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Supporting information for Hemmer-Hansen et al.: A genomic island linked to ecotype
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divergence in Atlantic cod
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Supporting figures
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Figure S1: Number of SNPs per scaffold for 1167 SNPs obtained through blasting SNP
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flanking sequences against the cod genome assembly.
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Figure S2: Distance to previous SNP for 704 SNPs located in scaffolds with more than one
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SNP.
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Figure S3: Population relationships among eastern Atlantic samples based on correspondence
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analysis with all markers (a, 750 loci) and with neutral markers only (Axes 1 and 2 in b) and
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axes 1 and 3 in c), 667 loci). Loci with a minor allele frequency below 10% were excluded
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from the analyses.
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Figure S4: Pairwise levels of population differentiation, estimated by Weir and Cockerhams θ
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(Weir & Cockerham 1984), for 1199 loci ordered within linkage groups for all population
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samples. Horizontal dashed and dotted lines represent mean and 95% confidence interval
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generated by bootstrapping over loci. Loci in linkage groups 1, 2, 7 and 12 are coloured red,
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blue, green and purple, respectively, while additional linkage groups are coloured in
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alternating shades of grey and loci with unknown linkage group are shown in black. Location
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within linkage group is unknown for loci to the right of the vertical line.
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Figure S5: Global FST among eastern Atlantic samples (red line) and number of loci in data
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sets (blue line) for different minor allele frequency thresholds used to filter the data.
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Figure S6: Pairwise levels of population differentiation, estimated by Weir and Cockerhams θ
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(Weir & Cockerham 1984), for 1113 loci ordered within linkage groups for temporally
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replicated samples. Horizontal dashed and dotted lines represent mean and 95% confidence
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interval generated by bootstrapping over loci. Loci in linkage groups 1, 2, 7 and 12 are
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coloured red, blue, green and purple, respectively, while additional linkage groups are
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coloured in alternating shades of grey and loci with unknown linkage group are shown in
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black. Location within linkage group is unknown for loci to the right of the vertical line.
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Figure S7: Observed levels of heterozygosity based on 925 loci, estimated as moving
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averages within linkage groups for temporally replicated samples, (a) Norway migratory, (b)
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Norway stationary, (c) North Sea cod and (d) Baltic Sea cod. Vertical dashed line marks the
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1st percentile over all linkage groups. Estimates for linkage groups 1, 2, 7 and 12 are coloured
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red, blue, green and purple, respectively, while additional linkage groups are coloured in
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alternating shades of grey.
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Supporting tables
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Table S1. Genotyped SNPs with SNPs equence, associated dbSNP reference number,
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information from the genome alignment and estimates of heterozygosity in each of the eight
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samples.
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Table S2. Pairwise FST with 95% confidence intervals from 1000 bootstrapped data sets for
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the full data set (1199 loci, below diagonal) and for a reduced data set where outliers
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identified through Bayesian regression were removed (1112 loci, above diagonal).
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Table S3. Results from Bayesian regression analysis based on 975 loci with minor allele
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frequency above 2%. Linkage group and position within linkage group are given for each
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locus. Global FST, posterior probability and Posterior Odds for a model with selection
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compared to a model without selection were estimated by the programme BAYESCAN.
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Results were controlled for multiple testing by setting the false discovery rate threshold at
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5%. Outliers marked with an asterix were not confirmed in an outlier test based on loci with
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minor allele frequencies above 10%.
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Table S4. Levels of population differentiation (Weir and Cockerhams θ (Weir & Cockerham
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1984)) between migratory and stationary ecotype samples for 57 loci with known linkage
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group position in linkage group 1 and outlier status from Bayesian regression analysis.
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References
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Weir B, Cockerham C (1984) Estimating F-Statistics for the Analysis of Population-
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Structure. Evolution, 38, 1358-1370.
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