Challenges and Opportunities for Genetics-Based Fisheries Management of Recently Diverged Stocks

Genetics-based approaches have informed fisheries management for decades, yet remain challenging to implement within systems involving recently diverged stocks or where low levels of gene flow persist. North American lakes containing stream- and shore-spawning kokanee (Oncorhynchus nerka) represent good examples of fisheries exhibiting both of these confounding factors. Nevertheless, the ability to distinguish kokanee ecotypes remains important to fisheries managers, as they may be differentially impacted by alternative management regimes.  To date, individual assignment and mixed composition analyses based on neutral microsatellite loci have produced unacceptably high error rates for improving upon more traditional approaches to stock assessment, namely visual counts.  To overcome these challenges, work in my lab has explored the informativeness of outlier loci for distinguishing among kokanee ecotypes. Outlier loci are those that deviate from expected neutral expectations and represent candidate gene regions exhibiting signatures of selection, in this case, potentially underlying ecotype divergence. In Okanagan Lake, BC, we identified eight outliers among 52 polymorphic expressed sequence tagged-linked microsatellite loci that detected ecotype-level divergence, whereas there was no evidence of among-ecotype or among-site divergence using neutral loci alone. The outlier loci exhibited the highest self-assignment accuracy to ecotype (92.1%), substantially outperforming 44 neutral loci (71.8%). Similarly, outlier loci achieved >95% correct estimation of simulated mixture samples, as opposed to <85% accuracy using neutral loci. These results were robust among sampling years, with assignment and mixed composition estimates for individuals sampled in 2010 mirroring baseline results. Overall, outlier loci constitute promising alternatives to neutral loci for informing fisheries management involving recently diverged stocks.