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  • Title

    Monitoring and Evaluation of the North Delta Food Subsidies and Colusa Basin Drain Study

    Lead California Department of Water Resource [DWR]
    Description The North Delta Food Subsidies – Colusa Basin Drain Study monitors and evaluates the effects of the North Delta Flow Action on the Delta food web.
    Science topics Delta Smelt, Fish, Flows, Water management
    Updated November 17, 2022
  • Title

    Directed Outflow Project

    Lead U.S. Bureau of Reclamation [USBR]
    Description The U.S. Bureau of Reclamation (USBR) and California Department of Water Resources (DWR), along with collaborators, are continuing efforts to evaluate the hypothesized benefits of outflow and outflow alteration for Delta Smelt. The collective aim of these efforts is to better inform management actions that will bolster and stabilize the Delta Smelt population. The planned five-year Directed Outflow Project (DOP) seeks to assist in evaluating the overarching hypothesis that habitat quality and quantity is improved in the summer/fall when X2 is below 81 km and the LSZ occurs in Suisun Bay and Marsh, and this improvement in habitat conditions will translate into a greater catch density, health, and growth for Delta Smelt using this area
    Science topics Delta Smelt, Fish, Flows, Water management
    Updated November 17, 2022
  • Title

    Monitoring and Assessment of Suisun Marsh Salinity Control Gates Action

    Lead California Department of Water Resource [DWR]
    Description The Suisun Marsh Salinity Control Gates (SMSCGs) have the potential to provide an increase in low-salinity-zone habitat for endangered Delta Smelt. Operation of the SMSCGs in summer and fall to improve Delta Smelt habitat are called for in the Biological Opinion and Incidental Take permit for the Central Valley Project and State Water Project. To support the adaptive management of the action, DWR is planning to monitor the change in water quality, phytoplankton, zooplankton, fishes, and clams resulting from the action.
    Science topics Delta Smelt, Phytoplankton, Salinity
    Updated November 17, 2022
  • Title

    Suisun Marsh Salinity Control Gates Action Pilot Study

    Lead California Department of Water Resource [DWR]
    Description In summer 2018 we used a unique water control structure in the San Francisco Estuary to direct a managed flow pulse into Suisun Marsh. Field monitoring showed that turbidity and chlorophyll were at higher levels in Suisun Marsh, representing better habitat conditions, than the upstream Sacramento River region throughout the study period. Fish monitoring data suggested that small numbers of Delta Smelt colonized Suisun Marsh from the Sacramento River during the 2018 Flow Action.
    Science topics Delta Smelt, Phytoplankton, Salinity
    Updated September 28, 2023
  • Title

    Delta Landscapes Project

    Lead San Francisco Estuary Institute [SFEI]
    Description The Delta Landscapes Project has developed a body of work to inform landscape-scale restoration of the Sacramento-San Joaquin Delta ecosystem. The project is built on knowledge, first published in 2012’s Delta Historical Ecology Investigation, of how the Delta ecosystem functioned in the early 1800s (prior to the California Gold Rush and subsequent landscape-level changes).
    Science topics Landscape metrics, Restoration planning, Marsh wildlife, Riparian wildlife, Terrestrial wildlife, Fish
    Updated April 29, 2022
  • Title

    Delta Salmon Rearing Project

    Lead San Francisco Estuary Institute [SFEI]
    Description This project summarizes existing research and knowledge around suitable rearing habitat for Chinook salmon in the Sacramento-San Joaquin Delta;identifies areas of suitability for rearing salmon using a combined suitability analysis of four mapped habitat parameters;and provides recommendations for types of restoration needed to improve or restore rearing habitat, as well as to identify where in the Delta these restoration efforts could be prioritized.
    Science topics Salmon rearing, Salmon migration, Habitat restoration
    Updated April 29, 2022
  • Title

    Delta Regional Monitoring Program Mercury Monitoring

    Lead Delta Regional Monitoring Program [RMP]
    Description Monitoring of sport fish and water was conducted by the Delta Regional Monitoring Program (Delta RMP) from August 2016 to April 2017 to begin to address the highest priority information needs related to implementation of the Sacramento–San Joaquin Delta Estuary Total Maximum Daily Load (TMDL) for Methylmercury (Wood et al. 2010). Two species of sport fish, largemouth bass (Micropterus salmoides) and spotted bass (Micropterus punctulatus), were collected at six sampling locations in August and September 2016. The length-adjusted (350 mm) mean methylmercury (measured as total mercury, which is a routinely used proxy for methylmercury in predator fish) concentration in bass ranged from 0.15 mg/kg or parts per million (ppm) wet weight at Little Potato Slough to 0.61 ppm at the Sacramento River at Freeport. Water samples were collected on four occasions from August 2016 through April 2017. Concentrations of methylmercury in unfiltered water ranged from 0.021 to 0.22 ng/L or parts per trillion. Concentrations of total mercury in unfiltered water ranged from 0.91 to 13 ng/L. Over 99% of the lab results for this project met the requirements of the Delta RMP Quality Assurance Program Plan, and all data were reportable. This data report presents the methods and results for the first year of monitoring. Historic data from the same or nearby monitoring stations from 1998 to 2011 are also presented to provide context. Monitoring results for both sport fish and water were generally comparable to historic observations. For the next several years, annual monitoring of sport fish will be conducted to firmly establish baseline concentrations and interannual variation in support of monitoring of long-term trends as an essential performance measure for the TMDL. Monitoring of water will solidify the linkage analysis (the quantitative relationship between methylmercury in water and methylmercury in sport fish) in the TMDL. Water monitoring will also provide data that will be useful in verifying patterns and trends predicted by numerical models of mercury transport and cycling being developed for the Delta and Yolo Bypass by the California Department of Water Resources (DWR).
    Science topics Biosentinels, Fish, Methylmercury, Restoration, Water
    Updated November 17, 2022
  • Title

    Habitat, hatcheries, and nonnative predators interact to affect juvenile salmon behavior and survival

    Lead University of California - Santa Cruz [UCSC]
    Description Chinook salmon are an iconic part of California’s environment and heritage, and important both economically and culturally. In the Sacramento River, the winter-run Chinook population is endangered, and there is strong interest in restoring these populations. To do so, resource managers need to better understand the pressures on wild populations. Predation by nonnative predators affects survival of young salmon but may also affect the behavior of salmon. Changes to salmon behavior also have costs but are not currently considered in management. Managers need information on how predators affect juvenile salmon behavior, how they might vary under different conditions, and how they scale up to affect populations.
    Science topics Chinook Salmon, Fishing
    Updated November 17, 2022
  • Title

    Effects of copper exposure on the olfactory response of Delta smelt [Hypomesus transpacificus]: Investigating linkages between morphological and behavioral anti-predator response

    Lead University of California - Davis [UC Davis]
    Description This study aimed to address the question of how water-borne copper can affect the ability of delta smelt to detect predator related odorants and conduct essential behaviors. To do this, the project included a thorough morphological and cytological study of the delta smelt olfactory organ, which had previously not been well-studied. The researchers also characterized the olfactory mediated antipredatory response to alarm cues and assessed the effects of copper exposure on the anti-predator behavior and morphology of the olfactory rosette of delta smelt.
    Science topics Copper, Delta Smelt, Toxicity
    Updated November 17, 2022
  • Title

    Effect of temperature and salinity on physiological performance and growth of longfin smelt: Developing a captive culture for a threatened species in the Sacramento- San Joaquin Delta

    Lead University of California - Berkeley [UC Berkeley]
    Description This research project aimed to improve understanding of the physiological requirements for survival and reproduction across the entire life history of longfin smelt (from egg to larvae to juvenile to reproducing adult). The overall goals of this project were to assist in developing a captive longfin smelt culture and assess longfin smelt responses to multiple stressors across all life stages, which has been difficult because of extremely low (<10%) larval survival of these fish.
    Science topics Delta Smelt, Longfin Smelt, Salinity, Temperature
    Updated November 17, 2022
  • Title

    Yolo Bypass Salmonid Habitat Restoration and Fish Passage

    Lead California Department of Water Resource [DWR]
    Description The Yolo Bypass Salmonid Habitat Restoration Project works to reconnect the floodplain for fish during the winter season and improve connectivity within the bypass and to the Sacramento River. The project provides seasonal inundation that mimics the natural process of the Yolo Bypass floodplain and improves connectivity within the bypass and to the Sacramento River.
    Science topics Chinook Salmon, Endangered species
    Updated April 29, 2022
  • Title

    Yolo Bypass Salmonid Habitat Restoration and Fish Passage: Scenario Analysis of Fremont Weir Notch – Integration of Engineering Designs, Telemetry, and Flow Fields

    Lead U.S. Army Corps of Engineers [USACE]
    Description This study analyzes 12 notch scenarios in the Fremont Weir in terms of entrainment of juvenile salmon. The goal is to quantify the relative entrainment rates (between 0 and 1) across the suite of scenarios and to identify possible strategies for enhancing entrainment outcomes. This study does not predict future entrainment as models generally do not predict future outcomes so much as highlight trends
    Science topics Chinook Salmon, Endangered species, Water conveyance / infrastructure
    Updated April 29, 2022
  • Title

    Defining habitat quality for young-of-year longfin smelt: Historical otolith-based reconstructions of growth and salinity history in relation to geography, climate, and outflow

    Lead University of California - Davis [UC Davis]
    Description This project aimed to use experiments to develop new otolith-based tools for longfin smelt and to then apply them to an extensive collection of archived wild Longfin Smelt specimens, to build a better understanding of longfin smelt life history, habitat use, and the interactions between stressors and abundance. In addition, the project aims to improve the understanding of how longfin smelt populations are affected by freshwater outflow. The project also aims to provide tools to support and evaluate habitat restoration, and facilitate development of a plan to recover this threatened species.
    Science topics Longfin Smelt, Outflow, Salinity
    Updated November 17, 2022
  • Title

