Landscape Genomics of Kokanee Salmon: Neutral and Adaptive Population Divergence and Their Implications for Fisheries Management

Sockeye salmon (Oncorhynchus nerka) exhibit a range of morphotypes and ecotypes, with the parallel evolution of smaller freshwater forms (kokanee) that now occur in many post-glacial lakes. Divergent kokanee ecotypes exist related to reproductive behaviour, including those that spawn in streams, along lakeshores and at depth in lakes. Shore and stream spawning ecotypes are morphologically identical and cannot be identified outside of the spawning season.  In some lakes different reproductive ecotypes co-occur. The environmental pressures that affect each ecotype may differ significantly; the inability to assign individuals to ecotype presents challenges for assessing stock-specific population trends. We used restriction site-associated DNA (RAD) sequencing to investigate neutral and adaptive divergence within and among paired co-occurring ecotypes of shore and stream spawning kokanee from four lakes across British Columbia, and between paired kokanee and anadromous sockeye populations in both the Columbia and Frazer River drainages (total n = 504). We identified highly diverged loci (outlier loci) between ecotype pairs within each lake, and inferred underlying mechanisms associated with ecotype divergence. Reconstructed patterns of neutral and putatively adaptive genetic variation have the potential to contribute to conservation management by informing prioritization of populations at risk and identifying ecotype within lakes to guide monitoring activities.