-
Longfin Smelt (Spirinchus thaleichthys), a CESA-listed threatened species, faces persistent population declines and high interannual variability in recruitment throughout the San Francisco Estuary. Recent data from CDFW Smelt Larva (SLS) and 20-mm Surveys reveal the Napa River can be a production hotspot, where catches of larval and juvenile Longfin Smelt far surpass those observed in other strata of the upper San Francisco Estuary. However, this abundance is not consistent across years. This poster investigates the drivers of this interannual variability in the Napa River.
Authors:
• Vanessa Mora*, California Department of Fish and Wildlife, vanessa.mora@wildlife.ca.gov
• Jessica Jimenez, California Department of Fish and Wildlife
• Jennifer Oceguera Zavala, California Department of Fish and Wildlife
• Colin Brennan, California Department of Fish and Wildlife
*Presenting author
-
Larval Longfin Smelt (LFS) were collected as part of a 5-year pilot study, first referred to as the Larval Entrainment Pilot Study (LEPS) and then developed into the Larval Entrainment Study (LES). LEPS and LES were conducted to determine the risk of larval entrainment in the lower San Joaquin River and South Delta area near Byron, CA, during the months January through April when larval LFS are most likely to be present. Longfin Smelt can be advected and transported by flows and affect the location of larvae in the Sacramento-San Joaquin Delta (Delta) and San Francisco Estuary regions. We looked at the effects of Delta hydrology, weather, time of day, and day of year on catch during January through April for the years 2022 (LEPS), 2023 and 2024 (LES). To look at the spatial component, we included Smelt Larva Survey (SLS) data in the analyses with LES since the SLS survey covers more of the Delta and San Francisco Estuary areas and, in some regions like the Napa River, has higher catches than LES. Using the combined LES and SLS datasets we expect to see regional shifts in catch over the season and in response to changes in hydrology and weather on a finer temporal scale. This in turn may help inform management of larval Longfin Smelt through incorporation of larval movement in response to environmental cues and preferred habitats.
Authors:
• Virginia Afentoulis*, California Department of Fish and Wildlife, virginia.afentoulis@wildlife.ca.gov
• Kyle Griffiths±, California Department of Fish and Wildlife
• Morgan Gilbert, California Department of Fish and Wildlife
• Tim Malinich, California Department of Fish and Wildlife
*Presenting author, ± Co-Presenting Author
-
Longfin Smelt (Spirinchus thaleichthys), once one of the most abundant osmerids in the San Francisco Estuary, was listed as endangered under the Endangered Species Act in July 2024. Today, the population stands at less than 1% of historical levels due to habitat degradation, altered freshwater flows, food limitation, climate change, and small population dynamics. To address this decline, the UC Davis Longfin Smelt Conservation and Culture Program (LFSCCP), supported by the California Department of Water Resources, integrates four specialized facilities to advance full life-cycle culture and recovery. The Otolith Geochemistry and Fish Ecology Laboratory (OGFL) leads broodstock collection from South Bay and Alviso Marsh, ensuring genetic diversity and healthy spawner acquisition. The Fish Conservation and Culture Laboratory (FCCL) focuses on spawning and early life stages, refining fertilization, incubation, and larval rearing protocols. The Putah Creek Facility (PCF) provides large-scale capacity for juvenile and adult culture, with recirculating aquaculture systems (RAS) supporting all life stages. Finally, the Bodega Marine Laboratory (BML) supports rearing of Longfin Smelt under full-strength seawater conditions, with new systems under construction to expand capacity. This poster presents the integrated culture framework developed by the LFSCCP, highlighting protocols for broodstock transport and conditioning, fertilization and larval rearing methods, and system design innovations supporting all life stages. Cross-facility coordination strategies and genetic management approaches will also be described to inform future recovery efforts. Results from 2024-2025 demonstrate the effectiveness of this framework: increased broodstock collections and improved transport survival from OGFL, higher hatching and larval success at FCCL, successful rearing of age-2 F1 fish at PCF, successful spawning of wild age-2 adults at BML, and new infrastructure at both PCF and BML to expand capacity. Together, these facilities form a collaborative network advancing Longfin Smelt culture science, increasing captive capacity, and building the foundation for long-term species recovery.