    Investigating the Factors that Affect Distribution, Abundance, and Recruitment of Age-0 Longfin Smelt in the upper San Francisco Estuary

    Lead Metropolitan Water District of Southern California
    Description
    Science topics Longfin Smelt
    Updated April 29, 2022
  • Title

    Mechanisms underlying the flow relationship of longfin smelt: I. Movement and feeding

    Lead San Francisco State University [SFSU]
    Description The project is to apply modern analytical methods, bioacoustic detection and particle tracking models to refine understanding of the vertical and longitudinal distribution of longfin smelt (Spirinchus thaleichthys) and how they are affected by flow and food availability. Funding will be used to conduct the research to protect and maintain the estuary's threatened longfin smelt population.
    Science topics Longfin Smelt
    Updated November 17, 2022
  • Title

    The Effect of Drought on Delta Smelt Vital Rates

    Lead University of California - Davis [UC Davis]
    Description This Project is necessary to obtain a better understanding of the effects of drought and management's response to drought on the Delta Smelt in order to avoid extinction. This study will test predication from other models to evaluate the impact of drought and management measures on Delta Smelt responses in terms of growth, phenotype diversity and survival during the spring and summer, when drought impacts are greatest.
    Science topics Delta Smelt, Drought
    Updated November 18, 2022
  • Title

    A Next-generation Model of Juvenile Salmon Migration through the Sacramento-San Joaquin Delta

    Lead University of California - Santa Cruz [UCSC]
    Description While migrating through the Delta and its tributaries, Chinook salmon and steelhead move through diverse habitats, encounter predators, interact with highly dynamic flows, and are impacted by a multitude of human-made structures. Funding for this Project will be use to develop integrated system-level models that will effectively manage salmonid populations and other key resources in the California Central Valley.
    Science topics Salmon migration
    Updated November 18, 2022
  • Title

    Reconstructing juvenile salmon growth, condition and Delta habitat use in the 2014-15 drought and beyond

    Lead University of California - Davis [UC Davis]
    Description This study uses otolith chemistry and microstructure to monitor how salmon use the Delta as rearing habitat and a migratory corridor, and the mechanisms cuing their outmigration from natal rivers. We will quantify the extent to which Delta-rearing contributes to salmon population resilency under different conditions (including drought and flood conditions) and provide baseline data to assess population responses to future habitat restoration and changing climate. Physical tags are limited to larger fish that are more sea-ready than fry, and are thus ineffective to estimate the full rearing potential of Delta habitats, while abundance surveys provide only a snapshot of information. Otolith reconstructions allow us to estimate “who” is using the Delta (which populations and life history types), for how long, and their growth rates relative to other rearing habitats. This project will generate empirical data that will inform management actions aimed at maximizing salmon abundance, life history diversity, and resilience to future stressors.
    Science topics Drought
    Updated April 29, 2022
  • Title

    Identify environmental drivers influencing habitat attributes and effect on salmonids survival.

    Lead State Water Contractors [SWC]
    Description
    Science topics None specified
    Updated April 29, 2022
  • Title

    Juvenile salmon distribution, abundance, and growth in restored and relict Delta marsh habitats

    Lead California Department of Fish and Wildlife [CDFW]
    Description Project is to conduct a study that will to determine whether observed salmon responses match the assumptions and expectations of habitat suitability and life-cycle models currently guiding resource management and habitat restoration in the Bay-Delta, while at the same time supplying much-needed quantitative information to improve these models. The broader purpose is to improve these models to allow more objective and accurate predictions of alternative management and restoration actions intended to recover Central Valley salmon populations. The overarching goal of this project is to quantify the distribution, abundance, residence time and growth of juvenile salmon within the Bay-Delta.
    Science topics None specified
    Updated April 29, 2022
  • Title

    Problems and Promise of Restoring Tidal Marsh to Benefit Native Fishes in the North Delta during Drought and Flood

    Lead University of California - Davis [UC Davis]
    Description The Project will improve scientific understanding of the North Delta ecosystem and to improve better basis for management and creation of restoration sites, as well as management of the region to benefit native fishes. The Project will improve scientific understanding of how fish populations are influenced by the interactions between wetlands and hydrology, geomorphology, water quality and food availability. Funding will be use to conduct water quality monitoring;hydrodynamic modeling;and fish and invertebrate surveys.
    Science topics None specified
    Updated April 29, 2022
  • Title

    Application of cutting-edge tools to retrospectively evaluate habitat suitability and flow effects for Longfin Smelt

    Lead University of California - Davis [UC Davis]
    Description The Longfin Smelt (Spirinchus thaleichthys) is a native forage fish, characteristic of the natural biological community of the San Francisco Estuary (SFE). This study will examine variation and interactions among hatch dates, instantaneous and total growth rates, habitat use, and timing of transitions among habitats with different salinities, and variation among years with very different climate and freshwater outflow conditions. This information is crucial for managing freshwater flows and can be used to evaluate the effects of tidal wetland restoration in the San Francisco Estuary.
    Science topics None specified
    Updated November 19, 2022
  • Title

    Contaminant Effects on Two California Fish Species and the Food Web That Supports Them

    Lead University of California - Davis [UC Davis]
    Description Water temperatures are increasing due to global climate change, and are predicted to reach levels that exceed the thermal tolerance of sensitive Delta species such as the Delta Smelt by 2050. Little is directly known about the differences in sensitivity between Inland Silverside and Delta Smelt to such stressors, or how either species responds to multiple stressors. Funding will be use to study how these two species respond to drought-induced stressors (temperature, salinity, and reduced dilution of contaminants) which will provide key insights, given that one is near extinction and the other is thriving under drought conditions.
    Science topics None specified
    Updated November 19, 2022
  • Title

    Defining the fundamental niche of Longfin Smelt [Spirinchus thaleichthys]: Physiological mechanisms of environmental tolerance.

    Lead University of California - Davis [UC Davis]
    Description This Project will evaluate reproductive output, embryo to larval development, and growth and maturation of Longfin Smelt (Spirinchus thaleichthys). This Project is designed to comprehensively assess effects of extreme events and their interaction with contaminant effects, and aims to fill knowledge gaps relating to turbidity (e.g., stress levels associated with predation risk), age-specific fecundity, egg and early larval buoyancy, and other essential requirements for captive rearing conditions that will aid the successful culture.
    Science topics None specified
    Updated April 29, 2022
  • Title

    Impact of Spatial and Temporal Dynamics of Water Flows on Migratory Behavior of Chinook Salmon Smolts in the South Delta

    Lead University of California - Davis [UC Davis]
    Description Funding for this study project will be use track the swimming movements of salmon smolts during migration using acoustic transmitters and detection arrays near the confluence of Old River and the San Joaquin River. Analyses will be carried out to determine swimming velocity relative to current velocity. Modeling will estimate fish distribution; fish transit times; entrainment of fish into channels of the south Delta; and alternative water export management scenarios that may result in reduced entrainment.
    Science topics None specified
    Updated November 19, 2022
  • Title

    Identifying the Causes of Feminization of Chinook Salmon in the Sacramento and San Joaquin River System

    Lead University of California - Berkeley [UC Berkeley]
    Description Purpose was to assess the potential importance of endocrine-disrupting chemical contaminants to salmon and other resident speices of waters that are discharged into the San Francisco-San Joaquin Delta.
    Science topics Chinook Salmon
    Updated April 29, 2022
  • Title

    Review of Four Juvenile Salmon Coded Wire Tag Experiements Conducted in the Delta

    Lead U.S. Fish and Wildlife Service [USFWS]
    Description The US Fish and Wildlife Service, Stockton Fish and Wildlife Office, has since the mid-1980s conducted several multi-year release-recovery experiments with coded-wire-tagged juvenile Chinook salmon. The objectives of the studies were (1) to estimate survival through the lower portions of the Sacramento and San Joaquin river systems, the California Delta, and (2) to quantify the factors affecting survival. Four of these studies, listed more or less by their historical start dates, are the Delta Cross Channel, Interior, Delta Action 8, and VAMP experiments.
    Science topics Chinook Salmon
    Updated April 29, 2022
  • Title

    Quantitative Indicators and Life History Implications of Environmental Stress on Sturgeon

    Lead University of California - Davis [UC Davis]
    Description The purpose of this project is to analyze the effects of the pollutants on the overall fitness of different life stages of the green and white sturgeon. This research will significantly enhance our understanding of stressors on sturgeon and allow further development of life history models.
    Science topics Water temperature, Salinity, Pelagic fish, Methylmercury, Sturgeon
    Updated April 29, 2022
  • Title

    The Consequences of Operational Decisions on Water Quality: Reconciling Delta Smelt, Salmon, and Human Needs

    Lead Contra Costa Water District [CCWD]
    Description The purpose of this project is to assess the consequences of actions taken to protect threatened or endangered Chinook salmon species relative to other upstream and in-Delta water management actions that have changed seasonal salinity in the Delta, thus reducing the ability of delta smelt to survive as a species;and, to investigate with modeling scenarios the potential to ameliorate this trade-off with specific operational actions.
    Science topics Delta Smelt, Chinook Salmon
    Updated April 29, 2022
  • Title

    Pilot Mark-Recapture Study to Estimate Delta Smelt Pre-Screen Loss and Salvage Efficiency

    Lead U.S. Fish and Wildlife Service [USFWS]
    Description The purpose of this project is to perform a study to determine whether it is feasible to quantify entrainment losses of juvenile and adult delta smelt due to water exports. This information is critical to better understanding the movement of Delta smelt in the system.
    Science topics Delta Smelt
    Updated April 29, 2022
  • Title

    Are Apparent Sex Reversed Chinook Salmon a Symptom of Genotoxicity?

