BergEtAl2017_AtlanticCod_TransatlanticDataset_PLINK-formatSNP array data for 316 individuals of Atlantic cod (Gadus morhua), genotyped at 8,165 loci in standard PLINK file format. The PLINK file format consists of two files, a map file and a ped file. In the map file, the first column defines the linkage group, the second column contains the loci names (dbSNP accession numbers), the third line describes the position within the linkage groups (here all are set to 0) and the fourth column defines the order of the SNPs within each linkage group. In the ped file, column one is used to separate the populations (pop-1 to pop-9), column 2 defines the individuals within each population (denoted as the population abbreviation followed by the individual number) where the populations are abbreviated as follows: Can-N_PB = Placentia Bay, Can-N_SG = Southern Gulf of St. Lawrence, Can-S_SB = Sambro, Can-S_GM = Gulf of Maine, Can-S_BB = Browns Bank, Ice_F = Iceland Frontal, Ice_C = Iceland Coastal, NEAC = Northeast Arctic cod, NCC = Norwegian coastal cod. The genotypes are given as numbers from column 7 and onwards, where 1=A, 2=C, 3=G, 4=T. (For a thorough description of the PLINK format, please see https://www.cog-genomics.org/plink). All SNPs are referred to by their database of Single Nucleotide Polymorphisms (dbSNP) accession numbers, available from: http://www.ncbi.nlm.nih.gov/SNP.BergEtAl2017_AtlanticCod_TransatlanticDataset.zip

Chromosomal rearrangements such as inversions can play a crucial role in maintaining polymorphism underlying complex traits and contribute to the process of speciation. In Atlantic cod (Gadus morhua), inversions of several megabases have been identified that dominate genomic differentiation between migratory and non-migratory ecotypes in the Northeast Atlantic. Here, we show that the same genomic regions display elevated divergence and contribute to ecotype divergence in the Northwest Atlantic as well. The occurrence of these inversions on both sides of the Atlantic Ocean reveals a common evolutionary origin, predating the more than 100,000 years old trans-Atlantic separation of Atlantic cod. The long-term persistence of these inversions indicates that they are maintained by selection, possibly facilitated by co-evolution of genes underlying complex traits. Our data suggest that migratory behaviour is derived from more stationary, ancestral ecotypes. Overall, we identify several large genomic regions - each containing hundreds of genes – likely involved in the maintenance of genomic divergence in Atlantic cod on both sides of the Atlantic Ocean.