This PDF file includes:

• Fig. S1. Principal components analysis of whole-genome variation among Pacific, Arctic, and Atlantic cods.
• Fig. S2. Phylogenetic networks, root mismatch, and ghost effects.
• Fig. S3. Phylogenetic networks, further examples.
• Fig. S4. Sampling localities of Pacific, Arctic, and Atlantic gadids on a world map centered on the Arctic.
• Table S1. ABBA-BABA D test for the whole genome of six gadid species with Arctic cod as the root.
• Table S2. ABBA-BABA D test for the whole genome of six gadid species with Polar cod as the root.
• Table S3. ABBA-BABA D test for individual linkage groups of six gadid species with Arctic cod as the root.
• Table S4. D_FOIL statistics of admixture and introgression.
• Table S5. Summary statistics of sequencing coverage.
• Table S6. Number of parsimony informative sites, number of blocks of 5000 parsimony-informative characters, and number of mdl generated “recombinational genes” used in the SNaQ (32) analysis of different linkage groups.

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