    Lead University of California - Davis [UC Davis]
    Description Goal was to test the relative importance of chemical stressors on population viability and genetic diversity for fall-run Chinook salmon (in association with environmental contaminant exposure in the Central Valley delta).
    Science topics Chinook Salmon
    Updated April 29, 2022
  • Title

    Estimating Juvenile Chinook Salmon Spring and Winter Run bundance at Chipps Island

    Lead U.S. Fish and Wildlife Service [USFWS]
    Description The purpose of this project will develop and implement a DNA sampling protocol for juvenile Chinook salmon captured at Chipps Island.
    Science topics Chinook Salmon
    Updated April 29, 2022
  • Title

    A Statistical Model of Central Valley Chinook Incorporating Uncertainty

    Lead R2 Resource Consultants Inc.
    Description The purpose of this project is to develop a statistical modeling approach to the two Central Valley Chinook Salmon species that incorporates mortality in all phases of salmon life history, and includes the effects of uncertainty in assessing population status, guiding future research, and making management decisions.
    Science topics Chinook Salmon
    Updated April 29, 2022
  • Title

    Quantifying Factors Affecting Migration Routing and Survival of Juvenile Late-Fall Chinook Salmon in the Sacramento-San Joaquin River Delta

    Lead U.S. Geological Survey [USGS]
    Description Juvenile Chinook salmon emigrating from natal tributaries of the Sacramento River must negotiate the Sacramento-San Joaquin River Delta where they disperse among the Delta's complex channel network. Natural processes and water management actions affect the fraction of the population using different migration routes through the Delta and survival within those routes, but quantifying these relationships has proven difficult. Since 2006, acoustic telemetry techniques have been used to quantify both movement among migration routes and survival within routes, providing the first insights into how route-specific survival contributes to population-level survival in the Delta. In this project, we propose to use existing acoustic telemetry data from multiple sources to 1) Quantify factors affecting migration routing of juvenile salmon emigrating from the Sacramento River, 2) Quantify factors affecting survival of juvenile salmon within specific migration routes, and 3) Simulate population-level survival through the Delta under a limited number of historical and operational scenarios. Collating telemetry data from multiple sources over numerous years offers a unique opportunity to identify important relationships that might otherwise be difficult to detect for any particular study in a given year. Quantifying such relationships is critical to informing resource management that seeks to balance use of water resources with recovery of endangered salmon populations.
    Science topics Chinook Salmon
    Updated April 29, 2022
  • Title

    Impact of Urbanization on Chinook Salmon, Steelhead Trout, and Their Prey: a Case Study of the American River

    Lead University of California - Berkeley [UC Berkeley]
    Description The American River provides spawning/rearing habitat for Chinook salmon and steelhead, yet passes through 30 miles of dense urban development. Urban runoff contains pyrethroid insecticides that cause the river to become toxic to standard testing species with every storm event. This study will go beyond observed toxicity, and address toxicity to chironomids, caddisflies, and mayflies, key diet components of juvenile fish in the river. A bioenergetic model will be used to evaluate effects of food web changes on young salmonids. Our key approach is the use of river-side systems with flowing river water that allow us to replicate realistic pesticide exposures, while controlling other variables. We will determine sensitivity to pyrethroids and fipronil of salmonid prey taxa, and expose them, as well as standard testing species, in the flow-through systems through six storm events. We will maintain experimental streams containing riverine benthic invertebrate communities, and measure response to the pyrethroid pulses. To supplement analyses of the indirect, food web-mediated effects, we will measure endocrine effects through vitellogenin induction in salmon and steelhead. Finally, one treatment includes river water from which organic contaminants have been removed by activated charcoal, to help establish cause of toxicity. The goal is to determine if known toxicity in the American River is a threat to benthic invertebrates and, through the food web, to salmon and steelhead.
    Science topics Chinook Salmon, Steelhead Trout, Above-highwater refugia, Other discharge contaminants, Food webs
    Updated April 29, 2022
  • Title

    Habitat Values of Native SAV [Submerged Aquatic Vegetation] in the Low Salinity Zone of San Francisco Estuary

    Lead San Francisco State University [SFSU]
    Description We will investigate the importance of native submerged aquatic vegetation (SAV) in providing food web support for native fish species in the low salinity zone of the San Francisco Bay-Delta. These SAV beds, composed primarily of Stuckenia pectinata (sago pondweed), are an extensive feature along many of the islands in Suisun Bay and the west Delta, yet almost nothing is known of their seasonal or interannual patterns, their invertebrate communities, or how their physical structure or food resources influence use by native fishes. We hypothesize that the position of these beds in the shallow subtidal zone along the islands increases habitat options adjacent to wetlands and channels for numerous fish species, including species of concern such as delta smelt and chinook salmon. The objectives of this project are to: 1) characterize patterns in habitat structure, community composition, and productivity of SAV beds in four locations in Suisun Bay and the western Delta over a three year period (with comparisons to non-native Egeria densa beds), 2) document the epifaunal invertebrate community composition and abundance in the Stuckenia beds, 3) assess fish use of these beds through seining and acoustic monitoring of hatchery-tagged fish, 4) utilize stable isotope analyses to evaluate food web relationships within and among the beds, and 5) begin preliminary evaluation of the potential to restore native SAV to subsided lands in this region.
    Science topics Chinook Salmon, Green sturgeon, White Sturgeon, Sacramento Splittail, Delta Smelt, Steelhead Trout
    Updated April 29, 2022
  • Title

    Foodweb Support for the Threatened Delta Smelt and Other Estuarine Fishes in Suisun Bay and the Western Sacramento-San Joaquin Delta

    Lead San Francisco State University [SFSU]
    Description The purpose of the project is to increase understanding of the foodweb supporting delta smelt and other estuarine species. This research is important because: 1) it could lead to increased foodweb support for the threatened delta smelt and 2) identify potential mechanisms underlying relationships of abundance or survival of some fish to freshwater flow.
    Science topics Delta Smelt
    Updated April 29, 2022
  • Title

    Quantifying the contribution of tidal flow variations to survival of juvenile Chinook salmon

    Lead U.S. Geological Survey [USGS]
    Description The purpose of this project is to quantify how tides in the Delta influence survival of juvenile salmon. Juvenile salmon survival increases when there is more flow and the river is less tidally influenced. We hypothesize that the increase in survival is because of reduced travel times causing less exposure to predators. This project will test this hypothesis using multiple models including ones that can predict how management actions that modify tidal patterns affect juvenile salmon survival.
    Science topics Chinook Salmon, Salmon migration, Surface water / flow, Tides, Water management
    Updated January 29, 2024
  • Title

    An Improved Genomics Tool for Characterizing Life History Diversity and Promoting Resilience in Central Valley Chinook Salmon

    Lead Michigan State University
    Description This study will improve our ability to protect the diversity of traits in Chinook salmon. The diversity of Chinook salmon migration timing is decreasing in the Central Valley. A key roadblock to protecting diversity is the current inability to rapidly and inexpensively identify large numbers of individuals from different populations during their migration to the ocean. This study addresses this information gap by leveraging pre-existing genomic data to develop a new technique that will allow scientists to identify individuals to life history type and location. For example, this study will potentially be able to identify Fall Run Chinook that are from the Sacramento versus the San Joaquin River basins. This information, in combination with data on water temperature and river flows, can determine the relationship between environmental conditions and juvenile salmon life history diversity. The information generated by this work will provide managers with the ability to accurately monitor the effect of key management actions on the different Central Valley Chinook salmon populations.
    Science topics Chinook Salmon, Estuaries, Fish, Habitat restoration, Resilience, Salmon rearing
    Updated November 29, 2022
  • Title

    Life History Variation in Steelhead Trout and the Implications for Water Management

    Lead University of California - Santa Cruz [UCSC]
    Description The purpose of this project is to explore the ways in which different stream hydrology and temperature can affect the growth and maturation of steelhead trout. Model examination will incude various stream flow management regimes may affect trout population dynamics region-wide.
    Science topics Steelhead Trout
    Updated April 29, 2022
  • Title

    Evaluating Juvenile Salmonid Behavioral Responses to Hydrodynamic Conditions in the Sacramento-San Joaquin Delta

    Lead State Water Contractors [SWC]
    Description This study combines detailed model predictions with salmonid tracking data to inform how river flows affect steelhead movement through the Delta. This project leverages an existing 6-year data set to support analysis of salmonid behavioral responses across a broad range of water years. The study will evaluate behavior relative to flow under existing regulatory requirements (Old and Middle River Flow and the Inflow to Export ratio), evaluate five new potential water management metrics identified by the Collaborative Adaptive Management Team Salmonid Scoping Team, and improve the understanding of what conditions affect survival.
    Science topics None specified
    Updated April 29, 2022
  • Title

    Impact of Temperature and Contaminants on Chinook Salmon Survival: A Multi-Stressor Approach

    Lead National Marine Fisheries Service [NMFS]
    Description The decline of native salmon species has resulted in their protection under the U.S. Endangered Species Act and the California Endangered Species Act. Disease and predation are primary drivers of mortality as salmon migrate. Multiple stressors, such as exposure to contaminants and elevated temperature, can impact rates of disease and predation of salmon as they migrate to the ocean. This study examines how contaminant exposures at different temperatures affects salmon health. Specifically, the study investigates the sensitivity of salmon to a contaminant mixture of bifenthrin (a pyrethoid pesticide) and triclosan (an antibacterial added to personal care products). Both contaminants can alter fish swimming behavior and critical physiological functions. Similarly, temperature stress can impact fish physiology and behavior, as well as exacerbate the adverse effects of contaminants.
    Science topics None specified
    Updated April 29, 2022
  • Title

    Synchrony of Native Fish Movements: Synthesis Science Towards Adaptive Water Management in the Central Valley (FishSync)

