Population Genomics of Pacific Cod in Japanese Waters Identifies Signature of Selection and Fine Scale Population Structure from Genome-Wide Markers

Identifying factors shaping the distribution of intraspecific genetic diversity is a focal area in ecology and evolutionary biology. In marine realm, there are fewer physical barriers preventing dispersal, hence, gene flow is suggested being extensive and high genetic diversity is diffused among populations. However, environmental variables such as currents, bathymetry, and temperature gradients can be possible factors shaping population structure and can cause natural selection. The Pacific cod Gadus macrocephalus is widely distributed ground fish and sustains one of the largest fisheries in the North Pacific. Providing genetic background of cod stocks can be useful information to improve our management. Here, we analyzed population structure of Pacific cod using genome-wide single nucleotide polymorphism (SNP) markers via Restriction-site associated DNA sequencing using Next-Generation-Sequencing in 234 individuals from 19 locations across Japanese coastal area. SNP markers showed two distinct populations separating at the southern part of Sea of Japan, which was supported by our previous study using ordinary nuclear markers. Fine scale population structure with the respect to water bodies was also observed with large amount of SNPs. We also identified several loci that are under diversifying selection. Identifying populations that are locally adapted provide useful information to maintain sustainable resources.