Raw ddRAD sequence data from 380 Atlantic cod (Gadus morhua).

In an effort to address fundamental questions of population structure of Atlantic cod in the western Atlantic Ocean, we performed a whole genome scan on hundreds of spawning adults and juveniles captured throughout Atlantic Canada. This collection of samples represents one of the most comprehensive sampling efforts to date in this region. We discovered a reduced proportion of homozygotes for a super-gene complex associated with adaptations to thermal gradients among adults, relative to juveniles. This is a potential indicator of age-dependent habitat use or ontogenetic selection for attributes associated with the many genes located in chromosomal inversion LG1. Our research is unique due to this comparison of juvenile and adult samples and the revelation that super-gene frequencies may be age-dependent.