The purpose of this project will develop and implement a DNA sampling protocol for juvenile Chinook salmon captured at Chipps Island.
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 trawl efficiency estimates using data from releases of coded wire tags (CWT), acoustic tags (AT), and by genetically sampling the trawl catch in 2025 and 2026. The project will (1) develop statistical models for estimating trawl efficiencies using 2016-2025 data for paired AT-CWT releases of winter run and fall-run Chinook Salmon; (2) use 2016-2025 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 for 2016-2025; (3) implement trawl efficiency studies for multiple salmon runs in 2025-2026 informed by the prior 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 2016-2025.
Description: The Enhanced Delta Smelt Monitoring (EDSM) program is a comprehensive, year-round monitoring initiative that employs multiple research crews conducting concurrent trawling operations across designated strata within the San Francisco Estuary. The program specifically targets post-larval Delta Smelt from April through June using 20mm trawling gear, while Kodiak trawling gear is utilized for the remainder of the year. Need: The ongoing decline of the Delta Smelt population has underscored the critical need for continuous improvement in the data supporting our understanding of the ecological and anthropogenic factors influencing Delta Smelt population dynamics. The EDSM program plays a vital role in providing essential biological data that informs management strategies aimed at mitigating the adverse effects of water operations on this endangered species. By capturing data across nearly all life stages of Delta Smelt, including near-real-time information on juvenile and adult stages, the EDSM program offers significant conservation benefits. This data is promptly disseminated to the Smelt Working Group and other resource managers to facilitate informed decision-making during the critical entrainment season. Objectives: -Estimate the total abundance of Delta Smelt, including standard errors or confidence intervals, on a weekly to bi-weekly basis across various life stages (post-larvae, juveniles, sub-adults, adults) throughout the year. -Assess the spatial distribution of Delta Smelt at a management-relevant temporal and spatial resolution. -Provide data that supports management decisions and addresses scientific inquiries related to sampling efficiency, drivers of Delta Smelt population patterns, and other conservation and management-related topics.
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.
The federal hatcheries mark and tag fish that are released into the river or bay using a combination of coded wire tags (CWT) and adipose fin clipping. The number of fish tagged and the identifiers are reported to the RMPC which is part of the RMIS. The Regional Mark Processing Center (RMPC) provides essential services to international, state, federal, and tribal fisheries organizations involved in marking anadromous salmonids throughout the Pacific region. These services include regional coordination of some tagging and fin marking programs, maintenance of databases for Coded Wire Tag Releases, Recoveries, and Locations, as well as the dissemination of reports of these data in electronic or printed form when requested. These databases are known collectively as the Regional Mark Information System (RMIS).
The overarching AIS goal is that "Risks of aquatic invasive species invasions are substantially reduced, and their economic, ecological, and human health impacts are minimized. This goal is addressed through a series of performance and workload measures. The AIS Program provides funding for Aquatic Invasive Species Coordinators for each Region within the Service and their respective aquatic nuisance species activities. These coordinators work closely with the public and private sector to develop and implement invasive species projects. One of the primary initiatives of the program is the prevention of invasive species via boats through the "100th Meridian Initiative" (overseen by individual AIS regional coordinators). This initiative aims to prevent the spread of aquatic invasive species by boats personal watercraft and other pathways. Through boat inspections and boaters assessments along the 100th meridian, partners can learn how to prevent the spread of zebra mussels and other AIS via transport of boats and personal watercraft.
The Delta Juvenile Fish Monitoring Program (DJFMP) has monitored natural-origin and hatchery-origin juvenile Chinook Salmon (Oncorhynchus tshawytscha) and other fish species within the San Francisco Estuary (SFE) since 1976 using a combination of midwater trawls and beach seines. Since 2000, three trawl sites and at least 58 beach seine sites have been sampled weekly or biweekly within the SFE and lower Sacramento and San Joaquin Rivers. The main objectives of the DJFMP are: 1. Document the long-term abundance and distribution of juvenile Chinook Salmon in the Delta. 2. Comprehensively monitor throughout the year to document the presence of all races of juvenile Chinook Salmon. 3. Intensively monitor juvenile Chinook salmon during the fall and winter months for use in managing water project operations (Delta Cross Channel gates and water export levels) on a real-time basis. 4. Document the abundance and distribution of Steelhead. 5. Document the abundance and distribution of non-salmonid species.
Observations of individual and population dispersal of delta smelt are essential for improving models that can inform management strategies potentially improving movement into favorable areas or reducing movement into areas of poor habitat quality and risk of pumping loss. However, delta smelt movement patterns are largely unknown. Pacific Northwest National Labs has developed a much smaller Juvenile Salmon Acoustic Telemetry System (JSATS) tag, called the "Shad tag." Recent experiments suggest these tags can be successfully implanted in delta smelt without having significant, negative effects on individual condition and swimming behavior. The next step to determine if the newest technology may provide a tool for acoustic observation of fish dispersal over small spatial scales. Filling this data gap is important because changes in delta smelt spatial distribution (i.e., movement or dispersal) play a significant role in the management and recovery of the species.
This project includes two years of field-based experiments necessary to move this technology into the field. The existing San Francisco Estuary's JSATS array was designed to detect larger, more powerful tags and may not be as effective at detecting the smaller, less powerful tags. Therefore, first, we will test the detectability of the Shad tag by the existing JSATS array and explore detectability at potential locations for new receivers at delta smelt-relevant locations. Secondly, we will design and deploy a 3D positioning array to test performance of such an array in upper San Francisco Estuary habitats. Finally, we will conduct several small releases of delta smelt implanted with the new Shad tag to assess the capacity of the JSATS receiver arrays to detect and position live fish. This feasibility study will lay the groundwork for the development of a receiver array and post detection signal processing algorithm to detect delta smelt tagged with Shad tags in later phases of the project.
Description
The Mossdale Trawl occurs two miles downstream of Mossdale Landing County Park (river miles 56), and upstream of the Old River confluence. Timing and production (indices and estimates) for the out-migrating fall-run Chinook salmon smolts has been monitored at this location since 1987. Additionally this trawl captures coded wire tagged Chinook smolts and is the primary capture site for these fish being used to estimate survival of Chinook smolts in the river system. Results from this project, therefore document information on the out-migration timing, survival, and the magnitude of nonmarked smolt production from the San Joaquin Basin passing into the South Delta. The trawl also captures steelhead outmigrants and provides an index of these outmigrants for the entire San Joaquin River Basin.
Project Need
This project needs to identify annual juvenile Chinook salmon production in the San Joaquin River Basin. This project provides data supporting water management in the San Joaquin River basin and the Delta. Enumerating steelhead (Oncorhynchus mykiss) migrating through the San Joaquin River into the south Delta. Developing method to differentiate fall and spring run juvenile Chinook salmon migrating in the San Joaquin River basin.
Project Objectives
• What is the annual juvenile Chinook salmon production in the San Joaquin River Basin? • How do water quantity and quality conditions affect smolt production trends? • How many Oncorhynchus mykiss passage at Mossdale trawl?
