This archive contains summarized analysis results for all SNPs, including package-specific significance tests. Files are: BayEnv2_XtX_results.csv: results from BayEnv2 and XtX analyses. SNP: SNP ss#; Chrom: Chromosome; Position: Position on chromosome(bp); XtX_median: median XtX over three replicate runs; Median_BF: median Bayes Factor over five replicate runs; Median_P: median Spearman's P over five replicate runs; Abs(Med_P) absolute value of median Spearman's P; Distance: environmental variable was freshwater migration distance; Catchment: environmental variable was upstream catchment area. Bayescan_results.csv: results from Bayescan analysis. SNP: SNP ss#; Chrom: Chromosome; Position: Position on chromosome(bp); prob: posterior probability for the model including selection; log10(PO): the logarithm of posterior odds to base 10 for the model including selection; qval: q-value for the model including selection; alpha: estimated alpha coefficient indicating the strength and direction of selection; fst: Fst averaged over populations. HapFLK_results.csv: results from HapFLK analysis SNP: SNP ss#; Chrom: Chromosome; Position: Position on chromosome(bp); hapflk: hapflk statistic; hapflk_scaled, hapflk_pvalue: rescaled hapflk and hapflk p value, calculated using the python function 'scaling_chi2_hapflk.py'; hapflk_qvalue: hapflk qvalue, calculated from p values using the package 'qvalue' in R; FLK_pzero: estimated allele frequency in the ancestral population; FLK_flk: flk statistic (not used in manuscript); FLK_pvalue: flk p-value; FLK_qvalue: flk qvalue, calculated using 'qvalue'. LFMM_results.csv: results from LFMM analyses SNP: SNP ss#; Chrom: Chromosome; Position: Position on chromosome(bp); median_z.score: median value of z-score over five replicate runs; Abs(z.score): absolute value of median z-score; adjusted.p.values: pvalue of median z-score, adjusted for lambda; qvalues: qvalues, calculated from p values using the package 'qvalue' in R; Distance: environmental variable was freshwater migration distance; Catchment: environmental variable was upstream catchment area; Runtime: phenotypic variable was median run time at river mouth for 1SW individuals. OutFLANK_results.csv: results from OutFLANK analysis. SNP: SNP ss#; Chrom: Chromosome; Position: Position on chromosome(bp);He: expected heterozygosity; FST: Fst for the locus; FSTNoCorr: Fst for the locus without sample size correction; T1, T1NoCorr: The numerator of the estimator for Fst; T2, T2NoCorr: The denominator of the estimator for Fst; meanAlleleFreq: mean minor allele frequency; GoodH: He exceeds specified threshold of 0.1; qvalues: locus q-value; pvalues: locus p-value; pvaluesRightTail: locus p-value based only on right tail. XPEHH_results.csv: results from XP-EHH analyses. SNP: SNP ss#; Chrom: Chromosome; Position: Position on chromosome(bp); Kara_Iesj (example): XP-EHH statistic for the comparison between KARA and IESJ, standard normalized over all chromosomes; Max(absXPEHH): maximum of the absolute value of XP-EHH over all 45 population comparisons. Empirical_Pvalues.csv: empirical P-values for each SNP for each analysis, calculated as (SNP rank / Total number of SNPs). Statistics used to rank SNPs were as follows: XTX: median XtX over all replicate runs; Bayescan: median alpha over all replicate runs; OutFLANK: Fst; HapFLK: hapFLK; XPEHH: maximum absolute score over all comparisons; LFMM_Distance,LFMM_Catchment: median absolute z-score over all replicate runs; BayEnv_Distance,BayEnv_Catchment: median absolute Spearman's P over all replicate runs.