Comparison of Length-at-Date Criteria and Genetic Run Assignments for Juvenile Chinook Salmon Caught at Sacramento and Chipps Island in the Sacramento–San Joaquin Delta of California

Patricia Brandes,Michael Banks,Brian Pyper,Tommy Garrison,David Jacobsen,Steve Cramer

doi:10.15447/sfews.2021v19iss3art2

Abstract

There are four distinct runs of Chinook Salmon (Oncorhynchus tshawytscha) in the Central Valley, named after their primary adult return times: fall, late-fall, winter, and spring run. Estimating the run-specific composition of juveniles entering and leaving the Sacramento–San Joaquin Delta is crucial for assessing population status and processes that affect juvenile survival through the Delta. Historically, the run of juvenile Chinook Salmon captured in the field has been determined using a length-at-date criteria (LDC); however, LDC run assignments may be inaccurate if there is high overlap in the run-specific timing and size of juveniles entering and leaving the Delta. In this study, we use genetic run assignments to assess the accuracy of LDC at two trawl locations in the Sacramento River (Delta entry) and at Chipps Island (Delta exit). Fin tissues were collected from approximately 7,500 juvenile Chinook Salmon captured in trawl samples between 2007 and 2011. Tissues were analyzed using 21 microsatellites to determine genetic run assignments for individuals, which we compared with LDC run assignments. Across years, there was extensive overlap among the distributions of run-specific fork lengths of genetically identified juveniles, indicating that run compositions based on LDC assignments would tend to underestimate fall-run and especially late-fall-run compositions at both trawl locations, and greatly overestimate spring-run compositions (both locations) and winter-run compositions (Chipps Island). We therefore strongly support ongoing efforts to include tissue sampling and genetic run identification of juvenile Chinook Salmon at key monitoring locations in the Sacramento–San Joaquin River system.

Highlights

The challenges of mixed stock salmon management extend to harvest in fisheries, and to distinguishing stock of origin among juveniles migrating to sea
Across field years 2008 through 2011, genetic run assignments were made for 2,565 juvenile Chinook Salmon collected from the Sacramento River and 5,108 juveniles collected at Chipps Island (Table 1; Figure 2)
length-at-date criteria (LDC) assignments were lower for fall run and much higher for spring run compared to genetic assignments because genetic fall run dominated the spring-run LDC (Table 1; Figure 2)

Summary

Introduction

The challenges of mixed stock salmon management extend to harvest in fisheries, and to distinguishing stock of origin among juveniles migrating to sea. In the Central Valley of California, four distinct runs of Chinook Salmon (Oncorhynchus tshawytscha) are named after their primary adult return times: fall, late-fall, winter, and spring run (Fisher 1994; Yoshiyama et al 1998). Juveniles of these runs intermix to various degrees during their seaward migrations in the lower Sacramento River and Sacramento–San Joaquin Delta (Figure 1; Yoshiyama et al 1998; Williams 2006). Juvenile monitoring studies with accurate run identification will be needed to evaluate and refine some of these various—and often costly—recovery actions (NMFS 2014; Peterson and Duarte 2020)

Methods

Results

Discussion

Conclusion