Authors:
• Kendall Ashley1*†, University of California, Davis, keashley@ucdavis.edu
• Zoe Kimball1, University of California, Davis
• Brianna Yetter1, University of California, Davis
• Heather Bell1, University of California, Davis
• Dennis E. Cocherell1, University of California, Davis
• Florian Mauduit1, University of California, Davis
• Mandi Finger3, University of California, Davis
• Md. Moshiur Rahman2, University of California, Davis
• Tien-Chieh Hung2, University of California, Davis
• Levi Lewis4, University of California, Davis
• Nann A. Fangue1, University of California, Davis
*Presenting author, †Early Career Award candidate
-
Longfin Smelt (Spirinchus thalieichthys) are a protected species in their southernmost range in the Sacramento – San Joaquin Delta (Delta) of California. The observed decline of the Longfin Smelt (LFS) population is attributed to factors such as decreased food availability, increasing temperatures, changes in flow within the estuary, and entrainment to the federal and state water projects. Entrainment is the redirection of LFS by exported water diversions out of the estuary by water projects located in the south Delta, and researchers are attempting to determine what proportion of the LFS population is vulnerable to entrainment. The California Dept. Of Fish and Wildlife and the Interagency Ecological Program (IEP) monitors the spatial distribution and presence of larval LFS across the Delta with the Smelt Larva Survey (SLS) and the Larval Entrainment Study (LES). Both were established to improve our understanding of factors influencing larval LFS entrainment. Here, we aim to measure the start and end of spawning periods by examining trends in the timing of larval LFS presence and abundance in the south Delta. We estimate spawning starts using the developmental rate of LFS eggs in conjunction with larval LFS observations. We compare data from LES to those of SLS, specifically focusing on the south Delta region. We expect LFS with yolk sacs to appear in clusters throughout each sampling season in the south Delta with corresponding abundances of growing LFS later in the season. Furthermore, spawning periods are expected to vary in length across years in response to environmental variables such as precipitation and river temperatures. Preliminary work suggests that recently hatched larvae are still present, and at risk of entrainment, in the south Delta following the end of the SLS season. A clearer understanding of LFS spawning trends, presence, and abundance will improve monitoring efforts and inform management of LFS.
Authors:
• Lalayna Hablutzel*†, California Department of Fish and Wildlife, Lalayna.hablutzel@wildlife.ca.gov
• Virginia Afentoulis, California Department of Fish and Wildlife
• Walter Kyle Griffiths, California Department of Fish and Wildlife
• Morgan Gilbert, California Department of Fish and Wildlife
• Tariq Celeste, California Department of Fish and Wildlife
• Tim Malinich, California Department of Fish and Wildlife
*Presenting author
-
The California Department of Fish and Wildlife’s Fish Restoration Program (FRP) conducts sampling for fish, macroinvertebrates, and zooplankton at wetland restoration and reference sites throughout the Sacramento-San Joaquin Delta and Suisun Marsh. Staff monitor sites to evaluate the FRP goal of restoring altered wetland habitats to a beneficial state for native fish species of interest, including Longfin Smelt (Spirinchus thaleichthys). While invertebrate species composition and density from regular sampling provide information on food availability, diet studies give insight into prey selection and foraging success. In 2019, Tule Red, a FRP restoration site in Suisun Marsh, was breached to Grizzly Bay. This re-established natural tidal action to a 460-acre parcel previously managed for duck hunting.
Our study examined differences in larval Longfin Smelt diet between a restoration site, Tule Red; a reference site, Ryer Island; and the adjacent water body, Grizzly Bay in April 2023 and April 2024. We used permutational multivariate analysis of variance (PERMANOVA) to examine differences in larval Longfin Smelt diet between sites. In addition, we compared gut contents of fish with species composition of zooplankton samples from the same time periods for evidence of prey selectivity. Finally, we measured feeding incidence to assess overall foraging success across sites. This study provides critical information concerning the role of tidal wetlands in supporting foraging success as well as variability in diet. Moreover, our research elucidates food source preferences and generally deepens our understanding of beneficial habitat.
