Assigning Individual Pacific Cod Gadus macrocephalus to Population of Origin Along an Isolation-By-Distance Gradient Using RAD Sequencing

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 problematic for management because distinct population boundaries, and thus spatial management units, cannot often be clearly delineated.  Assignment tests could potentially be used to identify population of origin, facilitating management by estimating seasonal migration patterns and distances, as well as detecting productive areas.  However, most IBD patterns are shallow and assignment tests have little power.  Here, we successfully applied restriction site-associated DNA (RAD) sequencing toward stock identification in the Pacific cod (Gadus macrocephalus), which exhibits a nearly perfect IBD pattern along the northeastern Pacific coast.  Using 6,756 single nucleotide polymorphisms (SNPs), we were able to reassign 95-100% of fish to their reference population of origin, with high confidence, while still reproducing the strong IBD pattern found in earlier studies.  Moreover, we identified over 200 SNPs that may be under selection across the sampled range.  These results lay the groundwork for future genetic stock identification and genetics-based management of Pacific cod.