Stream or Shore? Outlier Loci Distinguish Kokanee Ecotypes to Inform Fisheries Management

Delineating and monitoring kokanee stocks for management is difficult because visual assignment of individuals to shore- and stream-spawning ecotypes is only possible during the spawning season, and enumerations of shore-spawners are likely inaccurate due to poor visibility in steep beach environments. Genetic markers are cost-effective tools used for estimating stock abundance in many fisheries, however kokanee are recently diverged (<15,000 years before present) and conventional neutral markers are not sufficient for distinguishing ecotypes. Here we used population genomic approaches to identify outlier loci, markers that deviate from expected neutral expectations and represent candidate gene regions exhibiting signatures of selection associated with spawning behaviour.  We applied these markers to address fisheries management questions in two BC lakes exposed to differing pressures.  In Wood Lake, the most popular recreational kokanee fishery in BC, outlier loci and sex-specific markers were effective for estimating relative proportion of stream- and shore-spawning ecotypes, monitoring long-term population trends, and assessing ecotype or sex-specific bias in angling. In Kootenay Lake, neutral and outlier loci reconstructed stock structure and distinguished ecotypes to inform assessment of the differential impact of water level management on stream- and shore-spawning kokanee.