Authors:
• Lauren Sique*†, California Department of Fish and Wildlife, lauren.sique@wildlife.ca.gov
• Michelle Avila±, California Department of Fish and Wildlife
• Darian Dungey, California Department of Fish and Wildlife
*Presenting author, †Early Career Award candidate, ± Co-Presenting Author
-
This poster presents the methods and data products of the Monitoring Survey Design Team (Design Team) that form the geographic basis for the design and analysis of the California Department of Fish and Wildlife (CDFW) long-term monitoring studies conducted in the San Francisco Estuary (SFE). These products are intended to serve as a foundation for a spatial design to standardize methods for estimating regional fish abundance across CDFW pelagic fish monitoring studies conducted in the SFE, including Smelt Larval Survey, 20mm, Summer Townet, Fall Midwater Trawl, and the San Francisco Bay Study, which are all part of the Interagency Ecological Program (IEP). Here, we present the methods behind new data resources intended to standardize the approach to defining spatial extents and the inputs used to determine critical catch per unit of effort (CPUE) estimates, including design-based abundance (DBA) indices with units and uncertainty. The spatial extent and methods for calculating expansion factors (water volume and surface area) provide an improved means to estimate pelagic fish abundance consistently across CDFW surveys in the SFE. Using the latest bathymetric data for the SFE (DWR & USGS, 2025), we have updated and increased standardization for volume and surface area expansion factors for CPUE, including implementing a spatially variable water surface elevation, making sample frame refinements, and creating a new hydrologic footprint for the SFE. We define the sample frame as the continuous geographic area containing the SFE, subdivided into smaller nested areas we term regions (n=7), strata (n=12), and subregions (n=35). Our operational footprint differs from the U.S. Fish & Wildlife Service (USFWS) Enhanced Delta Smelt Monitoring (EDSM) program, but our method for defining the hydrological footprint and geographic regions, are adaptations of EDSM’s. Our hydrological footprint is a customized selection of USFWS National Wetlands Inventory (NWI) features, including estuarine, marine, riverine, and lake features.
Authors:
• Celeste M. Dodge*, California Department of Fish and Wildlife, celeste.dodge@wildlife.ca.gov
• Steven B. Slater, California Department of Fish and Wildlife
• Aroon R. Melwani, Applied Marine Sciences, Inc.
*Presenting author
-
The Sacramento–San Joaquin Delta is home to a broad range of scientific and management efforts led by government agencies, academic institutions, non-governmental organizations, and private research groups. To support transparency, accountability, and opportunities for collaboration concerning these efforts, the Delta Science Program created the Delta Science Tracker as a publicly accessible, web-based platform to organize and share information on Delta-focused research, monitoring, and management projects. Designed to support the vision of “One Delta, One Science,” the Tracker enables those involved in the Delta to easily find activities, discover new connections, and communicate outcomes. The Delta Science Tracker acts as a catalyst for collaboration, connecting scientists, managers, and decision-makers across disciplines and regions. Early use of the Tracker has revealed gaps and overlaps in research, helped funders and managers monitor investments toward Science Action Agenda priorities, and promoted communication among different partners. By fostering this kind of transparency and coordination, the Tracker enhances our capacity to support resilient decision-making and effective stewardship of the greater Delta and estuary. Going forward, the Delta Science Tracker will continue to play a key role in providing access to information about and outcomes of critical science activities aimed at informing decision-making needs for the Delta’s water, ecosystems, and communities in the face of climate change and other mounting challenges.
Authors:
• Nicholas Rowlands*†, Delta Stewardship Council, Nicholas.rowlands@deltacouncil.ca.gov
• Maggie Christman, Delta Stewardship Council
*Presenting author, †Early Career Scientist (not participating in Early Career Awards)
-
SHERLOCK (Specific High-sensitivity Enzymatic Reporter unLOCKing) is a CRISPR-based genetic method used to detect specific DNA or RNA sequences with high sensitivity. In conservation, SHERLOCK is used to quickly and accurately detect invasive and endangered species. DWR’s Genetic Monitoring (GeM) Lab uses SHERLOCK for diverse projects, including Chinook Salmon Spring-Run Juvenile Production Estimate and to estimate take of listed Chinook Salmon runs at water export facilities. This work is sometimes extremely time-sensitive and informs real-time water operations. Therefore, we need to produce results quickly to provide information to water operators. Typically, SHERLOCK reactions are prepared fresh each day. To minimize SHERLOCK processing time, and increase work efficiency, it would be ideal to deploy pre-frozen SHERLOCK reactions for sample testing. Through experimentation, we tested how long, after reactions are prepared, can they be frozen before results become unreliable. We found that reactions can be prepared and frozen 90 days in advance with minimal decrease in sensitivity, which saves considerable time compared to fresh preparation. We can also pre-freeze positive and negative controls into reactions, further increasing efficiency. Therefore, for time-sensitive samples we can simply thaw the frozen reactions and add only the samples, streamlining the entire process. Study findings help improve the efficiency and flexibility of SHERLOCK workflows, making both high-throughput and field-based sample processing faster and more practical, without compromising accuracy.
