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  • Title

    Delta Wetland Resilience and Blue Carbon

    Lead San Francisco Estuary Institute [SFEI]
    Description This project estimates carbon storage for the past, present and future Delta, as well as GHG fluxes and elevation change based on chosen restoration and rice farming scenarios in the future Delta using the Delta Landscape Scenario Planning Tool. The project also investigates how well the current organic matter parameterizations and inorganic sediment parameterization in the Marsh Equilibrium Model (MEM) represent Delta marsh accretion processes. Knowledge of marsh accretion and migration will be used to develop a spatial conceptual model of marsh resilience in the Delta.
    Science topics Carbon, Greenhouse gas GHG, Resilience, Sea level rise, Subsidence, Wetlands
    Updated October 13, 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 Landscape Scenario Planning Tool

    Lead San Francisco Estuary Institute [SFEI]
    Description The Delta Landscapes Scenario Planning Tool is a set of resources to assist users with developing, analyzing, and evaluating different land use scenarios in the Delta. The tool is designed to inform ongoing and future restoration planning efforts by assessing how proposed projects will affect a suite of landscape metrics relating to desired ecosystem functions.
    Science topics Fish, Landscape metrics, Marsh wildlife, Restoration planning, Riparian wildlife, Sea level rise, Terrestrial wildlife
    Updated November 17, 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

    Low-Cost Satellite Remote Sensing of the Sacramento-San Joaquin Delta to Enhance Mapping for Invasive and Native Aquatic Vegetation

    Lead University of California - Davis [UC Davis]
    Description Invasive aquatic vegetation (IAV) acts as an ecosystem engineer by changing habitat conditions and water quality. This negatively affects the survival of native species. Over the past 15 years, IAV has more than doubled its footprint in the Sacramento-San Joaquin Delta waterways. The State of California spends millions of dollars each year to control IAV in the Delta-Suisun region and costs are likely to continue to rise. Gaining a better understanding of the spread, life history characteristics, and potential vulnerabilities of these species can lead to more effective control strategies. The recent launch of the Sentinel-2 satellite can fill temporal gaps left by annual airborne surveys. This study will create a data pipeline for sustained, low-cost satellite-based monitoring of aquatic and marsh vegetation year-round. To quantify one of the Delta Plan performance measures, the time and degree of floodplain inundation for the Yolo Bypass will be measured. This study will result in new metrics to measure progress toward habitat goals in several restoration sites.
    Science topics Aquatic vegetation, Invasive / non native species
    Updated November 18, 2022
  • 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

    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

    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

    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

    Assessing sea-level rise and flooding changes in the Sacramento/San Joaquin Delta using historical water-level records

    Lead California State University [CSU]
    Description The project aims to recover, digitize, and analyze more than 1300 station years of ‘lost-and-forgotten’ water level records collected from 1857 to 1982 in the Sacramento-San Joaquin Delta. These measurements, augmented by modern data, will improve our understanding of tidal, flood, and sea level trends in the system. By determining ‘hotspots’ of habitat and flood risk sensitivity, the results may be used to better focus future scientific and management priorities, to protect the environment, manage flood risk, and enhance community resilience to climate change
    Science topics Backwater, Climate change, Environmental drivers, Estuaries, Land elevation, Levees, Outflow, Sea level rise, Stage, Subsidence, Surface water / flow, Tides, Velocity, Vessels and shipping channels, Water, Wind
    Updated October 10, 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

    Pixel-Wise Footprint Analysis of GPP Using High-Resolution NDVI/NIRv Data

    Lead University of California - Berkeley [UC Berkeley]
    Description Spectral indices such as NDVI have long been found to be good predictors of plant productivity at many spatial scales from the canopy to the landscape. Spectral indices are an important tool for upscaling GPP fluxes we measure at the ecosystem scale through Eddy Covariance up to larger spatial scales. Other indices, such as NIRv (expressed as NDVI * total NIR) have also been shown to be potentially more accurate predictors of GPP using in-situ spectral measurements than NDVI alone. Additionally, associating spectral signals within modeled flux footprint areas has been shown to improve the predictive capability of spectral indices compared to estimates using remotely sensed data centered directly on top of flux towers. Most if not all of these spatially explicit footprint analyses have been done by aggregating footprints into polygons based on their 50%-90% estimated flux contributions, and then associating those polygons with fluxes and spectral signals within them. This approach has been necessary largely because of the spatial scales involved with satellite remote sensing products, reaching a practical minimum of 3m, downsampled from 4.8m imagery by Planet Labs. By combining pixel-weighted flux footprint contributions with ultra-high resolution (3cm) spectral drone data, we will examine and compare how different spatial scales and indices affect the capability of spectral data to predict fluxes which are not directly measured.
    Science topics None specified
    Updated January 30, 2024