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mec12284-sup-0001-TableS1.xlsxapplication/msexcel230KTable S1 Genotyped SNPs with SNPs equence, associated dbSNP reference number, information from the genome alignment and estimates of heterozygosity in each of the eight samples.
mec12284-sup-0002-TableS2.docxWord document23KTable S2 Pairwise FST with 95% confidence intervals from 1000 bootstrapped data sets for the full data set (1199 loci, below diagonal) and for a reduced data set where outliers identified through Bayesian regression were removed (1112 loci, above diagonal).
mec12284-sup-0003-TableS3.xlsxapplication/msexcel68KTable S3 Results from Bayesian regression analysis based on 975 loci with minor allele frequency above 2%. Linkage group and position within linkage group are given for each locus. Global FST, posterior probability and Posterior Odds for a model with selection compared to a model without selection were estimated by the programme BAYESCAN. Results were controlled for multiple testing by setting the false discovery rate threshold at 5%. Outliers marked with an asterix were not confirmed in an outlier test based on loci with minor allele frequencies above 10%.
mec12284-sup-0004-TableS4.xlsxapplication/msexcel14KTable S4 Levels of population differentiation [Weir and Cockerhams θ (Weir & Cockerham 1984)] between migratory and stationary ecotype samples for 57 loci with known linkage group position in linkage group 1 and outlier status from Bayesian regression analysis.
mec12284-sup-0005-FigS1.pdfapplication/PDF78KFig. S1 Number of SNPs per scaffold for 1167 SNPs obtained through blasting SNP flanking sequences against the cod genome assembly.
mec12284-sup-0006-FigS2.pdfapplication/PDF82KFig. S2 Distance to previous SNP for 704 SNPs located in scaffolds with more than one SNP.
mec12284-sup-0007-FigS3.pdfapplication/PDF246KFig. S3 Population relationships among eastern Atlantic samples based on correspondence analysis with all markers (a, 750 loci) and with neutral markers only (Axes 1 and 2 in b) and axes 1 and 3 in c), 667 loci). Loci with a minor allele frequency below 10% were excluded from the analyses.
mec12284-sup-0008-FigS4.pdfPDF document14377KFig. S4 Pairwise levels of population differentiation, estimated by Weir and Cockerhams θ (Weir & Cockerham 1984), for 1199 loci ordered within linkage groups for all population samples. Horizontal dashed and dotted lines represent mean and 95% confidence interval generated by bootstrapping over loci. Loci in linkage groups 1, 2, 7 and 12 are coloured red, blue, green and purple, respectively, while additional linkage groups are coloured in alternating shades of grey and loci with unknown linkage group are shown in black. Location within linkage group is unknown for loci to the right of the vertical line.
mec12284-sup-0009-FigS5.pdfPDF document93KFig. S5 Global FST among eastern Atlantic samples (red line) and number of loci in data sets (blue line) for different minor allele frequency thresholds used to filter the data.
mec12284-sup-0010-FigS6.pdfPDF document3099KFig. S6 Pairwise levels of population differentiation, estimated by Weir and Cockerhams θ (Weir & Cockerham 1984), for 1113 loci ordered within linkage groups for temporally replicated samples.
mec12284-sup-0011-FigS7.pdfPDF document1192KFig. S7 Observed levels of heterozygosity based on 925 loci, estimated as moving averages within linkage groups for temporally replicated samples, (a) Norway migratory, (b) Norway stationary, (c) North Sea cod and (d) Baltic Sea cod.
mec12284-sup-0012-Supporting information legends.docxWord document24KAppendix S1 Captions of Figure S1–S7 and Table S1–S4 along with reference Weir & Cockerham (1984).

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