    Lead University of California - Davis [UC Davis]
    Description Salmon and other native California fishes are in decline and increasingly targeted for enhanced conservation. Acoustic telemetry technologies have emerged, allowing researchers to track fish routes through the Central Valley. Yet while the use of acoustic telemetry has widened, little synthesis has occurred on the large, growing, and expensive datasets that already exist. The main goal of the project is to conduct a synthesis study of existing and high priority telemetry datasets for native and non-native fishes in the Central Valley. Using synchrony of movement rates, through space and time, we will develop a novel behavior-based statistical framework to gain understanding into the environmental conditions that promote movement/passage of diverse native fishes in the Central Valley. The project includes a Technical Advisory Group, composed of members of multiple conservation teams. The group will inform each step of study, strengthen syntheses, and enable rapid communication of results to decision makers. In total, the project will analyze 10 to 15 high-quality telemetry datasets encompassing a range of native fishes and life stages. This synthesis will yield major insights into water management practices that could help improve survival of native fish.
    Science topics Chinook Salmon, Fish, Salmon migration, Steelhead Trout, Sturgeon, White Sturgeon
    Updated December 4, 2022
  • Title

    Improving Green Sturgeon Population and Migration Monitoring

    Lead University of California - Santa Cruz [UCSC]
    Description Green sturgeon is a listed species under the federal Endangered Species Act. This project supports the recovery and management of the southern distinct population segment of green sturgeon by improving population and migration monitoring. Improved monitoring is recommended in multiple initiatives to help protect this species, such as the Green Sturgeon Recovery Plan. There is some uncertainty on whether the most appropriate green sturgeon monitoring techniques are being used. This project compares the different estimation and monitoring techniques to identify the superior protocol. To compare the effectiveness of different techniques, scientists will monitor green sturgeon in the Sacramento River using sonar technology. Monitoring data will be used to estimate the population size and death rates due to by-catch. This project will also review and synthesize past acoustic telemetry data to determine if the data can be modeled to improve population size estimates.
    Science topics Green sturgeon
    Updated April 29, 2022
  • Title

    Risk of fish predation within and across tidal wetland complexes

    Lead University of California - Davis [UC Davis]
    Description This study focuses on understanding how restored tidal wetlands with different physical configurations function as refuge and rearing habitat for fishes, including native and imperiled species such as delta smelt and juvenile Chinook salmon. This research will assess the spatial distribution of predation risk as it varies within and across tidal wetlands. The proposed research will generate a statistical model that helps predict predation outcomes from various restored tidal wetland designs and channel configurations. This will be a powerful tool for managers to forecast how proposed habitat restoration or water management actions may impact native fish populations.
    Science topics Tidal wetlands
    Updated April 29, 2022
  • Title

    Estuarine fish community responses to climate, flow, and habitat

    Lead University of California - Berkeley [UC Berkeley]
    Description The goal of this research is to better understand how climate change will affect fishes with different life histories and habitat associations across the San Francisco Estuary. Existing datasets will be incorporated in synthetic analyses and cutting-edge statistical models to identify fish community responses to climate, flows, and habitats along the estuarine salinity gradient. This synthesis-science project will use rich long-term datasets that have been collected by Bay-Delta researchers for decades that will then be analyzed in a reproducible and open science framework. It will also support efforts by the Interagency Ecological Program’s Climate Change Project Work Team.
    Science topics Estuaries
    Updated April 29, 2022
  • Title

    The effect of temperature on predation of juvenile salmonids

    Lead University of California - Davis [UC Davis]
    Description This study will investigate fish swim performance in response to temperature, using salmon and two of its known predators: largemouth bass and Sacramento pikeminnow. The researcher will assess swim performance metrics and predation risk inside and outside the ideal thermal range of each species to determine if a temperature advantage predicts salmon survival in predation scenarios. This project’s results will provide a mechanistic understanding of how temperature stress may influence mortality risk of juvenile Chinook salmon through predation, which will offer a more holistic perspective on the management of this species
    Science topics Temperature
    Updated April 29, 2022
  • Title

    Understanding the Scale and Mechanisms of Connectivity between Splittail Populations and the Implications for Management

    Lead U.S. Bureau of Reclamation [USBR]
    Description Our proposal seeks to add four elements, telemetry, genetics, physiology, and modeling, to an existing research effort on splittail. The study addresses the hypothesis that there is no difference in population dynamics between the two distinct splittail populations. To address this hypothesis we are conducting a collaborative, interdisciplinary study that includes an intensive field effort combined with state-of-the-art laboratory tools that can determine the natal origins, historical habitat use, feeding, and general health of adult splittail. With this proposal we seek to leverage additional funds that were not previously available to add the four new elements. The telemetry component will take advantage of the expansive existing array of receivers deployed in the estuary to evaluate the movements and migration of splittail. The genetic component will provide a precise means to assign individuals to their respective population, determine sex ratios, and to estimate the effective size of the populations. The physiology component will determine if the newly discovered Petaluma/Napa population of splittail exhibits different requirements and tolerances than the Central Valley population. The modeling component will apply the cumulative information gained by the overall study to evaluate the sensitivity of splittail persistence to demographic variability in population dynamics. This work will directly address the Priority Research Topics presented in the PSP.
    Science topics Sacramento Splittail
    Updated April 29, 2022
  • Title

    Survivial and Migratory Pattern of Central Valley Juvenile Salmonids

    Lead University of California - Davis [UC Davis]
    Description The purpose of this project is to determine the survival and movement patterns of late-fall Chinook salmon smolts and steelhead smolts as they migrate downstream. This information is important to better understand how salmon move through the system.
    Science topics None specified
    Updated April 29, 2022
  • Title

    A Multi-Stock Population Dynamics Framework for the Recovery of Sacramento River Chinook Salmon

    Lead University of Washington [UW]
    Description The purpose of this project is to construct a multi-stock salmon population model and management strategy evaluation (MSE) tool that addresses the cross-linkages between water use and fishery ecosystem response. Recent federal court judgment concluded that insufficient evidence was provided for prescribing specific flow restrictions in two recent conservation measures. The inability to provide adequate evidence was a byproduct of not having the correct quantitative tools at hand. We propose to build these tools by furthering technological developments of previous analyses of Central Valley Chinook population dynamics. Specifically, our work will integrate multiple salmon populations together into a single model that can reconstruct historical population dynamics such that environmental conditions and water resource use can be used as predictors of biological responses of multiple populations. Our goal is to integrate populations into a single model so that the effect of water management and fishery management policies can be examined in light of all fish populations simultaneously. This pertains to the biological interactions between the populations as well as the way in which fisheries impact individual populations depending on growth and maturation rate of each population. All analysis will be framed in the context of historical and proposed water use patterns.
    Science topics Flows
    Updated April 29, 2022
  • Title

    Linking Trophic Ecology with Slough and Wetland Hydrodynamics, Food Web Production and Fish Abundance in Suisun Marsh

    Lead University of California - Davis [UC Davis]
    Description Suisun Marsh remains one of the most productive regions of the San Francisco Estuary (SFE), fueling interest in the Marsh as a model for restoring estuarine function to the region in the future. The UC Davis Suisun Marsh Fish Survey has 30 years of data on physical structure, water quality, benthic and pelagic invertebrates and fish. We will use these and other data to explore patterns of fish abundance in relation to zooplankton, slough geomorphology, and regional hydrodynamics. Our goal is to understand and predict the kinds of physical variability and structure that create attractive habitat for fish, in order to 1) serve as a template for wetland and subtidal habitat restoration in the Estuary and 2) anticipate the effects of sea level rise, levee failure and salinity increases that are expected to have a large impact on the Marsh in the near future. A comprehensive literature and data search will pull together known information for synthesis. Cluster analysis will identify slough complexes into types of functional habitat. Predictive maximum likelihood, hierarchical and multivariate autoregressive models will be used to predict how foodwebs and fish respond to environmental factors. Finally, coupled hydrodynamic-life history models for zooplankton will demonstrate how production is regulated by slough morphology. Results will be integrated as a white paper on the history, current functioning, and future of the Marsh.
    Science topics Levees, Climate change
    Updated April 29, 2022
  • Title

    Modeling the Delta Smelt Population of the San Francisco Estuary

    Lead San Francisco State University [SFSU]
    Description The purpose of this project is to develop an individual-based particle-tracking model examining population behavior of Delta smelt under different scenarios.
    Science topics Delta Smelt
    Updated April 29, 2022
  • Title

    Aquatic Habitat Sampling Platform: Standardized Fish Community Sampling Across Habitat Types

    Lead U.S. Bureau of Reclamation [USBR]
    Description Description The Aquatic Habitat Sampling Platform (AHSP) is an integrated aquatic species and habitat sampling system that can effectively monitor aquatic organisms and reveal habitat associations while having minimal or no “take” of sensitive species. Further development and deployment of the AHSP will expand data collection to shallow and off-channel habitat, while offering the capability to transition to deeper and open water habitats, providing reliable sampling efficiency estimates (e.g., probability fish detection) and “catch” per unit effort (i.e., number of individual species per volume of water sampled) and improving our knowledge about populations, habitat associations and major stressors of key organisms within the San Francisco Estuary (Estuary). Need Within the Estuary, numerous monitoring techniques are used. However, monitoring weaknesses for determining fish status and trends include: 1) restricted locations available for some techniques;2) limited ability to simultaneously assess zooplankton and fish larvae;and 3) difficulty in estimating fish population size due to lack of gear efficiency information (Honey et al. 2004). Furthermore, past attempts at integrated abundance indices from more than one sampling method have had limited success. Although there continues to be considerable collaborative monitoring and research devoted to understanding Central Valley fish species, coordination among activities has been difficult. Other issues include permitting take of listed species and time-consuming monitoring with extended periods of down time due to sample post-processing of fish and invertebrate species. Identification of key microhabitats for each lifestage and attributes and linking associated physical parameters such as habitat features (e.g., depth, structure, channel type) and water quality is needed. Objectives • Test AHSP operation within the Estuary while providing information highly relevant to pressing Delta management issues (IEP 2016); • Provide detailed information on distribution and approximate abundance of adult Delta Smelt within identified habitat types (Biological Opinion on the Long-Term Operational Criteria and Plan for coordination of the Central Valley Project and State Water Project;https://www.fws.gov/sfbaydelta/documents/SWPCVP_OPs_BO_12-15_final_OCR.pdf);and • Assess habitat associations and diurnal behavior of Delta Smelt and other fishes (Durand 2015).
    Science topics Delta Smelt
    Updated April 29, 2022
  • Title

