Considerations for the Development of a Juvenile Production Estimate for Central Valley Spring-Run Chinook Salmon

Abstract

Effective species management depends on accurate estimates of population size. There are, however, no estimates of annual juvenile production for Central Valley spring-run Chinook Salmon (“spring run”), a highly imperiled species in California, making it difficult to evaluate population status and effectively manage key issues such as entrainment of this species at water diversions. In recognition of this critical information gap, we initiated an effort to develop a juvenile production estimate (JPE) for spring run, defined here as an annual forecast of the number of juvenile Central Valley spring-run Chinook Salmon that enter the Sacramento–San Joaquin Delta (“Delta”) from the Sacramento Valley. This metric would allow for a more robust scientific assessment of the population, which is needed to effectively manage water to reduce effects on spring run, a key condition of state permit requirements. To help guide this effort, we organized a workshop for stake-holders, managers, and scientists to review some of the key aspects of spring-run biology, examine the management and conservation importance of a JPE, identify knowledge gaps, introduce new tools, and discuss alternative approaches to forecasting the number of spring run emigrating from the Sacramento River drainage and into the Delta. This paper summarizes the spring-run biology, monitoring, and emergent methods for assessment considered at the workshop, as well as the guiding concepts identified by workshop participants necessary to develop a JPE for spring-run Chinook Salmon.

Genomics and 20 years of sampling reveal phenotypic differences between subpopulations of outmigrating Central Valley Chinook salmon

“…However, effective management of diversity depends on an accurate understanding and monitoring framework for individual components of diversity, which can be difficult to develop and typically becomes more challenging at finer scales. Genetic approaches hold promise for improving monitoring frameworks (Baerwald et al., 2023 ; Cordoleani et al., 2020 ; Meek et al., 2020 ; Nelson et al., 2022 ), but the accuracy of genetic approaches can face challenges from low differentiation as well as heterogeneity in sample qualities. Here, we utilized thousands of SNPs from next generation sequencing data and showed that a step‐wise approach based on a hierarchy of genetic differentiation, thorough threshold development, and method validation can address these challenges and facilitate confident assignments to origin even for subpopulations with low levels of differentiation in highly heterogeneous datasets.…”

“…The phenological and demographic distinctness of these units facilitates both their study and management and the ESA statuses of the winter and spring runs provide conservation mandates. However, major management challenges remain (Nelson et al., 2022 ). A primary obstacle is the difficulty of distinguishing different runs during the juvenile phase of the life cycle, which has impeded the development of basic monitoring tools such as juvenile production estimates for individual runs (Cordoleani et al., 2020 ; Nelson et al., 2022 ).…”

“…However, major management challenges remain (Nelson et al., 2022 ). A primary obstacle is the difficulty of distinguishing different runs during the juvenile phase of the life cycle, which has impeded the development of basic monitoring tools such as juvenile production estimates for individual runs (Cordoleani et al., 2020 ; Nelson et al., 2022 ). However, new genetic tools are being implemented to improve monitoring and management of the major populations within the CV (Baerwald et al., 2023 ; Meek et al., 2020 ; Nelson et al., 2022 ).…”

“…Other components of diversity are also important contributors to stability both across and within the major runs, but are less understood, often impossible to monitor under the current framework, and are not currently a focus of management (Cordoleani et al., 2020 , 2021 ). Two prime, interrelated examples are (1) variation within the juvenile phase of the Chinook life cycle and (2) subpopulation level diversity (Bourret et al., 2016 ; Brennan et al., 2019 ; Cordoleani et al., 2021 ; Herbold et al., 2018 ; Nelson et al., 2022 ; Sturrock et al., 2020 ). Juveniles exhibit variation in their timing and age of outmigration, size, and habitat utilization (Bourret et al., 2016 ; Cordoleani et al., 2021 ; Singer et al., 2020 ; Sturrock et al., 2015 ; Williams, 2006 ), and the relative success of a particular juvenile strategy can vary dramatically depending on how it aligns with environmental factors in a given year (Cordoleani et al., 2021 ; Herbold et al., 2018 ; Sturrock et al., 2020 ).…”

“…Currently, length‐at‐date (LAD) designations are used to categorize outmigrating juveniles into major populations of origin (winter, spring, and fall/late‐fall runs). However, LAD designations have been shown to have very high error rates and they do not account for subpopulation diversity within the spring run (Brandes et al., 2021 ; Nelson et al., 2022 ). The major populations within the CV are genetically distinct, and a lesser degree of genetic differentiation exists between some spring run subpopulations, as well as fall and late‐fall runs (Banks et al., 2014 ; Clemento et al., 2014 ; Hedgecock et al., 2001 ; Meek et al., 2020 ).…”