The PDF file includes:

• Fig. S1. Fine-scale analysis of individual divergence and LD within LG1 using whole-genome data obtained from Barney et al. (19).
• Fig. S2. Significance of association per SNP with migration phenotype in a LFMM, categorizing SNPs with a false discovery rate q value of <0.05 as significant.
• Fig. S3. Comparison of historical and recent (2004) effective size of LG1 homozygous noninverted, LG1 homozygous inverted, and heterozygous individuals in Labrador, Newfoundland, and offshore sites and proportion of each genotype group at each site.
• Fig. S4. Recent effective population size relative to maximum effective population size within each group of LG1 homozygous noninverted, LG1 homozygous inverted, and heterozygous Northern cod groupings calculated using LinkNe assuming a bin size of 0.01 M, plotted with reconstructed estimates of historical biomass measured from 1500 to 2004 (11) relative to the maximum value.
• Fig. S5. Comparison of historical and recent (2004) effective size in subsamples of 41 LG1 homozygous noninverted individuals.
• Legends for tables S1 to S3

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Other Supplementary Material for this manuscript includes the following:

• Table S1 (Microsoft Excel format). Site code, geographic location (latitude, longitude, name), dataset source, number of genotyped individuals, migratory behavior, and sites used to infer migratory behavior from Robichaud and Rose (20) for 511 Atlantic cod (G. morhua) samples.
• Table S2 (Microsoft Excel format). Single Nucleotide Polymorphism Database (dbSNP) information for all 24 migration-associated SNPs identified across all genome-wide association methods, and gene names and functions of closest known gene for each SNP as described by Berg et al. (10).
• Table S3 (Microsoft Excel format). Effective size estimates calculated by LG1 rearrangement genotype using LinkNe.