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  • 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

    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

    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

    Directed Field Collections

    Lead California Department of Fish and Wildlife [CDFW]
    Description Description The Direct Field Collections element (-089) provides funding support for expanded field collections, allowing CDFW to provide other, IEP-approved researchers access to research-capable boats and experienced operators, and thus the ability to safely sample the upper San Francisco Estuary. This element most recently facilitated investigations associated with the Fall Low Salinity Habitat (FLaSH) project and the Directed Outflow Project (DOP). Need This element allows CDFW and thus IEP to provide boat and operator time to assist collaborating researchers leading approved IEP projects with “on-the-water” sampling. There is no mandate for this element. Objectives To provide CDFW operational flexibility to assist collaborating researchers leading approved IEP projects with access to CDFW boat operators and boats to complete "onthe-water" sampling.
    Science topics None specified
    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

    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

    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

    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 February 1, 2024
  • Title

    Analysis of Delta Salinity during Extended Drought – Pilot Project

    Lead California Department of Water Resource [DWR]
    Description Managing California water operations for multiple priorities under long term drought conditions is becoming an increasing challenge which is compounded by potential sea level rise. This project is a pilot exercise to demonstrate the utility of hydrodynamic and salinity transport models in to understand options for salinity management under extended drought combined with climate change and sea level rise. The project will also consider how to make model outputs available and relevant to other modeling and environmental management decision making efforts. The full range of potential sea level rise, restoration and operational actions is extensive, involving many potential combinations of individual actions. Therefore, it is difficult to fully explore potential actions with high resolution multi-dimensional models. The proposed approach is to use high resolution multi-dimensional flow and transport models to evaluate changes in transport in the Delta under sea level rise, restoration, and operational scenarios. The predicted changes to salinity for a given scenario will inform operations modeling in CALSIM through re-calibration of an ANN to approximately account for the changed salinity response of the estuary. Operations modeling incorporating the revised ANN will then estimate Delta inflows and overall water cost to meet Delta standards for the scenario. “Round-trip” modeling will be performed using the detailed Delta models to verify that the predicted hydrologic inputs allow appropriate compliance with water quality standards and will provide other metrics related to Delta transport.
    Science topics Conductivity, Drought, Landscape change, Restoration planning, Sea level rise, Water operations / exports
    Updated January 29, 2024