    Central Valley Salmonid Coordinated Genetic Monitoring [Year 4]

    Lead U.S. Bureau of Reclamation [USBR]
    Description Description This work will include tasks to rapidly identify winter-run Chinook juvenile salmon at the CVP/SWP salvage facilities, process juvenile salmonid tissues from various CVPIA and IEP fish monitoring stations, and support coordination of genetic monitoring across the CVP and SJRRP programs. PIs: Josh Israel (USBR);Scott Blankenship (Cramer Fish Science);Ken Bannister (USFWS);John Carlos Garza (NOAA-Fisheries);Brett Harvey (DWR);Noble Hendrix (QEDA);Rachel Johnson (NOAA-Fisheries);Mariah Meek (UC Davis);Kevin Reece (DWR) Need This study is needed due to the limited accuracy of Lenght at Date stock identification. Inaccurate identification of Chinook salmon is problematic because it compromises the management value of data collected from standard monitoring programs. This project will improve the science and management value of the Central Valley salmon monitoring network, supported through IEP and Central Valley Project Improvement Act (CVPIA) monitoring stations, by accurately determining stock identification of multiple Chinook salmon stocks across their distribution. Classification tables will be developed to characterize monthly and seasonal accuracy between length-at-date and genetic race assignment at IEP and BiOp monitoring locations. This multi-year dataset will be used to evaluate the likelihood of accurate assignment and potential biophysical explanatory variables influencing genetic accuracy. Objectives Improve accuracy of CVPIA and IEP monitoring programs by providing genetic stock identification information for tissues collected from Red Bluff, Knights Landing, DJFMP, salvage facilities and San Joaquin River fish monitoring stations. Samples will be collected from all four runs of Chinook salmon based on length-at-date (i.e., samples will be collected from Chinook of various sizes throughout the sampling period).
    Science topics Chinook Salmon
    Updated April 29, 2022
  • Title

    Enhanced Acoustic Tagging, Analysis, and Real-Time Monitoring

    Lead National Oceanic and Atmospheric Administration [NOAA]
    Description Description This project tracks the movement and survival of wild and hatchery juvenile Chinook salmon with a large acoustic receiver network (JSATS), including real-time receivers, and the development of real-time metrics and retrospective modeling of juvenile salmon migration data. Need There is a well-documented need for improved detection and associated modeling of salmon migration and survival in the Central Valley. Understanding salmon survival and movement dynamics in the Delta and its tributaries is critical to the operation of state and federal water projects, recovery of ESA-listed species, and sport and commercial fisheries management. Objectives • Maintain 20 real-time JSATS receivers: will provide information on migrating salmon smolt location and timing of Delta entry and exist, which is key for informing time-sensitive decisions • Deployment of autonomous JSATS receiver array: this will provide fine-scale reach-specific survival and movement rates • Development of new metrics for the real-time data: this will inform key management relevant questions, such how many fish are entrained at critical junctions • Development of real-time website to convey movement and survival rates of acoustic tagged juvenile salmonids at various real-time locations in the Sacramento River and Delta.
    Science topics Salmon migration
    Updated April 29, 2022
  • Title

    Physiological and Behavioral Effects of Domestication on Delta Smelt

    Lead California Department of Water Resource [DWR]
    Description Description Due to the continued population decline of Delta Smelt and the threat of extinction, conservation efforts may include future supplementation practices using the refuge population of Delta Smelt at the Fish Conservation and Culture Laboratory (FCCL) in Byron, CA to assist in maintaining the wild population. Prior to any supplementation planning, it is first critical to determine if Delta Smelt with varying levels of domestication indices (i.e. level of hatchery ancestry) respond differently, both physiologically and behaviorally, to various habitat conditions. This project aims to provide a better understanding of the effects of domestication on captive Delta Smelt (Hypomesus transpacificus) by assessing the refuge population at the FCCL. Three studies will be conducted exploring if domestication index (i.e. the level of hatchery ancestry) affects the physiological and behavioral performance of Delta Smelt in response to physical handling and climate change stressors. Need Physiological and behavioral changes of hatchery fish due to domestication could lead to unintended detrimental effects in the wild;therefore, research characterizing the alterations of hatchery Delta Smelt across levels of domestication indices are warranted to understand the effects of captivity and how they might shape future supplementation and conservation strategies. For example, identification of differences among groups of Delta Smelt with varied domestication index may create the need for domestication management and the implementation of altered hatchery practices. This project will provide relevant and timely information for conservation managers and adaptive restoration strategies and dovetail with the recommendations from the 2017 Delta Smelt Supplementation Workshop. As such, this study is included in the supplementation studies work plan which came out of that workshop. Specifically, this project fits within two topics in the IEP Science Strategy: Effects of Climate Change and Extreme Events and Restoring Native Species and Communities. Objectives 1. To characterize domestication effects on hatchery Delta Smelt by synthesizing existing/historical datasets on growth and reproduction of fish at the FCCL since the start of the hatchery program. 2. To identify the impacts of domestication index on the physiological stress response of Delta Smelt following handling stress. 3. To determine the effects of domestication index on individual and group swimming behavior, responses to predation, and responses within the context of climate change factors including warming and increased salinity.
    Science topics Delta Smelt
    Updated April 29, 2022
  • Title

    Developing an eDNA metabarcoding protocol to improve fish and mussel monitoring in the San Francisco Estuary

    Lead National Oceanic and Atmospheric Administration [NOAA]
    Description Description We propose to develop an eDNA metabarcoding protocol to complement existing IEP monitoring surveys and assess the effects of management activities such as habitat restoration or flow alteration. We will develop a reference sequence database for native and invasive fish, mussels, and other macroinvertebrates present in the San Francisco Estuary (SFE). We will optimize a molecular and computational pipeline for metabarcoding and ground truth the method against three SFE monitoring efforts, each using different sampling gear. We will investigate the relationship between eDNA sequence read count and fish biomass or abundance (EDSM survey). Finally, we will determine the ability of metabarcoding to detect fish and macroinvertebrate assemblages across large and small spatial scales and over time. Need Our overarching goal is to develop a non-invasive, low cost monitoring tool that can be used in conjunction with existing IEP monitoring programs or used alone to assess biological community composition at locations of interest in the SFE. This proposal is related to the 2020 – 2024 IEP Science Strategy by creating a new monitoring tool that can assist in two main areas: 1) Restoring Bay-Delta native fishes and community interactions and 2) assessing effects of flow alteration on Bay-delta aquatic resources. Broadly, this study will inform management decisions by supporting and augmenting existing monitoring surveys in the SFE. It will also lead to a richer and more complete understanding of SFE ecology. This study is not explicitly required by law or agreement, and to our knowledge is neither a recommended action nor a result from an IEP review or synthesis effort. Objectives Objective 1: Develop robust molecular methods and a computational pipeline for detection of SFE fish and macroinvertebrates by eDNA metabarcoding of water samples. Objective 2: Compare eDNA metabarcoding head-to-head with existing and historical monitoring data from three ongoing ecological surveys using diverse conventional sampling gear and evaluate accuracy of fish abundance and biomass estimates from eDNA metabarcoding data. Objective 3: Evaluate factors that influence eDNA detection of species of interest (e.g. rare or invasive species) and suites of species (e.g. benthic fishes and invertebrates) on two spatial scales, within and between habitats, along with temporal variation.
    Science topics Fish
    Updated April 29, 2022
  • Title

    Predation Dynamics Across Reach-Specific Gradients in Juvenile Salmon Survival

    Lead U.S. Geological Survey [USGS]
    Description Description The overarching goal of this project is to determine if predation by piscivorous fishes is an important explanatory driver of survival of juvenile Chinook Salmon emigrating through the north Delta. To achieve this goal, we seek to determine if variation in reach-specific characteristics of predation dynamics covary with survival of acoustictagged juvenile Chinook Salmon collected during the study period. This will be accomplished by comparing reach-specific characteristics of the piscivore community and its observed and modeled consumption of juvenile Chinook Salmon across a range of environmental conditions. Need This is not a mandated study but it addresses an important research need. Objectives • How does the piscivore community (species composition, size structure, and abundance) vary across specific migratory pathways (river reaches) in the North Delta? • To what extent do environmental conditions (e.g., water temperature, turbidity, and discharge) control the consumption of juvenile Chinook Salmon? • Do characteristics of the predator community explain variation in survival of acoustic tagged salmon collected during the study period?
    Science topics Predation
    Updated April 29, 2022
  • Title

    Estimating Abundance of Juvenile Winter-run Chinook Salmon Entering and Exiting the Delta [SAIL]

    Lead U.S. Fish and Wildlife Service [USFWS]
    Description Description This is a continuation of a five year project funded by CDWR and CDFW and the Central Valley Project Improvement Act in 2017. The objective of the project is to improve estimates of population abundances for fall, winter and spring run juvenile Chinook Salmon at Sacramento and Chipps Island by improving efficiency estimates using data from releases of coded wire tags (CWT), acoustic tags (AT), and by genetically sampling the trawl catch in 2018. The project will (1) develop statistical models for estimating trawl efficiencies using 2016-2018 data for paired AT-CWT releases of winter run and fall-run Chinook Salmon;(2) use 2018 genetic sampling of trawl catch in combination with efficiency estimates to estimate population abundances of fall, spring and winter run at Sacramento and Chipps Island in 2018;(3) implement trawl efficiency studies for multiple salmon runs in 2018 informed by the 2016 and 2017 results and in coordination with hatcheries for inclusion of AT fish with existing CWT releases;and (4) combine trawl efficiencies with genetic samples of trawl catch to provide estimates of fall, spring and winter-run salmon abundance (with estimated precision) entering and exiting the Delta in 2018. Need There is growing appreciation that a salmon monitoring network that could quantitative estimates of abundance is desirable to improve our knowledge and resolution of life stage success and movement across the landscape (Salmon SAIL conceptual models 2016). Objectives (1) Estimate the population-level status and trends for winter run;and status of spring and fall run;(2) evaluate production estimates for juvenile winter-run Chinook Salmon entering the Delta used in water project take development;(3) provide estimates of winter and fall run-specific freshwater cohort strength to support ocean harvest management decisions;(4) establish a time series of winter, spring and fall run-specific production estimates at key locations for incorporation into life cycle models.
    Science topics Chinook Salmon
    Updated April 29, 2022
  • Title

