Population substructure of harbor seals (Phoca vitulina richardsi) in Washington State using mtDNA

We examined the pupping phenology and genetic variation between the currently defined stocks of harbor seals, Phoca vitulina richardsi (Gray, 1864), in Washington’s coastal and inland waters and looked in detail at genetic variation within the inland waters of Washington. We analyzed mtDNA variation in 552 harbor seals from nine areas in Washington State and the Canada–US transboundary waters. A total of 73 haplotypes were detected; 37 individuals had unique haplotypes. Pupping phenology and levels of genetic variation between the outer coastal stock (WA Coastal Estuaries, WA North Coast) and the inland waters stock (British Columbia, Boundary Bay, San Juan Islands, Smith/Minor Islands, Dungeness Spit, Hood Canal, Gertrude Island) corroborated the appropriateness of the present stock boundary. However, within the inland waters stock, Hood Canal and Gertrude Island were significantly different from the coastal stock, from the rest of the inland waters stock, and from each other. This indicates a total of four genetically distinct groups in Washington State, suggesting that managing the inland waters as a single stock may be erroneous.