The Time of Origin and Genetic Diversity of Three Isolated Kokanee Populations in Southwest Alaska

<p>We examined the time of origin and genetic diversity of native kokanee, the nonanadromous ecotype of Sockeye Salmon <i>Oncorhynchus nerka</i>, 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 estimates of the time of origin for kokanee in Jo-Jo Lake (170 years before present [ybp]) and Devil’s Cove Lake (6,583 ybp) were consistent with the relative age of barriers isolating each lake. However, data from Dakavak Lake (1,379 ybp) suggested that the barrier was older than hypothesized. Indices of intrapopulation diversity were lower for kokanee than for Sockeye Salmon. Estimates for kokanee population divergence (<i>R</i>_ST; the <i>F</i>_ST analog for microsatellites) among the three lakes were consistent with time of origin estimates. Furthermore, the most recently isolated kokanee (Jo-Jo Lake population) were most closely related to neighboring Sockeye Salmon. Only the kokanee from Jo-Jo Lake exhibited a relatively low historical effective population size (<i>N_e</i> ≈ 107) and evidence of a genetic bottleneck. Taken together, the results of this study show that although rare, kokanee in Alaska are not ephemeral and can persist in isolation for hundreds of generations despite the colder temperatures and shorter growing season, that are thought to limit their sustainability in Alaska.</p> <p>Received April 26, 2017; accepted July 25, 2017 Published online September 25, 2017</p

KATM Kokanee and Sockeye Salmon genotypes

Genotype data from 13 microsatellite loci for Kokanee and Sockeye Salmon from the Katmai National Park and Preserve in southwest Alask

Raw_data

Quantification cycle values and scores for Northern pike DNA in water samples collected at multiple lakes across time

Schematic of the locations of eDNA sampling.

<p>Locations of pre (○)and post (●)-rotenone treatments are identified in Derks, East Mackey, Union, and West Mackey Lakes near Soldotna, AK. Post-treatment samples were collected at all pre-treatment sample locations. The background base map is exclusive property of Environmental Systems Research Institute, Inc. (Esri).</p

Physical habitat and fish stocking data for caged and carcass experiments.

<p>Physical habitat and fish stocking data for caged and carcass experiments.</p

Schematic of the locations of Northern pike cages relative to eDNA sampling locations.

<p>Northern pike carcass locations were identical to cage locations in Tiny, Gensle, Little Bear, and Denise lakes near Soldotna, AK. The background base map is exclusive property of Environmental Systems Research Institute, Inc. (Esri).</p