    Reconstructing Juvenile Salmon Growth, Condition, and Delta Habitat Use in 2014-15 Drought and Beyond [SAIL]

    Lead University of California - Davis [UC Davis]
    Description Description Life history diversity buffers salmon populations over space (e.g. the use of natal and non-natal rearing habitats and time (e.g. variable migration timing resulting in greater probability of meeting optimal ocean conditions). Historically the Sacramento-San Joaquin Delta provided critical salmon rearing habitat, but urban expansion, water diversions and species introductions have resulted in inhospitable conditions unlikely to meet rearing needs. This study fills critical data gaps regarding Delta rearing by juvenile Chinook salmon – primarily to determine the annual migrant portfolio (proportion of different populations and life stages) and the relative success of Delta vs. natal rearing (inferred by rearing duration, growth rate, diet and condition). We quantify the extent to which Delta rearing contributes to salmon population resiliency under different environmental conditions, including drought (2014-15) and flood conditions (2017, 2019), and provide baseline data to provide insights into population-level responses to future habitat restoration and climate change. The study uses annual collections of fall & late fall run salmon samples from sites upstream (Mossdale/Sherwood Harbor), within, and downstream (Chipps Island) of the Delta sampled by the IEP Delta Juvenile Fish Monitoring Program (DJFMP). Need Annual monitoring surveys routinely sample salmon entering and leaving the Delta, but the extent to which these juveniles rear there is virtually unknown, and has been highlighted as a critical data gap for parameterizing the NMFS Chinook salmon life cycle model (S. Lindley NOAA pers. comm.). There are limited tools available to monitor habitat use by native fishes, with most efforts providing a snapshot of fish presence/absence or abundance. Tagging studies provide key information about migratory pathways and survival through stretches of the Delta, but are typically limited to larger individuals and often use hatchery smolts with different rearing needs and seareadiness to the smaller individuals most likely to use Delta habitats. Otoliths represent a unique tool to reconstruct fish age, natal origin, growth history, movement patterns, and habitat use, even in fry <40mm fork length. Objectives We will use juvenile salmon collected by the IEP Delta Juvenile Fish Monitoring Program to assess: 1. Contributions of different rivers & hatcheries to sites upstream, within & downstream of the Delta. 2. Delta habitat use (frequency, duration) and success (growth rates, condition and diet). 3. Mechanisms governing juvenile salmon outmigration timing from the natal tributary.
    Science topics None specified
    Updated April 29, 2022
  • Title

    Enhanced Delta Smelt Monitoring [EDSM]

    Lead U.S. Fish and Wildlife Service [USFWS]
    Description Description The Enhanced Delta Smelt Monitoring (EDSM) program is a year-round monitoring program comprised of multiple crews trawling concurrently at multiple sites in predefined strata within the San Francisco Estuary. Post-larval Delta Smelt are targeted approximately April through June using 20mm trawling gear, and Kodiak trawling gear is employed the remainder of the year. Gear efficiency experiments and shallow water sampling elements are incorporated when possible. Need The declining Delta Smelt population has highlighted the need to keep improving the array of information that supports our understanding of the factors affecting Delta Smelt population dynamics and management decisions to minimize adverse effects of water operations on the population. EDSM has biological significance and potential conservation benefit by providing data to resource managers on nearly all life stages of endangered Delta Smelt and near-real-time data on the juvenile and adult life stages. EDSM data is provided to the Smelt Working Group and other managers in near realtime to help inform management decisions during the entrainment season. Objectives • To estimate the total abundance of Delta Smelt, along with standard errors or confidence intervals, on a weekly to bi-weekly basis for various life stages (postlarvae, juveniles, sub-adults, adults) throughout the year; • To estimate the spatial distribution of Delta Smelt at a management relevant temporal and spatial resolution;and • To provide data that support management decisions and address scientific questions to further understanding of sampling efficiency, drivers of Delta Smelt population patterns, and other conservation and management-relevant topics.
    Science topics Delta Smelt
    Updated April 29, 2022
  • Title

    Integrating Measurement of Fish Body Condition within the Delta Juvenile Fish Monitoring Program [DJFMP]

    Lead U.S. Fish and Wildlife Service [USFWS]
    Description Description The aim of this pilot effort is to begin assessing methods and developing protocols for incorporating measurement of fish body condition (Fulton’s Condition Index, K) into standard Delta Juvenile Fish Monitoring Program (DJFMP) sampling. Need The goal of this study is to examine the utility of fish body condition as a measure for DJFMP to evaluate underlying factors driving fish health and survival in the Sacramento and San Joaquin River-Delta system. This will provide a more complete assessment of how condition metrics vary for common fish species that are sensitive to differences in environmental conditions, filling a fundamental data gap in our existing monitoring program. Objectives • Establish a pilot sampling design and methods for collection of data from fish sampled through DJFMP. • Assess the utility and expand the use of body condition to include up to 7 species of commonly sampled fishes. • Develop protocols for incorporating new methods into DJFMP sampling.
    Science topics Fish
    Updated April 29, 2022
  • Title

    Extracting Better Information from Long-Term Monitoring Data: Estimating Occupancy and Abundance of Near-Shore Fishes in the Sacramento-San Joaquin River Delta

    Lead U.S. Fish and Wildlife Service [USFWS]
    Description Description The purpose of this study is to expand IEP monitoring and inference to other dominant near-shore, littoral habitats not sampled by beach seines through the use of boat electrofishing. To accomplish this we will sample key littoral fish species across various near-shore habitats in order to determine how best to estimate abundance, occupancy, capture probabilities, and related environmental drivers. Need Expanding DJFMP sampling to other habitats throughout the Delta will allow our program to detect and monitor fishes and ecological trends through time, alleviating a recognized data gap. Current sampling relies on data collected through non-random fixed point sampling of unobstructed habitats, which limits the utility of our data to inform management decision. Objectives • Design boat electrofishing survey methods to expand DJFMP’s monitoring into habitats and locations not sampled by beach seining. • Design and develop field and data analysis methods for estimating capture probability and abundance using boat electrofishing techniques. • Predict spatio-temporal distribution of habitats occupied by key littoral species.
    Science topics Habitat
    Updated April 29, 2022
  • Title

    SAIL [Coordinated Enhanced Acoustic Telemetry Program]

    Lead U.S. Bureau of Reclamation [USBR]
    Description These monitoring efforts can provide critical information on juvenile salmonid distribution and survival, which inform biologists and managers interpretations of the exposure and intensity of CVP and SWP water operation risks on tagged populations in Central Valley rivers and the Bay- Delta. Understanding salmon survival and migration dynamics in the Delta and its tributaries is critical to the recovery of ESA-listed species, and sport and commercial fisheries management. For example, estimating the population size of endangered Sacramento River Winter-run Chinook (SRWRC) as they enter and exit the Delta is considered critical for informing Delta water management actions (Interagency Ecological Program (IEP) SAG 2013). “The use of realtime acoustic receivers that immediately transmit acoustic tagged (AT) fish detections needs to be included in the expanded network” (Johnson et al., in press). Tracking the fate of individual tagged fish will be accomplished with AT and used to develop estimates of survival and movement for other non-AT fish also part of that group. Population level sampling programs will use survival estimates generated by AT and applied to other mass marked (coded wire tagging) groups to develop improved capture efficiency for these sampling programs. Objectives: • Deploy and service field monitoring acoustic telemetry stations at locations important to fish and water management. • Implant, transport, and release acoustically tagged juvenile ESA-listed wild and hatchery juvenile salmonids. • Analysis and synthesis to support production and development of new metrics for understanding the survival, distribution, and entrainment of juvenile salmonid along the Sacramento River and its floodways, as well as, the Bay-Delta. Six-Year Steelhead Study Continuation Reclamation’s Proposed Action for ROC on LTO Section 4.10.5.12.3 Additional Measures includes a San Joaquin Basin Steelhead Telemetry Study -- Continuation of the 6-Year Steelhead telemetry study for the migration and survival of San Joaquin Origin Central Valley Steelhead. This investigation involves undertaking experiments utilizing acoustically-tagged salmonids to confirm proportional causes of mortality due to flows, exports, and other project and non-project adverse effects on steelhead smelt out-migrating from the San Joaquin Basin and through the southern Delta. This study is to coincide with different periods of operations and focus on clipped hatchery steelhead (Oncorhynchus mykiss). The period of interest is between February 15 and June 15, which coincides with a majority of O. mykiss outmigration from the Stanislaus River and recoveries of steelhead smolts in the Mossdale fish monitoring efforts. This period is to include changes in CVP/SWP operations that include reductions in exports, reductions in reverse flows in Old and Middle rivers (OMR), and San Joaquin River pulse flows to assess the influence of flow and exports on juvenile steelhead survival. This study is designed to evaluate juvenile steelhead route selection at channel divergences in the south Delta and along the mainstem San Joaquin River, and how these behaviors influence survival in specific reaches and through the Delta to Chipps Island.
    Science topics None specified
    Updated April 29, 2022
  • Title

    Pacific States Marine Fisheries Commission Coleman-Nimbus Tagging

    Lead U.S. Bureau of Reclamation [USBR]
    Description 25% of fall- run Chinook tagged and clipped and annual report on hathchery contributions to fisheries and watersheds
    Science topics None specified
    Updated April 29, 2022
  • Title

