Survival of a threatened salmon is linked to spatial variability in river conditions

Abstract

Extirpation of the Central Valley spring-run Chinook Salmon ESU (Oncorhynchus tshawytscha) from the San Joaquin River is emblematic of salmonid declines across the Pacific Northwest. Habitat restoration and fish reintroduction efforts are ongoing, but recent telemetry studies have revealed low outmigration survival of juveniles to the ocean. Previous investigations have focused on modeling survival relative to river discharge and geographic regions, but have largely overlooked the effects of habitat variability. To evaluate the link between environmental conditions and survival of juvenile spring-run Chinook Salmon, we combined high spatial resolution habitat mapping approaches with acoustic telemetry along a 150 km section of the San Joaquin River during the spring of 2019. While overall outmigration survival was low (5%), our habitat-based classification scheme described variation in survival of acoustic-tagged smolts better than other candidate models based on geography or distance. There were two regional mortality sinks evident along the longitudinal profile of the river, revealing poor survival in areas that shared warmer temperatures but that diverged in chlorophyll-α, fDOM, turbidity and dissolved oxygen levels. These findings demonstrate the value of integrating river habitat classification frameworks to improve our understanding of survival dynamics of imperiled fish populations. Importantly, our data generation and modeling methods can be applied to a wide variety of fish species that transit heterogeneous and diverse habitat types.

Interpopulation variation in thermal physiology among seasonal runs of Chinook salmon

“…Remaining early-migrating populations are constrained to the low elevation habitat of the Sacramento River and must contend with summer water temperatures, made tolerable through regulated cold-water releases from upstream reservoirs (Johnson and Lindley 2016). Proposed conservation actions, via reintroduction (Lusardi and Moyle 2017;USFWS 2018) or habitat restoration (Hause et al 2022) require matching the thermal environment to a population's thermal physiology. Determining interpopulation variation in thermal physiology is an essential step in preparing salmonid conservation for environmental change.…”