Genome-wide SNPs reveal novel genetic relationships among Atlantic cod (Gadus morhua) from the south coast of Newfoundland, Canada (subdivision 3Ps), Northern cod stock complex, and Gulf of St Lawrence

The south coast of Newfoundland, Canada (Northwest Atlantic Fisheries Organization (NAFO) Subdivision 3Ps) is known to be a mixing zone for Atlantic cod (Gadus morhua). Tagging and genetic studies have shown cod from the Northern and Southern Gulf of St. Lawrence (NAFO Divisions 3Pn, 4RST), Southern Grand Banks (3NO), and the Northern cod stock complex (2J3KL) frequent the waters of 3Ps at various times throughout the year, but the extent of genetic mixing is unknown. However, 3Ps has not been the central focus of previous large-scale genomic analyses of population structure, a knowledge gap that we address using single nucleotide polymorphisms. Using 38,111 neutral markers from reduced representation next-generation sequencing data, we determined the provenance of 3Ps cod relative to the Northern stock complex, Gulf of St. Lawrence, Bay of Fundy, and Gulf of Maine. We present evidence for genetic similarity between 3Ps and the Northern stock complex, particularly NAFO Division 3L. Additionally, genetic clustering analyses suggest 3Ps to be a mixed stock, containing individuals from the Northern stock complex and Gulf of St. Lawrence. Genetic clustering also suggests that there are two subtle subclusters of Northern stock complex and 3Ps cod, indicating there may be subtle population structure within the Northern stock complex and surrounding zones. This new information on population structure gives insight into connectivity and may be useful in future management for rebuilding cod populations.