Authors:
• Pachia Lee*†, California Department of Water Resources, pachia.lee@water.ca.gov
• Scott Meyer, California Department of Water Resources
• Sean Canfield, California Department of Water Resources
• Sarah Brown, California Department of Water Resources
• Melinda Baerwald, California Department of Water Resources
*Presenting author, †Early Career Award candidate
-
White Sturgeon (Acipenser transmontanus) are large, slow-growing, and late-maturing fish that move between river spawning grounds and downstream feeding areas. The southernmost population of the species, found in the Sacramento-San Joaquin system (i.e., Lower Sacramento River, San Joaquin River, and San Francisco Estuary), appears to be in decline. In November 2023, this population was petitioned for listing under both the federal Endangered Species Act (ESA) and the California Endangered Species Act (CESA). To better understand how White Sturgeon use the system, we analyzed 13 years (2013–2025) of acoustic detections from fish collected and tagged in the San Joaquin River (n = 107). Data from the U.S. Fish and Wildlife Service (Lodi) were combined with detections from the Pacific Aquatic Telemetry Hub (PATH) across the Sacramento–San Joaquin system. Over the study period, 50 tagged White Sturgeon (46%) were detected only in the San Joaquin River, 49 used both the Lower Sacramento and San Joaquin rivers, three were found only in the Lower Sacramento River (aside from the tagging year), one that was not detected above the confluence of the Sacramento-San Joaquin, and four were never detected after tagging. Thirteen fish (12%) moved below Alfred Zampa Memorial Bridge, 37 (34%) were observed in both the Sacramento and San Joaquin rivers within the same water-year, and 42 (40%) were detected in the Southern Delta. Four individuals were also detected in the Calaveras River, roughly 12 miles upstream of its confluence with the San Joaquin River. We explore these patterns further using age, sex, Delta inflow and outflow, and other environmental conditions to better understand the factors influencing these movements. Our findings help clarify how and when White Sturgeon use different parts of the Sacramento-San Joaquin system and provide useful information for future management and recovery efforts.
Authors:
• Gabriela Garcia*†, U.S. Fish and Wildlife Service, gabriela_garcia@fws.gov
• Taylor Senegal, U.S. Fish and Wildlife Service
*Presenting author, †Early Career Award candidate
-
Bigscale Logperch (Percina macrolepida) are a nonnative perch species found throughout the Sacramento-San Joaquin River Delta system. Logperch are understudied in the Delta, and little is known about their breeding behavior, habitat use, or species to species interaction within the system. The Lodi Fish and Wildlife Office’s Delta Juvenile Fish Monitoring Program (DJFMP) has encountered this species since the beginning of sampling efforts in 1976. The present study examines the spatial and temporal prevalence of adult and juvenile logperch within the Delta and how those patterns vary across years. Adult logperch are caught year-round by DJFMP—with the highest catch occurring in the Lower Sacramento and Upper San Joaquin Rivers. DJFMP begins to detect juvenile logperch in May and June. We hypothesize that environmental conditions influence the timing and abundance of juvenile logperch catch. This research provides more context for nonnative Logperch in the delta system. The location and timing of logperch spawning may coincide with other native species; the impact on habitat use and availability of Bigscale Logperch in the Delta system would be valuable to research further.
