Genetic monitoring of steelhead in the Klickitat River to estimate productivity, straying, and migration timing

Salmonids with complex life history variation present challenges for conservation management, but genetic approaches alongside fisheries monitoring can address questions regarding viability of natural populations. We genotyped adult (n=3,108) and juvenile (n=2,624) samples of anadromous Oncorhynchus mykiss that were collected in the Klickitat River, WA, USA at traps in the lower drainage to examine tributary level productivity, straying from outside sources and variation in adult migration timing. Genetic assignment of steelhead from this system indicated that the majority were produced within or near tributaries of the middle Klickitat River (juvenile mean = 72.8%; adult mean = 87.3%). Analyses with parentage-based tagging identified that most hatchery-origin adults were assigned to the Skamania Hatchery (80.8%) as expected since this has been the release stock for decades within the Klickitat River drainage. Hatchery-origin adults were also identified from programs operating outside the Klickitat River, which were primarily strays from Snake River hatcheries. Most natural-origin steelhead were assigned to the Klickitat River, but there were also natural-origin fish identified as strays from other regions of the Columbia River (22.3% of natural returns). We also examined genes known to be associated with migration timing in adult steelhead observed at the trap and observed a strong relationship between migration date and alleles for early and late migration, but individual outliers were detected across seasons. Our results indicate that genetic variation of steelhead in the Klickitat River has been influenced by hatchery programs as well as natural-origin straying from other sub-basins, but genetic diversity remains high throughout the sub-basin, and both early and late migration alleles are maintained. The genetic diversity present in Klickitat River steelhead may enable this Endangered Species Act listed (threatened) species to better adapt to stochastic environmental conditions compared to less diverse populations.生活史变异复杂的鲑科鱼类（Salmonids）对保护管理工作构成显著挑战，但遗传学研究方法结合渔业监测手段，可有效解答自然种群生存力相关的核心问题。本研究对采自美国华盛顿州克利基塔特河下游流域拦鱼栅的溯河洄游型虹鳟（Oncorhynchus mykiss）成体（n=3108）及幼体（n=2624）样本进行基因分型，旨在探究支流尺度的种群生产力、外源个体洄游扩散现象以及成体洄游时间的变异特征。针对该体系内钢头鳟（steelhead）的遗传归属分析结果显示，绝大多数个体起源于克利基塔特河中游支流及其周边区域（幼体占比均值为72.8%，成体占比均值为87.3%）。基于亲权标记法（parentage-based tagging）的分析结果表明，如预期所示，多数养殖起源的成体个体被归为斯卡马尼亚孵化场（Skamania Hatchery）来源（占比80.8%）——这是因为该孵化场数十年来一直是克利基塔特河流域的放流种群来源。同时也鉴定出了来自克利基塔特河流域以外放流项目的养殖起源成体，这些个体主要为来自斯内克河（Snake River）孵化场的洄游扩散个体。绝大多数野生起源的钢头鳟被归属至克利基塔特河，但也有22.3%的野生回归个体被鉴定为来自哥伦比亚河（Columbia River）其他区域的洄游扩散个体。本研究还对拦鱼栅处采集的成体钢头鳟中已知与洄游时间相关的基因进行分析，结果发现洄游日期与早、晚洄游相关等位基因之间存在显著关联，但不同季节均检测到个别极端异常个体。本研究结果显示，克利基塔特河钢头鳟的遗传变异受到孵化场放流项目以及来自其他子流域野生个体洄游扩散的共同影响，但整个子流域的遗传多样性仍维持在较高水平，且早、晚洄游相关等位基因均得以保留。相较于遗传多样性较低的种群，克利基塔特河钢头鳟所具备的遗传多样性，可帮助这一被列入《濒危物种法》（Endangered Species Act）“受威胁”等级的物种更好地适应随机波动的环境条件。