Central Valley Project, Genetic Determination of Population of Origin 2011-2021

Central Valley Chinook Salmon populations differ in their Endangered Species Act listing status. It is often difficult to distinguish individuals from the different Evolutionarily Significant Units. As such, many of the salmon monitoring and evaluation efforts in the Central Valley and San Francisco Bay-Delta are hampered by uncertainty about population (stock) identification and proportional effects of management actions (Dekar et al. 2013; IEP 2019). Studies have identified that the current identification method (length-at-date models) of juvenile Chinook salmon (Fisher 1992) captured in the watershed vary in their accuracy, particularly for spring-run (NMFS 2013; Harvey et al. 2014; Merz et al. 2014). The inaccuracy of the size-based methods is likely due to differences in fish distribution during early rearing, habitat-specific growth rates, and inter-annual variability in temperatures and food availability that lead to overlap in size ranges among stocks. The primary objective of this project was the genetic classification (to race; Evolutionary Significant Unit) of Chinook Salmon captured from State Water Project and Central Valley Project fish protection facilities and Interagency Ecological Program monitoring programs. The population-of-origin was determined for sampled fish by comparing their genotypes to reference genetic baselines. Genetic methods, having less statistical uncertainty that size-based models for population identification, were intended to directly target (and reduce) one source of uncertainty in the estimation of loss (take) from water diversions (operations) and develop the information necessary for understanding stock-specific distribution, habitat utilization, abundance, and life history variation. This project supports recommendations from the Interagency Ecological Program’s Salmon and Sturgeon Assessment of Indicators by Life Stage and Interagency Ecological Program Science Agenda efforts to improve Central Valley salmonid monitoring (Johnson et al. 2017; IEP 2019). Literature Cited Dekar, M., P. Brandes, J. Kirsch, L. Smith, J. Speegle, P. Cadrett and M. Marshall. 2013. USFWS Delta Juvenile Fish Monitoring Program Review. Background Document. Prepared for IEP Science Advisory Group, June 2013. US Fish and Wildlife Service, Stockton Fish and Wildlife Office, Lodi, CA. 224 p. Fisher, F.W. 1992. Chinook Salmon, Oncorhynchus tshawytscha, growth and occurrence in the Sacramento-San Joaquin River system. California Department of Fish and Game, Inland Fisheries Divisions, draft office report, Redding. Harvey, B.N., D.P. Jacobson, M.A. Banks. 2014. Quantifying the uncertainty of a juvenile Chinook Salmon Race Identification Methyod for a Mixed-Race Stock. North American Journal of Fisheries Management. IEP, Interagency Ecological Program. 2019. Interagency Ecological Program Science Strategy 2020-2024: Invenstment Priorities for Interagency Collaborative Science. Johnson, R.C., S. Windell, P. L. Brandes, J. L. Conrad, J. Ferguson, P. A. L. Goertler, B. N. Harvey, J.Heublein, J. A. Israel, D. W. Kratville, J. E. Kirsch, R. W. Perry, J. Pisciotto, W. R. Poytress, K. Reece, and B. G. Swart. 2017. Increasing the management value of life stage monitoring networks for three imperiled fishes in California's regulated rivers: case study Sacramento Winter-run Chinook salmon. San Francisco Estuary and Watershed Science 15: 1-41. National Marine Fisheries Service (NMFS). 2013. Endangered and Threatened Species: Designation of a Nonessential Experimental Population of Central Valley Spring-Run Chinook Salmon Below Friant Dam in the San Joaquin River, CA. Federal Register 70: 79622, December 31, 2013.

中央谷奇努克鲑（Central Valley Chinook Salmon）种群在《濒危物种法》（Endangered Species Act）下的保护名录状态各不相同。区分不同进化显著单元（Evolutionarily Significant Unit，ESU）的个体往往极具难度。正因如此，中央谷与旧金山湾-三角洲地区开展的诸多鲑鱼监测与评估工作，均因种群（群体）识别以及管理措施的比例效应存在不确定性而受阻（Dekar et al. 2013; IEP 2019）。

有研究表明，当前用于识别流域内捕获的奇努克鲑幼鱼的日龄体长模型（length-at-date models，Fisher 1992），其识别精度存在差异，对春型种群的识别尤为不准确（NMFS 2013; Harvey et al. 2014; Merz et al. 2014）。基于体长的识别方法之所以存在精度缺陷，大概率是因为幼鱼早期育幼阶段的分布差异、生境特异性生长速率，以及温度与食物可获得性的年际变化，导致不同群体的体长范围出现重叠。

本项目的核心目标，是对从州水资源工程（State Water Project）、中央谷工程（Central Valley Project）鱼类保护设施，以及跨机构生态项目（Interagency Ecological Program，IEP）监测计划中捕获的奇努克鲑进行遗传分类，以确定其所属宗群（即进化显著单元）。研究人员通过将采样个体的基因型与参考遗传基准进行比对，确定其原产地种群。相较于基于体长的种群识别模型，遗传方法的统计不确定性更低，旨在直接针对（并降低）引水工程（作业）导致的种群损失（取获量）估算中的一类不确定性来源，并为解析种群特异性分布、生境利用、种群丰度以及生活史变异提供必要的数据支撑。

本项目响应了跨机构生态项目基于生活史阶段的鲑鱼与鲟鱼指标评估，以及跨机构生态项目科学议程中关于改善中央谷鲑科鱼类监测的相关建议（Johnson et al. 2017; IEP 2019）。

参考文献
Dekar, M., P. Brandes, J. Kirsch, L. Smith, J. Speegle, P. Cadrett 与 M. Marshall. 2013. 美国鱼类及野生动物管理局三角洲幼鱼监测项目评估. 背景文件. 为跨机构生态项目科学咨询小组编制，2013年6月. 美国鱼类及野生动物管理局斯托克顿鱼类与野生动物办公室，加州洛迪. 共224页.
Fisher, F.W. 1992. 萨克拉门托-圣华金河系统内奇努克鲑（Oncorhynchus tshawytscha）的生长与分布. 加州鱼类与狩猎局内陆渔业处，办公室报告草案，雷丁.
Harvey, B.N., D.P. Jacobson, M.A. Banks. 2014. 混合种群奇努克鲑幼鱼宗群识别方法的不确定性量化. 《北美渔业管理杂志》("North American Journal of Fisheries Management").
跨机构生态项目(IEP). 2019. 2020-2024年跨机构生态项目科学战略：跨机构协作科学投资优先级.
Johnson, R.C., S. Windell, P. L. Brandes, J. L. Conrad, J. Ferguson, P. A. L. Goertler, B. N. Harvey, J. Heublein, J. A. Israel, D. W. Kratville, J. E. Kirsch, R. W. Perry, J. Pisciotto, W. R. Poytress, K. Reece, 与 B. G. Swart. 2017. 提升加州调控河流中三种濒危鱼类基于生活史阶段的监测网络管理价值：以萨克拉门托冬季奇努克鲑为例. 《旧金山河口与流域科学》("San Francisco Estuary and Watershed Science") 15: 1-41.
国家海洋渔业局(NMFS). 2013. 濒危与受威胁物种：加州圣华金河弗里蒙特坝下游中央谷春型奇努克鲑非必需实验种群的指定. 《联邦公报》("Federal Register") 70: 79622，2013年12月31日.