Contemporary genetic structure affects genetic stock identification of steelhead trout in the Snake River basin

Genetic stock identification is a widely applied tool for the mixed-stock management of salmonid species throughout the North Pacific Rim. The effectiveness of genetic stock identification is dependent on the level of differentiation among stocks which is often high due to the life history of these species that involves high homing fidelity to their natal streams. However, the utility of this tool can be reduced when natural genetic structuring has been altered by hatchery translocation and/or supplementation. We examined the genetic population structure of ESA-listed steelhead in the Snake River basin of the United States. We analyzed 9,613 natural-origin adult steelhead returning to Passive Integrated Transponder detection sites throughout the basin from 2010 through 2017. Individuals were genotyped at 180 single nucleotide polymorphic genetic markers and grouped into 20 populations based on their return location. While we expected to observe a common pattern of hierarchical genetic structuring due to isolation by distance, we observed low genetic differentiation between populations in the upper Salmon River basin compared to geographically distant populations in the lower Snake River basin. These results were consistent with lower genetic stock assignment probabilities observed for populations in this upper basin. We attribute these patterns of reduced genetic structure to the translocation of lower basin steelhead stocks and ongoing hatchery programs in the upper Salmon River basin. We discuss the implications of these findings on the utility of genetic stock identification in the basin and discuss opportunities for increasing assignment probabilities in the face of low genetic structure.

遗传种群识别（Genetic Stock Identification, GSI）是环北太平洋区域广泛应用于鲑科鱼类混合种群管理的技术工具。其效能取决于种群间的遗传分化水平；这类物种因具有对出生溪流高度归巢的生活史特征，种群间遗传分化通常较高。然而，当天然遗传结构因人工孵化场的种群移殖与/或增补发生改变时，该技术的应用效用便会降低。
本研究针对美国斯内克河（Snake River）流域内列入《濒危物种法案》（Endangered Species Act, ESA）的硬头鳟开展种群遗传结构分析。我们分析了2010至2017年间，返回流域内各被动集成应答器（Passive Integrated Transponder, PIT）检测点的9613尾野生成年硬头鳟样本，对所有个体的180个单核苷酸多态性（Single Nucleotide Polymorphism, SNP）遗传标记进行基因分型，并根据其洄游返回位点划分为20个种群。
尽管我们预期会观察到由距离隔离效应导致的层级化遗传结构这一常见模式，但与斯内克河下游流域地理距离较远的种群相比，萨蒙河上游流域的种群间却呈现出较低的遗传分化水平。该结果与该上游流域种群较低的遗传种群识别成功率相符。我们将这种遗传结构弱化的现象归因于萨蒙河上游流域开展的下游流域硬头鳟种群移殖，以及持续进行的人工孵化场繁育项目。最后，本研究探讨了上述发现对该流域内遗传种群识别技术应用的影响，并针对低遗传分化背景下提升种群识别成功率的可行路径展开讨论。