Selective Differentiation and Population Boundaries from RAD Sequencing Along a Microsatellite Isolation By Distance Gradient in Pacific Cod (Gadus macrocephalus)

Many marine species are characterized by an isolation-by-distance pattern (IBD), where more geographically distant samples are also more genetically differentiated. IBD patterns are well established in population genetics theory, can be explained by stepping stone migration models or limited dispersal within a continuous population, and can be used to estimate mean dispersal distances. However, they are problematic for management, because population boundaries and thus spatial management units cannot be identified. Genetic markers under selection, on the other hand, may provide more fine scale and informative estimates of population structure, as demonstrated for several Atlantic species. Here, we present data from genome-wide RAD sequencing surveys in Pacific cod Gadus microcephalus, which was previously shown to exhibit a tight IBD pattern using microsatellites. In addition, we assess selective differentiation between commercially exploited coastal cod and a rapidly declining population in Puget Sound, which was recently listed as a NOAA Species of Concern. Data are currently being collected, but we expect to find clear population structure along the coast, and high differentiation between Puget Sound and coastal cod at some genomic regions.