Among highly migratory fish species, nursery areas occupied by juveniles often differ from adult habitats. To better understand the spatial dynamics of Canada’s Northern cod stock, juveniles caught off the east coast of Newfoundland and Labrador were compared to adults from the same region as well as individuals from other areas in Atlantic Canada using ddRAD-derived SNPs. A reduced proportion of homozygotes with a chromosomal inversion located in LG1 was detected between juvenile and adult samples in the Northern cod stock region, potentially indicating age-dependent habitat use or ontogenetic selection for attributes associated with the many genes located in LG1. No neutral genetic differences were found between samples from the Northern cod stock; however, significant differences were found between some of these samples and cod collected from St. Pierre Bank, Bay of Fundy, Browns Bank and the southern Scotian Shelf. Clustering analysis of variants at neutral loci provided evidence for three major genetic units: 1) the Newfoundland Atlantic Coast, 2) eastern and southern Gulf of St. Lawrence and Burgeo Bank, and 3) the Bay of Fundy, Browns Bank and southern Scotian Shelf. Both adaptive and neutral population structure within the Northern cod stock should be considered by managers to promote rebuilding.

DNA was prepared using a ddRAD protocol and 125PE sequenced 60-96 individuals/lane on an Illumina HiSeq2500. SNPs were selected using STACKS and various software described in "Life-stage dependent supergene haplotype frequencies and metapopulation neutral genetic patterns of Atlantic cod, Gadus morhua, from Canada’s Northern cod stock region and adjacent areas." Please refer to publication for individual codes.