SFEWS Vol. 20, Issue 2 | June 2022
#ChinookSalmon #SacramentoSplittail #tidalmarsh #floodplain #openwater #drought #flood #juvenileproductionestimate #JPE #lifehistory #raceidentification #springrun #SacramentoRiver #CADelta #quantile #regressionforest #Steelhead #machinelearning #entrainmentloss #SanFrancisco #estuary #SFE #BayDelta #gillnet #gearselectivity #Drainage #waterquality #agriculturaldrainage #returnflow #diversions #Delta #island #groundwater #nitrogen #phosphorous #metals
Considerations for the Development of a Juvenile Production Estimate for Central Valley Spring-Run Chinook Salmon
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.
Machine Learning Forecasts to Reduce Risk of Entrainment Loss of Endangered Salmonids at Large-Scale Water Diversions in the Sacramento–San Joaquin Delta, California
Incidental entrainment of fishes at large-scale state and federal water diversion facilities in the Sacramento-San Joaquin Delta, California, can trigger protective management actions when limits imposed by environmental regulations are approached or exceeded. These actions can result in substantial economic costs, and likewise they can affect the status of vulnerable species. Here, we examine data relevant to water management actions during January–June; the period when juvenile salmonids are present in the Delta.
Gill Net Selectivity for Fifteen Fish Species of the Upper San Francisco Estuary
Gill-net size selectivity for 15 fish species occurring in the upper San Francisco Estuary was estimated from a data set compiled from multiple studies which together contained 7,096 individual fish observations from 882 gill net sets. The gill nets considered in this study closely resembled the American Fisheries Society’s recommended standardized experimental gill nets for sampling inland waters. Relationships between gill-net mesh sizes and the sizes for each fish species retained in them were estimated indirectly using generalized linear modeling and maximum likelihood.
Nutrient and Trace Element Contributions from Drained Islands in the Sacramento–San Joaquin Delta, California
Inventorying nutrient and trace element sources in the Sacramento-San Joaquin Delta (the Delta) is critical to understanding how changes—including alterations to point source inputs such as upgrades to the Sacramento Regional Wastewater Treatment Plant (SRWTP) and landscape-scale changes related to wetland restoration—may alter the Delta’s water quality. While island drains are a ubiquitous feature of the Delta, limited data exist to evaluate island drainage mass fluxes in this system. To better constrain inputs from island drains, we measured monthly discharge along with nutrient and trace element concentrations in island drainage on three Delta islands and surrounding rivers from June 2017 to September 2018.
Climate Change Impacts on San Francisco Estuary Aquatic Ecosystems: A Review ample header
In the San Francisco Estuary, signals of climate change are apparent in the long-term monitoring record. Here we synthesize current and potential future climate change effects on three main ecosystems (floodplain, tidal marsh, and open water) in the upper estuary and two representative native fishes that commonly occur in these ecosystems (anadromous Chinook Salmon, Oncorhynchus tshawytscha and estuarine resident Sacramento Splittail, Pogonichthys macrolepidotus).
Volume 16, Issue 4, 2018
Hourly Analyses of the Large Storms and Atmospheric Rivers that Provide Most of California’s Precipitation in Only 10 to 100 Hours per Year
California is regularly affected by floods and droughts, primarily as a result of too many or too few atmospheric rivers (ARs). This study analyzes a 2-decade-long hourly precipitation data set from 176 California weather stations and a 3-hourly AR chronology to report variations in rainfall events across California and their association with ARs. On average, 10–40 and 60–120 hours of rainfall in southern and northern California, respectively, are responsible for more than half of annual rainfall accumulations. Approximately 10% to 30% of annual precipitation at locations across the state is from only one large storm. On average, northern California receives 25 to 45 rainfall events annually (40% to 50% of which are AR-related). These events typically last longer and have higher event-precipitation totals than those in southern California. Northern California also receives more AR landfalls with longer durations and stronger Integrated Vapor Transport (IVT). On average, ARs contribute 79%, 76%, and 68% of extreme-rainfall accumulations (i.e., top 5% events annually) in the north coast, northern Sierra, and Transverse Ranges of southern California, respectively.
The San Francisco Bay Area terrain gap in the California Coast Range allows more AR water vapor to reach inland over the Delta and Sacramento Valley, and thus influences precipitation in the Delta’s catchment. This is particularly important for extreme precipitation in the northern Sierra Nevada, including river basins above Oroville Dam and Shasta Dam.
This study highlights differences between rainfall and AR characteristics in coastal versus inland northern California — differences that largely determine the regional geography of flood risks and water reliability. These analyses support water resource, flood, levee, wetland, and ecosystem management within the catchment of the San Francisco Estuary system by describing regional characteristics of ARs and their influence on rainfall on an hourly time-scale.
