Delta Flow Factors Influencing Stray Rate of Escaping Adult San Joaquin River Fall-Run Chinook Salmon (Oncorhynchus tshawytscha)

Data from the U.S. Fish and Wildlife Service are used to investigate the relationship between water temperature and survival of hatchery-raised fall-run chinook salmon (Oncorhynchus tshawytscha) smolts migrating through the Sacramento – San Joaquin Delta of California. A formal statistical model is presented for the release of smolts marked with coded-wire tags (CWTs) in the lower Sacramento River and the subsequent recovery of marked smolts in midwater trawls in the Delta. This model treats survival as a logistic function of water temperature, and the release and recovery of different CWT groups as independent mark–recapture experiments. Iteratively reweighted least squares is used to fit the model to the data, and simulation is used to establish confidence intervals for the fitted parameters. A 95% confidence interval for the upper incipient lethal temperature, inferred from the trawl data by this method, is 23.01 ± 1.08 °C This is in good agreement with published experimental results obtained under controlled conditions (24.3 ± 0.1 and 25.1 ± 0.1 °C for chinook salmon acclimatized to 10 and 20 °C, respectively): this agreement has implications for the applicability of laboratory findings to natural systems.

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

10.1101/2021.08.24.456882 ◽

2021 ◽

Author(s):

Colby L. Hause ◽

Gabriel P. Singer ◽

Rebecca A. Buchanan ◽

Dennis E. Cocherell ◽

Nann A. Fangue ◽

...

Keyword(s):

Pacific Northwest ◽

Chinook Salmon ◽

Habitat Restoration ◽

Oncorhynchus Tshawytscha ◽

Central Valley ◽

Data Generation ◽

Habitat Variability ◽

River Habitat ◽

San Joaquin River ◽

The Pacific

AbstractExtirpation 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.

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Factors Influencing Run Strength of Upper Yukon River Chinook Salmon (Oncorhynchus tshawytscha)

10.22215/etd/2020-13966 ◽

2020 ◽

Author(s):

James Sebes

Keyword(s):

Chinook Salmon ◽

Oncorhynchus Tshawytscha ◽

Yukon River ◽

Factors Influencing

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Effects of the proposed California WaterFix North Delta Diversion on survival of juvenile Chinook salmon (Oncorhynchus tshawytscha) in the Sacramento-San Joaquin River Delta, northern California

Open-File Report ◽

10.3133/ofr20181078 ◽

2018 ◽

Author(s):

Russell W. Perry ◽

Adam C. Pope

Keyword(s):

Chinook Salmon ◽

Oncorhynchus Tshawytscha ◽

River Delta ◽

Northern California ◽

Juvenile Chinook Salmon ◽

San Joaquin River ◽

Juvenile Chinook

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Mitochondrial DNA Polymorphism in Unique Runs of Chinook Salmon (Oncorhynchus tshawytscha) from the Sacramento-San Joaquin River Basin

Conservation Biology ◽

10.1046/j.1523-1739.1994.08030863-11.x ◽

1994 ◽

Vol 8 (3) ◽

pp. 882-884 ◽

Cited By ~ 16

Author(s):

Jennifer L. Nielsen ◽

Douglas Tupper ◽

W. Kelley Thomas

Keyword(s):

Mitochondrial Dna ◽

River Basin ◽

Chinook Salmon ◽

Dna Polymorphism ◽

Oncorhynchus Tshawytscha ◽

Mitochondrial Dna Polymorphism ◽

San Joaquin River

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Evaluation of a floating fish guidance structure at a hydrodynamically complex river junction in the Sacramento–San Joaquin River Delta, California, USA

Marine and Freshwater Research ◽

10.1071/mf15285 ◽

2017 ◽

Vol 68 (5) ◽

pp. 878 ◽

Cited By ~ 2

Author(s):

Jason G. Romine ◽

Russell W. Perry ◽

Adam C. Pope ◽

Paul Stumpner ◽

Theresa L. Liedtke ◽

...

Keyword(s):

Chinook Salmon ◽

Oncorhynchus Tshawytscha ◽

Time Of Day ◽

River Delta ◽

Sacramento River ◽

Migration Route ◽

Juvenile Chinook Salmon ◽

Percentage Points ◽

San Joaquin River ◽

Lower Discharge

Survival of out-migrating juvenile Chinook salmon (Oncorhynchus tshawytscha) in the Sacramento–San Joaquin River delta, California, USA, varies by migration route. Survival of salmonids that enter the interior and southern Delta can be as low as half that of salmonids that remain in the main-stem Sacramento River. Reducing entrainment into the higher-mortality routes, such as Georgiana Slough, should increase overall survival. In spring 2014, a floating fish-guidance structure (FFGS) designed to reduce entrainment into Georgiana Slough was deployed just upstream of the Georgiana Slough divergence. We used acoustic telemetry to evaluate the effect of the FFGS on Chinook entrainment to Georgiana Slough. At intermediate discharge (200–400m3 s–1), entrainment into Georgiana Slough was five percentage points lower when the FFGS was in the on state (19.1% on; 23.9% off). At higher discharge (>400m3 s–1), entrainment was higher when the FFGS was in the on state (19.3% on; 9.7% off), and at lower discharge (0–200m3 s–1) entrainment was lower when the FFGS was in the on state (43.7% on; 47.3% off). We found that discharge, cross-stream fish position, time of day, and proportion of flow remaining in the Sacramento River contributed to the probability of being entrained to Georgiana Slough.

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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

San Francisco Estuary and Watershed Science ◽

10.15447/sfews.2021v19iss3art2 ◽

2021 ◽

Vol 19 (3) ◽

Author(s):

Patricia Brandes ◽

◽

Brian Pyper ◽

Michael Banks ◽

David Jacobsen ◽

...

Keyword(s):

Chinook Salmon ◽

Oncorhynchus Tshawytscha ◽

Central Valley ◽

River System ◽

Population Status ◽

Juvenile Chinook Salmon ◽

Late Fall ◽

San Joaquin River ◽

Juvenile Chinook ◽

Specific Timing

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.

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