Sources of coaster brook trout (Salvelinus fontinalis) revealed by genomic analysis of brook trout populations along Minnesota's shoreline with Lake Superior

Knowledge of population-level relationships and how these relationships pertain to different life history forms is critical to developing effective management plans for native trout, char, and salmon. In the Lake Superior basin, identifying effective restoration strategies for coaster brook trout (Salvelinus fontinalis), a lake-inhabiting form of brook trout, is hampered by limited information on genetic connectivity and source-sink dynamics among brook trout populations. Here, we infer these relationships by surveying 8,178 single nucleotide polymorphisms in 234 brook trout from seven rivers along the Minnesota shoreline with Lake Superior, including from reaches above and below natural waterfalls that prevent upstream movement. We identified well-differentiated above-barrier populations that supply brook trout to below-barrier reaches. We also compared within-river brook trout to 26 coaster brook trout from Lake Superior. We identified at least four source populations for these coaster brook trout, three of which were located within rivers. Additionally, we estimated NE for within-river populations and detected a decline across recent generations, with the most recent estimates approaching critical thresholds. Finally, comparisons with 94 domestic brook trout representing nine hatchery strains revealed a lack of domestic introgression into wild populations, demonstrating the importance of natural reproduction to population persistence. Our results offer novel insights into sources of coaster brook trout and highlight the role of within-river populations in supporting the coaster life history. Management efforts focused on instream restoration may be more important to rehabilitating coaster brook trout than previously thought, and are urgently needed given the population-level conservation status reported here.

厘清种群水平的相互关系及其与不同生活史型的关联，是制定本土鳟类、红点鲑及鲑鱼有效管理方案的核心前提。在苏必利尔湖流域，针对洄游溪鳟（coaster brook trout，*Salvelinus fontinalis*，溪红点鲑的湖泊栖息型类群）制定高效修复策略的工作，因溪红点鲑种群间遗传连通性与源汇动态的相关研究数据不足而进展受阻。本研究通过对苏必利尔湖明尼苏达沿岸7条河流的234尾溪红点鲑进行8178个单核苷酸多态性（single nucleotide polymorphisms, SNP）位点分型，推断上述种群关系，采样覆盖了阻断上游洄游的天然瀑布上下游河段的个体。研究发现，瀑布屏障上游的种群分化程度极高，且可为下游河段的溪红点鲑种群提供个体补充。本研究同时将河溪内的溪红点鲑种群与26尾采自苏必利尔湖的洄游溪鳟进行了比对分析，结果显示这些洄游溪鳟至少存在4个源种群，其中3个分布于河流之中。此外，本研究估算了河溪内种群的有效种群大小（effective population size, Ne），并检测到近几代种群数量持续下降，最新估算值已接近临界阈值。最后，本研究将野生种群与代表9个孵化场品系的94尾养殖溪红点鲑进行比对，结果显示野生种群未受到养殖个体的基因渐渗，这表明自然繁殖对于种群存续至关重要。本研究结果为洄游溪鳟的源种群来源提供了全新见解，并凸显了河溪内种群对维持洄游型生活史的关键作用。相较于此前认知，聚焦于河流生境修复的管理措施，或许对洄游溪鳟的种群恢复更为关键；结合本研究报道的种群保护现状，这类管理工作亟待开展。