- 1 supplemental PDF
Resource managers rely on long-term monitoring surveys conducted in the San Francisco Estuary to evaluate the status and trends of resident fish populations in this important region. These surveys are potentially confounded because of the incomplete detection of individuals and species, the magnitude of which is often related to the same factors that affect fish populations. We used multistate occupancy estimators to evaluate the distribution, abundance, and detection probability of four fish species collected during 1995–2015 with three long-term surveys. Detection probabilities varied positively with fish abundance and negatively with Secchi depth. Detection varied among species and was greatest for the 20-mm Survey and least for the midwater trawl used for the midwater trawl used in the San Francisco Bay Study. Incomplete detection resulted in underestimates of occupancy and abundance across species and surveys and were greatest for the Bay Study. However, trends in occupancy and abundance of the study period appeared to be unbiased. Fish occupancy and abundance were generally related to salinity or specific conductance, day-of-the year, and water temperature, but the nature of the relations varied among surveys and species. There also was strong spatial and temporal dependence in species-specific occupancy and abundance that changed through time and were unrelated to the covariates considered. Our results suggest that managers consider incorporating methods for estimating detection and adjusting data to ensure data quality. Additionally, the strong spatio-temporal patterns in the monitoring data suggest that existing protocols may need to be modified to ensure that data and inferences reflect system-wide changes rather than changes at a specific set of non-randomly selected locations.
- 2 supplemental PDFs
Non-Native Fish Predator Density and Molecular-Based Diet Estimates Suggest Differing Impacts of Predator Species on Juvenile Salmon in the San Joaquin River, California
The Sacramento-San Joaquin Delta is a major survival bottleneck for imperiled California salmonid populations, which is partially due to a multitude of non-native fish predators that have proliferated there throughout the 20th century. Understanding the diets of salmonid predators is critical to understanding their individual impacts, role in the food web, and the implications for potential management actions. We collected the stomach contents of Striped Bass Morone saxatilis, Largemouth Bass Micropterus salmoides, Channel Catfish Ictalurus punctatus and White Catfish Ameiurus catus sampled from three 1-km reaches in the lower San Joaquin River in 2014 and 2015 during the peak juvenile salmon outmigration period. We tested each stomach (n = 582) for the presence of juvenile Chinook Salmon Oncorhynchus tshawytscha and other prey items using a genetic barcoding technique. Channel Catfish had significantly higher frequency of Chinook Salmon in their stomachs (27.8% of tested Channel Catfish contained Chinook Salmon DNA), compared to the other three predators (2.8% to 4.8%). However, non-native fish species occurred at greater frequencies in the diets of all four predator species than salmon. Using depletion estimation from electrofishing, we were able to generate population densities for Striped Bass and Largemouth Bass in our reaches. Largemouth Bass were evenly distributed throughout all three reaches, at a mean density of approximately 333 (± 195 SE) per km of river. Striped Bass were patchily distributed, ranging from 21 to 1,227 per km. Extrapolating the frequency of salmon detected in stomachs to the predator abundance estimates, we estimate that the population of Largemouth Bass we sampled consumed between 3 and 5 Chinook Salmon per day per 1-km study reach (consumption rate of 0.011 salmon per predator per day), whereas the Striped Bass population consumed between 0 and 24 Chinook Salmon per day (0.019 salmon per predator per day).
Alternative Juvenile Production Estimate (JPE) Forecast Approaches for Sacramento River Winter-Run Chinook Salmon
Sacramento River winter-run Chinook salmon are listed under the Endangered Species Act as Endangered and there are substantial efforts to estimate, predict, and limit mortalities at various stages of their life cycle. One such effort is the annual forecast of the number of juvenile winter-run entering the Sacramento-San Joaquin Delta. The natural-origin Juvenile Production Estimate (JPE) is defined as the number of winter-run juveniles produced from natural spawning areas that enter the Delta, and its forecast is used to determine the allowable level of winter-run incidental take at the state and federal pumping facilities located in the south Delta. Current monitoring programs in the Sacramento Basin do not allow for direct estimation of the JPE and thus various methods have been used to forecast this value annually. Here we describe three alternative methods for forecasting the natural-origin JPE. The methods range from the status quo approach (Method 1), which expresses the JPE forecast only as a point estimate, to two other methods that account for forecast uncertainty to various degrees. A comparison of JPE forecasts for 2018 across the three methods indicates that relative to Method 1, Methods 2 and 3 result in lower JPE forecasts, by 24 and 18 percent, respectively, primarily owing to lower forecasts of the fry-to-smolt transition and the smolt survival rate occurring downstream of Red Bluff Diversion Dam. Because post-hoc estimates of juvenile winter-run abundance at the entrance to the Delta do not currently exist, we are unable to evaluate forecast skill among the three methods.
- 1 supplemental PDF