DOI: 10.6073/pasta/642c767a1b9b8417b14b07d49d3e7173
title: Genetic assignments for Spring Evolutionary Significant Unit reanalysis, Central Valley Chinook Salmon populations, CA, 2011-2024

description: Central Valley Chinook Salmon populations differ in their Endangered Species Act listing status. It is difficult to visually distinguish individuals from the different Evolutionarily Significant Units (ESU). 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 genetic lineage; Evolutionary Significant Unit) of Chinook Salmon captured from State Water Project and Central Valley Project fish protection facilities and Interagency Ecological Program compliance monitoring programs. The genetic lineage 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).
 
 The data contained in this project are reanalysis of salvaged Chinook Salmon individuals that were formerly assigned to Spring Evolutionary Significant Unit using previously used methods. These individuals were reprocessed with new methods described herein.
 
 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.