Authors:
• Shanna Kowalewski*†, U.S Fish and Wildlife Service, shanna_kowalewski@fws.gov
• Meg Carmen±, U.S Fish and Wildlife Service
• Vanessa Tobias, U.S Fish and Wildlife Service
• Jennie Wiggins, U.S Fish and Wildlife Service
*Presenting author, †Early Career Award candidate, ± Co-Presenting Author
Longfin Smelt (Spirinchus thaleichthys), a CESA-listed threatened species, faces persistent population declines and high interannual variability in recruitment throughout the San Francisco Estuary. Recent data from CDFW Smelt Larva (SLS) and 20-mm Surveys reveal the Napa River can be a production hotspot, where catches of larval and juvenile Longfin Smelt far surpass those observed in other strata of the upper San Francisco Estuary. However, this abundance is not consistent across years. This poster investigates the drivers of this interannual variability in the Napa River.
Authors:
• Vanessa Mora*, California Department of Fish and Wildlife, vanessa.mora@wildlife.ca.gov
• Jessica Jimenez, California Department of Fish and Wildlife
• Jennifer Oceguera Zavala, California Department of Fish and Wildlife
• Colin Brennan, California Department of Fish and Wildlife
*Presenting author
Larval Longfin Smelt (LFS) were collected as part of a 5-year pilot study, first referred to as the Larval Entrainment Pilot Study (LEPS) and then developed into the Larval Entrainment Study (LES). LEPS and LES were conducted to determine the risk of larval entrainment in the lower San Joaquin River and South Delta area near Byron, CA, during the months January through April when larval LFS are most likely to be present. Longfin Smelt can be advected and transported by flows and affect the location of larvae in the Sacramento-San Joaquin Delta (Delta) and San Francisco Estuary regions. We looked at the effects of Delta hydrology, weather, time of day, and day of year on catch during January through April for the years 2022 (LEPS), 2023 and 2024 (LES). To look at the spatial component, we included Smelt Larva Survey (SLS) data in the analyses with LES since the SLS survey covers more of the Delta and San Francisco Estuary areas and, in some regions like the Napa River, has higher catches than LES. Using the combined LES and SLS datasets we expect to see regional shifts in catch over the season and in response to changes in hydrology and weather on a finer temporal scale. This in turn may help inform management of larval Longfin Smelt through incorporation of larval movement in response to environmental cues and preferred habitats.
Authors:
• Virginia Afentoulis*, California Department of Fish and Wildlife, virginia.afentoulis@wildlife.ca.gov
• Kyle Griffiths±, California Department of Fish and Wildlife
• Morgan Gilbert, California Department of Fish and Wildlife
• Tim Malinich, California Department of Fish and Wildlife
*Presenting author, ± Co-Presenting Author
Longfin Smelt (Spirinchus thaleichthys), once one of the most abundant osmerids in the San Francisco Estuary, was listed as endangered under the Endangered Species Act in July 2024. Today, the population stands at less than 1% of historical levels due to habitat degradation, altered freshwater flows, food limitation, climate change, and small population dynamics. To address this decline, the UC Davis Longfin Smelt Conservation and Culture Program (LFSCCP), supported by the California Department of Water Resources, integrates four specialized facilities to advance full life-cycle culture and recovery. The Otolith Geochemistry and Fish Ecology Laboratory (OGFL) leads broodstock collection from South Bay and Alviso Marsh, ensuring genetic diversity and healthy spawner acquisition. The Fish Conservation and Culture Laboratory (FCCL) focuses on spawning and early life stages, refining fertilization, incubation, and larval rearing protocols. The Putah Creek Facility (PCF) provides large-scale capacity for juvenile and adult culture, with recirculating aquaculture systems (RAS) supporting all life stages. Finally, the Bodega Marine Laboratory (BML) supports rearing of Longfin Smelt under full-strength seawater conditions, with new systems under construction to expand capacity. This poster presents the integrated culture framework developed by the LFSCCP, highlighting protocols for broodstock transport and conditioning, fertilization and larval rearing methods, and system design innovations supporting all life stages. Cross-facility coordination strategies and genetic management approaches will also be described to inform future recovery efforts. Results from 2024-2025 demonstrate the effectiveness of this framework: increased broodstock collections and improved transport survival from OGFL, higher hatching and larval success at FCCL, successful rearing of age-2 F1 fish at PCF, successful spawning of wild age-2 adults at BML, and new infrastructure at both PCF and BML to expand capacity. Together, these facilities form a collaborative network advancing Longfin Smelt culture science, increasing captive capacity, and building the foundation for long-term species recovery.
