COS 150-3 - Fine-scale genetic structure of Atlantic Cod’s (Gadus morhua) populations in NW Atlantic detected using low coverage whole genome sequencing

Background/Question/Methods

Population genomic research has revealed the importance of chromosomal rearrangements such as inversions for the maintenance of genetic diversity in wild populations. In Atlantic cod (Gadus morhua), four major inversions have been described, one in each of chromosomes 1, 2, 7 and 12. Two of these inversions (chromosomes 1 and 12) appear to drive much of the genetic differentiation observed in Canadian populations. Analysis at a local geographic scale around Newfoundland or across multidecadal scales since Newfoundland stocks collapsed in the early 1990s, have not, however, yet been performed. Here we focused on the Grand Banks and nearby areas. Using low coverage whole genome sequencing (lcwgs) we analyzed genetic differentiation across temporal (1990s vs 2010s) and geographic scales (at least 10 locations).

Results/Conclusions

We report results based on >300 individuals with ~2.4x average depth and 60-90% genome coverage. Temporal comparisons revealed no changes in genetic diversity. Although overall genetic differentiation across geographic locations was low, preliminary results indicate individuals cluster following patterns driven by the inversions in chromosome 1 and 12, with further clustering based on geographic location. Within these subclusters, collections from the northern Grand Banks were genetically distinguishable from those from the southern Grand Banks. This differentiation was not associated with any of the four major inversions. Instead, it appears to be driven by a genomic region associated with differences between spring and winter spawners. This study contributes to our understanding of the patterns of genetic diversity and structure among Atlantic cod populations around Newfoundland. Increasing our knowledge of cod populations can help with recovery efforts.