    Sacramento River Basin Salmonid Monitoring with Pacific States

    Lead U.S. Bureau of Reclamation [USBR]
    Description This study aims to monitor effectiveness of salmonid habitat improvement projects in the Sacramento River basin. Annual Chinook escapement estimates in Sacramento River and upper river tributaries and American, and habitat project juvenile monitoring.
    Science topics Chinook Salmon
    Updated April 29, 2022
  • Title

    FCCL Conservation Hatchery Operation for Delta Smelt Refuge Population Maintenance and Research Support

    Lead U.S. Bureau of Reclamation [USBR]
    Description This facility houses the Delta Smelt Refuge population and produces Delta Smelt for release into the Delta. It is also responsible for the genetic management of the captive population and support of studies on supplementation.
    Science topics Delta Smelt
    Updated April 29, 2022
  • Title

    Fish out of breath: Assessing, developing, and validating physiological bioindicators of hypoxia across the Delta

    Lead University of California - San Diego [UCSD]
    Description This proposal seeks to generate two management tools to optimize ongoing conservation efforts (e.g. wetland restoration, fish supplementation) by accomplishing the following 4 objectives: Objective 1) use controlled laboratory experiments to identify temperature-dependent hypoxia tolerance data (Pcrit) for ChinookSalmon smolts and juvenile Delta Smelt. Objective 2) compile existing temperature and DO monitoring data across the SFE. Objective 3) generate metabolic indices using the newly-generated physiological data (Obj. 1) and existing environmentalinformation (Obj. 2) to examine spatial and temporal patterns in metabolic stress for each species. Objective 4) explore and develop an otolith-based bioindicator to identify past hypoxia exposure.
    Science topics Chinook Salmon, Delta Smelt, Dissolved oxygen, Temperature
    Updated May 8, 2024
  • Title

    Restoring tidal marsh foodwebs: assessing restoration effects on trophic interactions and energy flows in the San Francisco Bay-Delta

    Lead University of California - Berkeley [UC Berkeley]
    Description The objective of this research on tidal marsh food webs is to examine whether and how restoration (via breaching dikes) may translate into recovery of diverse energy pathways and trophic interactions between basal resources, primary consumers, and predators. By comparing food webs at several tidal marshes, I will answer the following questions: (1) How does food web structure vary between reference and restored tidal marshes over time (seasons and years) and across a salinity gradient? (2)What mechanisms explain variation in food web structure within and between reference and restored tidal marshes–are they related to energy flows (food quantity, quality, transfer efficiency), community composition, or both? (3) What role do non-native species play in potentially shifting food web structure–e.g., changing community membership, sequestering energy from natives? This project builds on a large breadth of research that has used stable isotopes to characterize tidal marsh food webs in the Bay-Delta and other regions.
    Science topics Food webs, Wetlands
    Updated May 8, 2024
  • Title

    Examining the relationship between Longfin Smelt and flow in the San Francisco Bay Delta

    Lead University of California - Berkeley [UC Berkeley]
    Description The overarching goal of this study is to investigate the time-varying effects of flow variation and food availability on longfin smelt population dynamics, via advanced modeling of a diverse set of environmental and ecological monitoring time series. Specifically, this project will:(1) Assess how key environmental drivers (flow, salinity, temperature) have changed over the past 5 decades (1967 to present) across the San Francisco Estuary (SFE); (2) Examine how longfin smelt population dynamics have changed over that time period, and whether/when breakpoints in abundance and trends exist (e.g., periods of 'decline' vs' stability'); (3) Quantify the effects of environmental on driving observed fluctuations in longfin smelt dynamics; (4) Determine whether/how environment-smelt relationships have changed in magnitude or sign over time; and if they changed, whether such changes have been spatially consistent across the SFE. These goals will inform ongoing conservation efforts of longfin smelt by determining the combinations of flow, habitat, and prey availability conditions that lead to stable population dynamics for the species.
    Science topics Fish, Flows, Longfin Smelt, Zooplankton
    Updated May 8, 2024
  • Title

    Science for adaptive management of juvenile spring-run Chinook salmon in the San Joaquin River

    Lead University of California - Davis [UC Davis]
    Description Spring-run Chinook salmon rehabilitation efforts are intensifying on the San Joaquin River. Over the last three years, UC Davis has successfully tracked movement, behavior, reach-specific survival, and route selection for reintroduced juvenile spring-run Chinook salmon in this ecosystem. In 2019, information on salmon tracking was combined with state-of-art habitat (fast limnological automated measurements or “FLAMe”) and physiological (e.g. fish condition, survival and transcriptomic) approaches. Results from this work are ongoing but have yielded actionable information on key habitats and management strategies for promoting salmon life-cycles in the San Joaquin River and central Delta. Now UC Davis will further explore promising recent findings. First, the analysis of an additional year of juvenile salmon tracking will occur to glean more survival information across different water year conditions. This information would be married with expanded FLAMe surveys in space and time along with a second year of physiological assays using caged fish. UC Davis will also evaluate the ‘transport effect’ on salmon, in an attempt to explain consistently high losses of JSATS-tagged salmon through the restoration area. Numerous other synergies exist with new and ongoing telemetry work that will be benefitted by a continuation of this work. The goal is to provide actionable science, and open access data, with a high potential to facilitate adaptive management in the San Joaquin River and central Delta.
    Science topics Chinook Salmon, Endangered species, Estuaries, Fish, Habitat restoration
    Updated October 3, 2023
  • Title

    Impact of Temperature and Contaminants on Chinook salmon survival: A Multi‐Stressor Approach

    Lead National Oceanic and Atmospheric Administration [NOAA]
    Description This project will examine how contaminant exposures at different temperatures impact a number of critical physiological functions and the associated genes that maintain salmon fitness. The project will determine the sensitivity of fall‐run Chinook salmon to a mixture of bifenthrin, a pyrethoid pesticide, and triclosan, an antibacterial added to personal care products, at optimal and high temperatures that Chinook salmon encounter during their outmigration through the Sacramento and San Joaquin rivers. The hypothesis is that these stressors will impact salmon predator and disease susceptibility and will interact, such that the cumulative effect on salmon could not be predicted from multiple single exposures. To test the hypothesis, fall‐run Chinook salmon parr will be exposed to sublethal concentrations of bifenthrin, triclosan, and a mixture of bifenthrin and triclosan at different temperatures. The impacts of these exposures on salmon will be assessed with the following endpoints: (1) predator susceptibility through altered response latencies and escape velocities;  (2) disease susceptibility in response to a disease challenge; and (3) differential gene expression by high‐throughput sequencing of the Chinook salmon transcriptome.
    Science topics Pesticides
    Updated September 28, 2023
  • Title

    Non-Invasive Environmental DNA Monitoring to Support Tidal Wetland Restoration

    Lead University of California - Davis [UC Davis]
    Description In this project we use single-species and multi-species environmental DNA (eDNA) approaches to monitor tidal wetland restoration sites and paired reference sites (existing, unrestored tidal wetlands located near restoration sites) in the San Francisco Bay Delta (SFBD). We are working in coordination with the CDFW Fish Restoration Program (FRP) and other collaborators so our eDNA detections can be paired with physical detections of fishes from their trawling efforts. Ultra-sensitive DNA single species detection methods are being used to identify restoration site use by listed species (Delta Smelt, Longfin Smelt, winter- and spring-run Chinook Salmon) while the DNA metabarcoding approach will evaluate entire fish communities (groups of different fish species) at restored and reference sites. Aside from revealing restored habitat use by other fishes, metabarcoding will reveal potential ecological interactions between Endangered Species Act listed and non-listed species, through concurrent detection in time and space. Sampling throughout the year will allow us to identify seasonal trends in fish use of restored and reference sites. This project will demonstrate the utility of eDNA detection as a non-invasive (no take), cost-effective monitoring tool that can complement conventional surveys of restored tidal wetlands in the SFBD. Our results can be incorporated into an adaptive monitoring framework for tidal wetland restoration, to increase success of future restoration projects.
    Science topics Chinook Salmon, Delta Smelt, Endangered species, Estuaries, Fish, Green sturgeon, Habitat, Habitat restoration, Invasive / non native species, Invertebrates, Longfin Smelt, Mollusks, Pelagic fish, Restoration, Restoration planning, Sacramento Splittail, Salmon migration, Salmon rearing, Steelhead Trout, Striped bass, Sturgeon, Tidal wetlands, Wetlands, White Sturgeon
    Updated May 24, 2024
  • Title

    From Microbes to Zooplankton, What Defines a Beneficial Wetland?