Authors:
• Kendall Ashley1*†, University of California, Davis, keashley@ucdavis.edu
• Zoe Kimball1, University of California, Davis
• Brianna Yetter1, University of California, Davis
• Heather Bell1, University of California, Davis
• Dennis E. Cocherell1, University of California, Davis
• Florian Mauduit1, University of California, Davis
• Mandi Finger3, University of California, Davis
• Md. Moshiur Rahman2, University of California, Davis
• Tien-Chieh Hung2, University of California, Davis
• Levi Lewis4, University of California, Davis
• Nann A. Fangue1, University of California, Davis
*Presenting author, †Early Career Award candidate
Longfin Smelt (Spirinchus thalieichthys) are a protected species in their southernmost range in the Sacramento – San Joaquin Delta (Delta) of California. The observed decline of the Longfin Smelt (LFS) population is attributed to factors such as decreased food availability, increasing temperatures, changes in flow within the estuary, and entrainment to the federal and state water projects. Entrainment is the redirection of LFS by exported water diversions out of the estuary by water projects located in the south Delta, and researchers are attempting to determine what proportion of the LFS population is vulnerable to entrainment. The California Dept. Of Fish and Wildlife and the Interagency Ecological Program (IEP) monitors the spatial distribution and presence of larval LFS across the Delta with the Smelt Larva Survey (SLS) and the Larval Entrainment Study (LES). Both were established to improve our understanding of factors influencing larval LFS entrainment. Here, we aim to measure the start and end of spawning periods by examining trends in the timing of larval LFS presence and abundance in the south Delta. We estimate spawning starts using the developmental rate of LFS eggs in conjunction with larval LFS observations. We compare data from LES to those of SLS, specifically focusing on the south Delta region. We expect LFS with yolk sacs to appear in clusters throughout each sampling season in the south Delta with corresponding abundances of growing LFS later in the season. Furthermore, spawning periods are expected to vary in length across years in response to environmental variables such as precipitation and river temperatures. Preliminary work suggests that recently hatched larvae are still present, and at risk of entrainment, in the south Delta following the end of the SLS season. A clearer understanding of LFS spawning trends, presence, and abundance will improve monitoring efforts and inform management of LFS.
Authors:
• Lalayna Hablutzel*†, California Department of Fish and Wildlife, Lalayna.hablutzel@wildlife.ca.gov
• Virginia Afentoulis, California Department of Fish and Wildlife
• Walter Kyle Griffiths, California Department of Fish and Wildlife
• Morgan Gilbert, California Department of Fish and Wildlife
• Tariq Celeste, California Department of Fish and Wildlife
• Tim Malinich, California Department of Fish and Wildlife
*Presenting author
The California Department of Fish and Wildlife’s Fish Restoration Program (FRP) conducts sampling for fish, macroinvertebrates, and zooplankton at wetland restoration and reference sites throughout the Sacramento-San Joaquin Delta and Suisun Marsh. Staff monitor sites to evaluate the FRP goal of restoring altered wetland habitats to a beneficial state for native fish species of interest, including Longfin Smelt (Spirinchus thaleichthys). While invertebrate species composition and density from regular sampling provide information on food availability, diet studies give insight into prey selection and foraging success. In 2019, Tule Red, a FRP restoration site in Suisun Marsh, was breached to Grizzly Bay. This re-established natural tidal action to a 460-acre parcel previously managed for duck hunting.
Our study examined differences in larval Longfin Smelt diet between a restoration site, Tule Red; a reference site, Ryer Island; and the adjacent water body, Grizzly Bay in April 2023 and April 2024. We used permutational multivariate analysis of variance (PERMANOVA) to examine differences in larval Longfin Smelt diet between sites. In addition, we compared gut contents of fish with species composition of zooplankton samples from the same time periods for evidence of prey selectivity. Finally, we measured feeding incidence to assess overall foraging success across sites. This study provides critical information concerning the role of tidal wetlands in supporting foraging success as well as variability in diet. Moreover, our research elucidates food source preferences and generally deepens our understanding of beneficial habitat.
