Data from: The time of origin and genetic diversity of three isolated Kokanee populations in southwest Alaska

We examined the time of origin and genetic diversity of native Kokanee, the nonanadromous ecotype of Sockeye Salmon Oncorhynchus nerka, from three isolated lakes in the Katmai National Park and Preserve in southwest Alaska. These Kokanee evolved independently from Sockeye Salmon when migration barriers arose, blocking ocean access. We used information about the relative age of each barrier to hypothesize the relative time of origin for Kokanee in each lake. In addition, we used data from 13 microsatellite loci to test our time of origin hypotheses and assess genetic diversity of Kokanee from these three lakes and proximate Sockeye Salmon populations. Coalescent-based esti mates of the time of origin of Kokanee in Jo-Jo (170 ybp) and Devil’s Cove (6, 583 ybp) lakes were consistent with the relative age of barriers isolating each lake. However, data from Dakavak Lake (1,379 ybp) suggested the barrier was older than hypothesized. Indices of intra-population diversity were lower for Kokanee than Sockeye Salmon. Estimates for Kokanee population divergence (RST) among the three lakes were consistent with time of origin estimates. Further, the most recently isolated Kokanee from Jo-Jo Lake were most closely related to neighboring Sockeye Salmon. Only the Kokanee from Jo-Jo Lake exhibited relatively low historical effective population size (Ne ≈ 107) and evidence of a genetic bottleneck. Taken together, the results of this study show that, while rare, Kokanee in Alaska are not ephemeral and can persist in isolation for hundreds of generations despite the colder temperatures and shorter growing season thought to limit their sustainability in Alaska.