    Lead San Francisco State University, Estuary & Ocean Science Center
    Description Our study will characterize species diversity at multiple levels of biological organization in the water column of restoring wetlands in the upper San Francisco Estuary and Delta (SFE), from bacteria to fishes. In doing so, we will also describe the foodweb benefits being provided to larval fishes, including longfin smelt, through additional dietary DNA analysis. We will use the species diversity we find in the water column to identify a subset of biota that are indicative of the conditions present in wetlands in different stages of restoration (early, intermediate, and mature) and identify connections between those indicators to the foodweb resources being provided to higher trophic levels. We will study 3-4 wetlands in each of 3 stages: early (unvegetated), intermediate (partially vegetated and partially channelized), and mature (fully vegetated and channelized) wetlands.
    Science topics Crustaceans, Cyanobacteria, Estuaries, Fish, Food webs, Habitat, Habitat restoration, Insects, Invertebrates, Longfin Smelt, Other species, Other zooplankton, Pelagic fish, Phytoplankton, Predation, Restoration, Salinity, Saltwater / freshwater marshes, Tidal wetlands, Wetlands, Zooplankton
    Updated January 31, 2024
  • Title

    Open-Source Resources for the Sacramento-San Joaquin Delta Telemetry Research Community

    Lead Cramer Fish Sciences
    Description There is a great deal of telemetry data amassed from studies in the Sacramento-San Joaquin Delta. It continues to grow every year with special studies and monitoring efforts. Multiple research priorities surrounding fish ecology in the Delta could be addressed, at least in part, by synthesizing the myriad telemetry data sets that exist; this work would benefit greatly from the centralization and standardization of data workflows surrounding telemetry research. With the guidance of a PIT Advisory Team, we plan to establish a collection of open-source, technology-agnostic, accessible resources to support a reproducible and transparent telemetry data workflow for researchers in the region. The workflow and resources do not invent new procedures, rather improve and standardize those already used by the telemetry research community. This will bring us in closer alignment with centralized, coordinated data workflows that have been successfully implemented in other regions and data communities. The final open-source set of resources will include a design and roadmap for implementing a central telemetry database and workflow, an R package for the preparation, QA/QC, and basic analysis of telemetry data, and a regional workshop offering training programs in the proposed telemetry data workflow.
    Science topics Chinook Salmon, Fish, Other species, Salmon migration, Steelhead Trout, Striped bass, Sturgeon
    Updated December 22, 2023
  • Title

    Standard Operating Procedure for Diagnosing and Addressing Predator Detections in Salmon Telemetry Data

    Lead University of Washington [UW]
    Description Tag predation is a complicating factor in juvenile salmon telemetry studies that can bias results, delay timely reporting, and prevent effective data synthesis. This project addresses the problem by (1) characterizing predatory fish movement patterns from existing telemetry data in the Delta; (2) developing a standard operating procedure for diagnosing and handling detections of predated tags in salmon telemetry studies; and (3) implementing the recommendations in a software package in Program R that includes code, a “library” of expected predator behaviors, and example vignettes. The R package will be freely available for download at www.cbr.washington.edu.
    Science topics Chinook Salmon, Endangered species, Fish, Intertidal / transition zones, Invasive / non native species, Predation, Salmon migration, Steelhead Trout, Striped bass
    Updated December 26, 2023
  • Title

    Impacts of predation and habitat on Central Valley Chinook smolt survival

    Lead University of Vermont, USGS Vermont Cooperative Fish and Wildlife Research Unit
    Description The Sacramento River in California’s Central Valley has been highly modified over the past 150 years due to mining, urbanization, and impoundment/diversion of river flow to provide water for municipal, industrial, and agricultural needs. Land use changes combined with high levels of harvest have been accompanied by drastic declines in native salmon populations, including the once abundant Chinook salmon (Oncorhynchus tshawytscha). Further, the region has been subject to the introduction and widespread establishment of non-native fish species, some of which are predators of juvenile salmon. Of the four historic ecotypes of Chinook salmon (fall, late-fall, winter, and spring runs), winter- and spring-runs have been most impacted and are currently listed as endangered and threatened respectively under the US Endangered Species act. Past research has illustrated how smoltification of juvenile salmon and outmigration from freshwater to the ocean is a time of increased mortality, and reduced survival at this life stage can impact the number of reproducing adults returning to the system in subsequent years. While these studies have provided valuable information on how habitat and environmental conditions experienced by migrating Chinook salmon smolts can affect survival, they have primarily focused on individual ecotypes during the portion of the year where downstream migrations occur. However, variation in smolt size and migration timing among ecotypes can expose migrating fish to differing environmental conditions and levels of exposure to predation, which can present distinct risks for outmigration survival. To identify the areas and environmental conditions which have the greatest relative impact on juvenile survival for each ecotype, this project will use over ten years of data (2012-2022) from acoustically tagged smolts representing all four Chinook salmon ecotypes in the Sacramento River/Central Valley. Combining these data will increase sample size relative to previous studies, the range of environmental conditions (e.g., temperature, flow, and predator abundance) modeled, the range of fish sizes, and thus, the statistical power of our analyses. We hypothesize that each ecotype will have different factors that will be the primary drivers of mortality experienced during outmigration. To test our hypotheses, we will implement Cormack-Jolly-Seber (CJS) mark-recapture models to estimate both the probability of survival through reaches of the Sacramento River delineated by acoustic receivers, and the detection probability in each reach. Survival will be modeled as a function of individual, release group, reach-specific, and time-varying covariates. Further, to examine the relative impact of predation on smolt survival, we will include an additional covariate representing predator-prey encounter rates using the Mean Free-path Length model. Finally, model selection will be applied to a series of CJS models to assess the relative impact of each covariate on smolt survival for each of the four Chinook ecotypes.
    Science topics Chinook Salmon, Environmental drivers, Fish, Flows, Habitat, Predation, Salmon migration, Water temperature
    Updated February 2, 2024
  • Title

    White Sturgeon Telemetry Synthesis

    Lead Cramer Fish Sciences
    Description Acoustic telemetry studies are expensive and logistically demanding. A new study to tag and monitor 315 White Sturgeon would require a massive field effort by a large team, but by pooling and leveraging existing datasets, this sample size and analysis will be achieved at a fraction of the cost and effort. In recognition of the efficiencies gained by this approach, the Delta Stewardship Council’s Science Program lists the synthesis and analysis of existing telemetry datasets in Science Action Area (SAA) 2. This project directly addresses SAA 2 by capitalizing on existing White Sturgeon telemetry data through the synthesis of three existing large telemetry dataset to understand system-wide White Sturgeon movements. This contract will synthesize existing long-term acoustic telemetry datasets in order to address high priority research questions for the management of White Sturgeon in the San Francisco Estuary system. These questions include: 1. What is the periodicity of spawning migrations by tagged White Sturgeon, and how do these estimates compare to those from previous, single-basin studies? 2. What is the scope and variability of inter-basin movements exhibited by tagged adult White Sturgeon across years? 3. Is there individual fidelity to specific migration routes or sites within each river basin? 4. Do White Sturgeon migrating through the Yolo Bypass experience delays in reaching spawning grounds relative to fish using the mainstem Sacramento River or San Joaquin River routes? 5. Is the onset of upstream migration movement by individuals associated with a characteristic flow rate or event? This contract will serve as a model for future telemetry synthesis studies by adhering to best practices in scientific computing for reproducible, transparent research, and by making all parts of the data and analysis accessible to the broader Delta research community.
    Science topics Environmental drivers, Fish, Flows, White Sturgeon
    Updated May 21, 2024
  • Title

    Monitoring Sacramento River winter-run Chinook salmon life history diversity, growth, and habitat use among varying hydroclimatic regimes

    Lead University of California - Berkeley [UC Berkeley]
    Description Sacramento River winter-run Chinook salmon have been endangered since 1994. Historically, the fish spawned during summer in cool tributaries upstream of Sacramento, but dams have limited spawning habitat to a small reach of the river. Today, survival of their offspring is heavily dependent on cool summer water releases from reservoirs, which also provide critical water supplies for irrigation, municipal, and industrial needs, as well as providing flood control and hydropower generation. During drought, this can lead to difficult management decisions. Understanding how winter run Chinook salmon respond to drought and water temperature is therefore vital to the management of this endangered population. This project tackled two outstanding questions about winter-run salmon ecology. The first was how winter-run Chinook use different rearing habitats during drought and non-drought periods, and the second was to explore which habitats provide enhanced growth during drought and non-drought periods. To answer these questions, UC Berkeley post-doc Pedro Morais used isotopic analysis of otoliths, or fish ear bones, which grow continuously throughout their lives and therefore carry a record of their environment and growth. Using otoliths, researchers can reconstruct details of fishes’ lives, including water temperature and migration patterns.
    Science topics None specified
    Updated February 1, 2024
  • Title

    Evaluating contributions of hatchery-origin fish to conservation of endangered Sacramento River winter run Chinook salmon during a drought

    Lead University of California - Davis [UC Davis]
    Description Hatchery-reared fish have been used to supplement endangered winter-run Chinook salmon in the upper Sacramento River since 1989. Intense drought in the past five years has led fisheries managers to substantially modify their hatchery protocols, increasing the total number of fish released and using hatchery-origin adults for producing juveniles. However, the impact of these practices is not fully understood. This project evaluated multiple aspects of how hatchery–reared fish contribute to natural production of winter-run Chinook salmon in the upper Sacramento River. The researchers assessed whether hatchery-reared fish are spawning in the wild and producing natural-origin offspring using a novel panel of genetic markers developed during the study. The study also assessed if inadvertent domestication selection was occurring in the hatchery during the drought years and if more highly related hatchery broodstock pairings returned fewer offspring than less related pairs.
    Science topics Drought
    Updated February 1, 2024
  • Title

    In search of refuge: Investigating the thermal life history of Delta Smelt through in-situ oxygen isotope ratio analysis of otoliths.

    Lead University of California - Davis [UC Davis]
    Description The inner ear bones of fish, or otoliths, grow continuously and their chemistry reflects the water conditions that a fish has experienced throughout its life. In this project, researchers used in-situ chemical analysis to determine the oxygen isotopic composition of otoliths, which can reflect the water temperature that a fish has experienced. They applied this method to archived adult Delta Smelt otoliths from multiple different water years spanning the time from before and during the recent drought. Using these data, they investigated the relationship between delta smelt abundance and environmental parameters, such as water temperature. More specifically they investigated whether delta smelt are able to find temperature refuges, even in drought years.
    Science topics Climate change, Delta Smelt, Endangered species, Fish, Temperature
    Updated February 26, 2024
  • Title

    Revealing the invisible contributors to the diets of larval longfin smelt and striped bass in the San Francisco Estuary.

    Lead San Francisco State University [SFSU]
    Description To better understand why the longfn smelt is threatened, the project compared the diet of larval longfn smelt to a thriving fsh with overlapping natal habitat and of similar size and morphology— the Pacifc herring. Using new genetic analysis methods, the project aimed to elucidate species composition of fsh diets in greater detail than has been done before and to measure diferences in composition and frequency of prey across habitats. In particular, the project aimed to identify prey items that were not previously seen using traditional diet analysis methods and assess whether any prey are indicative of natal habitats
    Science topics Fish, Longfin Smelt
    Updated February 26, 2024