Authors:
• Lauren Sique*†, California Department of Fish and Wildlife, lauren.sique@wildlife.ca.gov
• Michelle Avila±, California Department of Fish and Wildlife
• Darian Dungey, California Department of Fish and Wildlife
*Presenting author, †Early Career Award candidate, ± Co-Presenting Author
This poster presents the methods and data products of the Monitoring Survey Design Team (Design Team) that form the geographic basis for the design and analysis of the California Department of Fish and Wildlife (CDFW) long-term monitoring studies conducted in the San Francisco Estuary (SFE). These products are intended to serve as a foundation for a spatial design to standardize methods for estimating regional fish abundance across CDFW pelagic fish monitoring studies conducted in the SFE, including Smelt Larval Survey, 20mm, Summer Townet, Fall Midwater Trawl, and the San Francisco Bay Study, which are all part of the Interagency Ecological Program (IEP). Here, we present the methods behind new data resources intended to standardize the approach to defining spatial extents and the inputs used to determine critical catch per unit of effort (CPUE) estimates, including design-based abundance (DBA) indices with units and uncertainty. The spatial extent and methods for calculating expansion factors (water volume and surface area) provide an improved means to estimate pelagic fish abundance consistently across CDFW surveys in the SFE. Using the latest bathymetric data for the SFE (DWR & USGS, 2025), we have updated and increased standardization for volume and surface area expansion factors for CPUE, including implementing a spatially variable water surface elevation, making sample frame refinements, and creating a new hydrologic footprint for the SFE. We define the sample frame as the continuous geographic area containing the SFE, subdivided into smaller nested areas we term regions (n=7), strata (n=12), and subregions (n=35). Our operational footprint differs from the U.S. Fish & Wildlife Service (USFWS) Enhanced Delta Smelt Monitoring (EDSM) program, but our method for defining the hydrological footprint and geographic regions, are adaptations of EDSM’s. Our hydrological footprint is a customized selection of USFWS National Wetlands Inventory (NWI) features, including estuarine, marine, riverine, and lake features.
Authors:
• Celeste M. Dodge*, California Department of Fish and Wildlife, celeste.dodge@wildlife.ca.gov
• Steven B. Slater, California Department of Fish and Wildlife
• Aroon R. Melwani, Applied Marine Sciences, Inc.
*Presenting author
The Sacramento–San Joaquin Delta is home to a broad range of scientific and management efforts led by government agencies, academic institutions, non-governmental organizations, and private research groups. To support transparency, accountability, and opportunities for collaboration concerning these efforts, the Delta Science Program created the Delta Science Tracker as a publicly accessible, web-based platform to organize and share information on Delta-focused research, monitoring, and management projects. Designed to support the vision of “One Delta, One Science,” the Tracker enables those involved in the Delta to easily find activities, discover new connections, and communicate outcomes. The Delta Science Tracker acts as a catalyst for collaboration, connecting scientists, managers, and decision-makers across disciplines and regions. Early use of the Tracker has revealed gaps and overlaps in research, helped funders and managers monitor investments toward Science Action Agenda priorities, and promoted communication among different partners. By fostering this kind of transparency and coordination, the Tracker enhances our capacity to support resilient decision-making and effective stewardship of the greater Delta and estuary. Going forward, the Delta Science Tracker will continue to play a key role in providing access to information about and outcomes of critical science activities aimed at informing decision-making needs for the Delta’s water, ecosystems, and communities in the face of climate change and other mounting challenges.
Authors:
• Nicholas Rowlands*†, Delta Stewardship Council, Nicholas.rowlands@deltacouncil.ca.gov
• Maggie Christman, Delta Stewardship Council
*Presenting author, †Early Career Scientist (not participating in Early Career Awards)
SHERLOCK (Specific High-sensitivity Enzymatic Reporter unLOCKing) is a CRISPR-based genetic method used to detect specific DNA or RNA sequences with high sensitivity. In conservation, SHERLOCK is used to quickly and accurately detect invasive and endangered species. DWR’s Genetic Monitoring (GeM) Lab uses SHERLOCK for diverse projects, including Chinook Salmon Spring-Run Juvenile Production Estimate and to estimate take of listed Chinook Salmon runs at water export facilities. This work is sometimes extremely time-sensitive and informs real-time water operations. Therefore, we need to produce results quickly to provide information to water operators. Typically, SHERLOCK reactions are prepared fresh each day. To minimize SHERLOCK processing time, and increase work efficiency, it would be ideal to deploy pre-frozen SHERLOCK reactions for sample testing. Through experimentation, we tested how long, after reactions are prepared, can they be frozen before results become unreliable. We found that reactions can be prepared and frozen 90 days in advance with minimal decrease in sensitivity, which saves considerable time compared to fresh preparation. We can also pre-freeze positive and negative controls into reactions, further increasing efficiency. Therefore, for time-sensitive samples we can simply thaw the frozen reactions and add only the samples, streamlining the entire process. Study findings help improve the efficiency and flexibility of SHERLOCK workflows, making both high-throughput and field-based sample processing faster and more practical, without compromising accuracy.
