Measurement of population structure of cod (Gadus morhua) in NAFO Subdivision 3Ps off southern Newfoundland by means of next-generation sequencing and genomic analysis

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University of New Brunswick


Once Canada’s biggest fishery, Atlantic Cod (Gadus morhua) stocks in the Northwest Atlantic collapsed in the 1990s, with recovery strategies proving unsuccessful. I focus on NAFO subdivision 3Ps off Newfoundland’s south coast. Tagging and genetic studies suggest 3Ps is a mixed stock of unknown composition. Greater power is required to see how 3Ps cod fits within Northwest Atlantic cod, which we address using Single Nucleotide Polymorphisms (SNPs). I compared 238 fish in 3Ps to three genetic clusters (Northern (NAFO 2J3KL), Saint Lawrence (NAFO 4SRT), Southern populations (NAFO 4X, 5YZ)) at 25,458 neutral SNPs. Supergene allele frequencies in juveniles and adults were also compared. I provide evidence for genetic similarity between 3Ps and Northern cod and evidence of two potential Northern cod subpopulations. Lastly, I observed decreasing supergene allele frequencies as 3Ps cod age. For species like cod with complex population structure, genomics helps understand population structure to inform recovery strategies.