Factors Affecting Spatiotemporal Variation in Survival of Endangered Winter‐Run Chinook Salmon Out‐migrating from the Sacramento River

Abstract

Among four extant and declining runs of Chinook Salmon Oncorhynchus tshawytscha in California's Central Valley, none has declined as precipitously as the Sacramento River winter run. Migratory winter-run Chinook Salmon employ a life history strategy to reside and feed in stopover habitats on their way from freshwaters to the ocean. Migratory winter run, on their way from freshwaters to the ocean, employ a life history strategy to reside and feed in stopover habitats that have been affected by anthropogenic disturbance. Using acoustic telemetry, we examined conditions that influenced reach-specific movement and survival of out-migrating juveniles during a prolonged, multi-year drought from 2013 to 2016, followed by one of the wettest years on record (2017). We modeled how time-varying individual riverine covariates and reach-specific habitat features influenced smolt survival. Model selection favored a model with mean annual flow, intra-annual deviations from the mean flow at the reach scale, reach-specific channel characteristics, and travel time. Mean annual flow had the strongest positive effect on survival. A negative interaction between mean annual flow and intra-annual reach flow indicated that within-year deviations at the reach scale from annual mean flow had larger effects on survival in low-flow years. These factors resulted in higher survival during years with pulse flows or high flows. Changes in movement behavior in response to small-scale changes in velocity were negatively associated with survival. Covariates of revetment and wooded bank habitat were positively associated with survival, but the effect of these fixed habitat features changed depending on whether they were situated in the upper or lower part of the river. Fish exhibited density-dependent stopover behavior, with slowed downstream migration in the upper river in the wet years and extending to the lower river in the most critically dry year. This paper contributes two key findings for natural resource managers interested in flow management and targeted habitat

A meta‐analysis and model comparison of juvenile salmon growth across different habitat types

“…This work will provide managers and modelers with a better understanding of the degree to which different habitats and temperature affect growth. Furthermore, these growth models can be integrated within lifecycle models to test hypotheses of how different size‐specific survival rates (Hassrick, Ammann, Perry, John, & Daniels, 2022; Perry et al, 2018) could affect long‐term population dynamics, ultimately informing efforts to recover threatened and endangered populations of Chinook salmon.…”

Imperfect detection and misidentification affect inferences from data informing water operation decisions

“…Numerous environmental factors have been hypothesized to influence the distribution of juvenile winter-run salmon in the Estuary. Previous studies have demonstrated relationships between juvenile salmon occupancy or abundance and flow characteristics, water clarity and temperature, weather, upstream juvenile production and distribution, and time (Brandes and McLain 2001;Sommer et al 2005;del Rosario et al 2013;Acierto et al 2014;Perry et al 2016;Hassrick et al 2022). However, few studies (e.g., del Rosario et al 2013;Hassrick et al 2022) have directly evaluated the influence of these factors on juvenile winter-run salmon occupancy, and no studies have accounted for sampling uncertainties, including imperfect detection and misidentification during their evaluation.…”

“…We obtained readily available data representing water quality and other environmental characteristics that were hypothesized to influence juvenile winter-run salmon occupancy and detection near Sacramento (Table 1; Brandes and McLain 2001;Sommer et al 2005;del Rosario et al 2013;Acierto et al 2014;Hassrick et al 2022). Water temperature was measured by DJFMP staff to the nearest 0.1°C approximately 0.5 m below the water surface by using a nonmercury thermometer, a YSI Model 85 meter, or a YSI PRO 2030 meter during or immediately before each Sacramento trawl tow and beach seine haul.…”

“…Bluff Diversion Dam and the Sacramento monitoring sites under the different flow scenarios were approximated using the SacPAS Fish Model version 2.7.4 (Beer et al 2017); the Delta Survival, Travel Time, and Routing Simulation Model (Perry et al 2018;Hance et al 2022); and the findings from Hassrick et al (2022).…”

Discharge‐Mediated Temperature Management in a Large, Regulated River, With Implications for Management of Endangered Fish

“…Red Bluff represents the end of the migratory corridor for adult salmon on the Sacramento, and the beginning of the migratory corridor for juvenile salmon that are born upstream, and so exposure time to potentially warm water temperatures downstream of here is a function of migration rates. Limited adult Chinook salmon telemetry data has shown travel times of 10–45 days to transit the non‐tidal lower Sacramento River before arriving to Red Bluff (Martin et al., 2015), and actively migrating juvenile Chinook salmon can take of 3–60 days to reach the tidal portions of the river after leaving Red Bluff (Hassrick et al., 2022; Michel et al., 2013).…”