SNPsMantel-Hecht-Moran FST full matricesInput files for Mantel test between Hecht Fst values and Moran et al. (2013) Fst values. Each set of Fst values are included in full matrix format in separate tabs of the Excel file. See Table S2 for corresponding triangular matrices and results of Mantel tests.Mantel-Hecht-MoranFSTfullmatrices.xlsxPCA-adegenet_neutralSNPsInput file for PCA in adgenet for all populations; 5,007 putatively adaptive SNPsRDA_BIOCLIMDATAInput file of environmental factors included for RDARDA_AlleleFreqInput file of allele frequencies for 19,703 SNPs for RDA