Authors:
• Pachia Lee*†, California Department of Water Resources, pachia.lee@water.ca.gov
• Scott Meyer, California Department of Water Resources
• Sean Canfield, California Department of Water Resources
• Sarah Brown, California Department of Water Resources
• Melinda Baerwald, California Department of Water Resources
*Presenting author, †Early Career Award candidate
White Sturgeon (Acipenser transmontanus) are large, slow-growing, and late-maturing fish that move between river spawning grounds and downstream feeding areas. The southernmost population of the species, found in the Sacramento-San Joaquin system (i.e., Lower Sacramento River, San Joaquin River, and San Francisco Estuary), appears to be in decline. In November 2023, this population was petitioned for listing under both the federal Endangered Species Act (ESA) and the California Endangered Species Act (CESA). To better understand how White Sturgeon use the system, we analyzed 13 years (2013–2025) of acoustic detections from fish collected and tagged in the San Joaquin River (n = 107). Data from the U.S. Fish and Wildlife Service (Lodi) were combined with detections from the Pacific Aquatic Telemetry Hub (PATH) across the Sacramento–San Joaquin system. Over the study period, 50 tagged White Sturgeon (46%) were detected only in the San Joaquin River, 49 used both the Lower Sacramento and San Joaquin rivers, three were found only in the Lower Sacramento River (aside from the tagging year), one that was not detected above the confluence of the Sacramento-San Joaquin, and four were never detected after tagging. Thirteen fish (12%) moved below Alfred Zampa Memorial Bridge, 37 (34%) were observed in both the Sacramento and San Joaquin rivers within the same water-year, and 42 (40%) were detected in the Southern Delta. Four individuals were also detected in the Calaveras River, roughly 12 miles upstream of its confluence with the San Joaquin River. We explore these patterns further using age, sex, Delta inflow and outflow, and other environmental conditions to better understand the factors influencing these movements. Our findings help clarify how and when White Sturgeon use different parts of the Sacramento-San Joaquin system and provide useful information for future management and recovery efforts.
Authors:
• Gabriela Garcia*†, U.S. Fish and Wildlife Service, gabriela_garcia@fws.gov
• Taylor Senegal, U.S. Fish and Wildlife Service
*Presenting author, †Early Career Award candidate
Bigscale Logperch (Percina macrolepida) are a nonnative perch species found throughout the Sacramento-San Joaquin River Delta system. Logperch are understudied in the Delta, and little is known about their breeding behavior, habitat use, or species to species interaction within the system. The Lodi Fish and Wildlife Office’s Delta Juvenile Fish Monitoring Program (DJFMP) has encountered this species since the beginning of sampling efforts in 1976. The present study examines the spatial and temporal prevalence of adult and juvenile logperch within the Delta and how those patterns vary across years. Adult logperch are caught year-round by DJFMP—with the highest catch occurring in the Lower Sacramento and Upper San Joaquin Rivers. DJFMP begins to detect juvenile logperch in May and June. We hypothesize that environmental conditions influence the timing and abundance of juvenile logperch catch. This research provides more context for nonnative Logperch in the delta system. The location and timing of logperch spawning may coincide with other native species; the impact on habitat use and availability of Bigscale Logperch in the Delta system would be valuable to research further.
Authors:
• Shanna Kowalewski*†, U.S Fish and Wildlife Service, shanna_kowalewski@fws.gov
• Meg Carmen±, U.S Fish and Wildlife Service
• Vanessa Tobias, U.S Fish and Wildlife Service
• Jennie Wiggins, U.S Fish and Wildlife Service
*Presenting author, †Early Career Award candidate, ± Co-Presenting Author