For the sea otter (Enhydra lutris), genetic population structure is an area of research that has not received significant attention, especially in Southwest Alaska where that distinct population segment has been listed as threatened since 2005 pursuant to the U.S. Endangered Species Act. In this study, 501 samples from 14 locations from Prince William Sound, Alaska to the Commander Islands in Russia were analyzed for variation at 13 microsatellite loci. Our results indicate a high degree of genetic divergence among the 14 locations (F_ST = 0.12) with gene flow conforming to the isolation by distance (IBD) model (r² = 0.491, p < 0.05). The 14 sampling locations formed six geographic associations in clustering and ordination analyses that likely correspond to remnant population lineages: 1) Southcentral Alaska, 2) Kodiak and North Alaska Peninsula, 3) South Alaska Peninsula and Bristol Bay, 4) Eastern Aleutian, 5) Western Aleutian, and 6) the Commander Islands. Except for South Alaska Peninsula and Bristol Bay, these clusters closely agree with previously defined stock and management unit boundaries. Our results reveal significant genetic population structure and are generally congruent with current management strategies for the threatened Southwest Alaska distinct population segment.

The file contains microsatellite data from 13 loci for 501 sea otters collected from 14 locations in Alaska and Russia. The individual's sex and latitude and longitude of sample collection are included with the multilocus genotype. Missing data are coded as "0" and "U" indicates that the sex of the individual is unknown.