Data from: Detection of outlier loci and their utility for fisheries management

Genetics-based approaches have informed fisheries management for decades, yet remain challenging to implement within systems involving recently diverged stocks or where gene flow persists. In such cases, genetic markers exhibiting locus-specific (“outlier”) effects associated with divergent selection may provide promising alternatives to loci that reflect genome-wide (“neutral”) effects for guiding fisheries management. Okanagan Lake kokanee (Oncorhynchus nerka), a fishery of conservation concern, exhibits two sympatric ecotypes adapted to different reproductive environments, however, previous research demonstrated the limited utility of neutral microsatellites for assigning individuals. Here, we investigated the efficacy of an outlier-based approach to fisheries management by screening >11,000 expressed sequence tags for linked microsatellites and conducting genomic scans for kokanee sampled across seven spawning sites. We identified eight outliers among 52 polymorphic loci that detected ecotype-level divergence, whereas there was no evidence of divergence at neutral loci. Outlier loci exhibited the highest self-assignment accuracy to ecotype (92.1%), substantially outperforming 44 neutral loci (71.8%). 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 for informing fisheries management involving recently diverged stocks, with potential applications for designating management units across a broad range of taxa.

数十年来，基于遗传学的方法一直为渔业管理提供决策支撑，但在涉及近期分化种群或存在持续基因流的渔业系统中，这类方法仍难以顺利实施。在此类场景下，与歧化选择相关的、表现出位点特异性“异常位点（outlier）”效应的遗传标记，或许可作为反映全基因组范围“中性（neutral）”效应的遗传位点的替代方案，用于指导渔业管理。
奥卡诺根湖的陆封红大马哈鱼（Okanagan Lake kokanee, *Oncorhynchus nerka*）是具有保护关注度的渔业资源，其存在两种适应不同繁殖环境的同域生态型，但此前研究显示，中性微卫星（neutral microsatellites）在个体归属鉴定中的应用效果有限。
本研究通过对11000余个表达序列标签（expressed sequence tags）中连锁的微卫星（microsatellites）进行筛选，并对7个产卵场采集的陆封红大马哈鱼样本开展基因组扫描，探究了基于异常位点的渔业管理方法的有效性。
我们在52个多态性位点中鉴定出8个异常位点，这些位点可有效检测到生态型水平的遗传分化，而中性位点则未表现出任何分化迹象。
异常位点在生态型自我归属鉴定中展现出最高准确率（92.1%），显著优于44个中性位点的71.8%准确率。
研究结果在不同采样年份间保持稳健，2010年采集样本的归属鉴定与混合组成估算结果与基准结果完全一致。
总体而言，异常位点可为涉及近期分化种群的渔业管理提供极具潜力的替代方案，有望在广泛的分类单元中用于划定渔业管理单元。