The Status of Rainbow Trout (Oncorhynchus mykiss) in the Stanislaus River Summary report of 2015 snorkel surveys

Delta Stewardship Council (Delta Council) | August 1st, 2016

The Use of Smolt Survival Estimates to Quantify the Effects of Habitat Changes on Salmonid Stocks in the Sacramento-San Joaquin Rivers, California

Canada Department of Fisheries and Oceans (DFO) | July 1st, 1989

The Vernalis Adaptive Management Program (VAMP): Report of the 2010 Review Panel

California State Water Resources Control Board (SWRCB) | May 11th, 2010

Panel members were asked by the Delta Science Program to carry out an independent review of a 12-year VAMP (Vernalis Adaptive Management Plan) experimental program design

Panel members were asked by the Delta Science Program to carry out an independent review of a 12-year VAMP (Vernalis Adaptive Management Plan) experimental program designed to develop water management measures that would provide protection to juvenile Chinook salmon migrating through the San Joaquin River system and associated Sacramento-San Joaquin River Delta (Delta) waterways. The Charge to the Panel was expressed as a series of three questions that the Panel was obligated to address: 1) Do the results to date from the VAMP study provide useful scientific information about the relationship between salmon survival and each of the following factors: Flows, Exports, and Barrier installation at the head of Old River? 2) How can the results from the VAMP to date be used to inform the State Water Resources Control Board's (SWRCB) current efforts to review and potentially revise the San Joaquin River flow objectives and their implementation? 3) How can the experiences to date from the VAMP study be used in a scientific manner to inform future monitoring and study efforts related to determining appropriate flow, operational, and water quality requirements to protect San Joaquin River fisheries (specifically Chinook salmon and steelhead)?

Trends in Fish and Invertebrate Populations of Suisun Marsh January 2017 - December 2017

University of California, Davis (UC Davis) | January 31st, 2019

Suisun Marsh, at the geographic center of the northern San Francisco Estuary, is important habitat for native and non-native fishes. The University of California, Davis,

Suisun Marsh, at the geographic center of the northern San Francisco Estuary, is important habitat for native and non-native fishes. The University of California, Davis, Suisun Marsh Fish Study, in partnership with the California Department of Water Resources (DWR), has systematically monitored the marsh's fish populations since January 1980. The study’s main purpose has been to determine environmental and anthropogenic factors affecting fish distribution and abundance. 

Underwater Videographic Observations of Domesticated Delta Smelt in Field Enclosures

U.S. Geological Survey (USGS) | May 24th, 2022

The delta smelt (Hypomesus transpacificus) is a small, euryhaline fish species endemic to the Sacramento–San Joaquin Delta; it is protected under the U.S. and Californi

The delta smelt (Hypomesus transpacificus) is a small, euryhaline fish species endemic to the Sacramento–San Joaquin Delta; it is protected under the U.S. and California Endangered Species Acts, and because of declines in population abundance, the delta smelt may be vulnerable to extinction. The California Department of Water Resources (DWR) is conducting studies to test the viability of using domesticated fish to supplement the wild population of delta smelt. These studies have focused on examining the health and survival of domesticated delta smelt placed inside enclosures (circular cages that are approximately 1.5 meters tall by 1 meter in diameter) into the wild. We completed two parts within this study using underwater cameras inside the enclosures to observe fish behavior and their responses to certain stimuli. In both parts of the study, delta smelt behaviors were broadly categorized into two basic categories: (1) normal and (2) alarm. Normal behavior was characterized as calm, non-polarized, and docile swimming behavior. Alarm behavior was characterized by sudden and rapid darting, polarized frantic swimming activity, and tighter schooling polarization of individuals. The first part of the study took place in a semi-controlled agricultural pond on the campus of the University of California, Davis. At this agricultural pond, we developed methods of observation and documented how fish behaved in response to enclosure disturbances associated with routine cleaning and service that is required during extended field deployments of the enclosures. We observed that delta smelt behavior changed from normal to alarm at the onset of an enclosure service and from alarm to normal within about 2 minutes after the service ended. The second part of the study was completed in cooperation with the DWR. In October 2019, DWR deployed three enclosures in the Sacramento River near Rio Vista, California. To monitor survival rate of delta smelt, DWR permitted us to deploy cameras in one enclosure to document the frequency and duration of alarm behaviors exhibited by delta smelt and the frequency, duration, and intensity of three types of disturbances: (1) noise generated from passing boats, (2) noise generated from the enclosure moving in response to wave energy, and (3) vertical movements of the enclosure generated from wave energy. Alarm behaviors averaged about 2 minutes in duration and occurred most frequently during the evening compared to midday or morning. Each disturbance variable exhibited substantial variability in duration and intensity and occurred least frequently during the morning and evening compared to midday. Alarm behaviors appeared to be most associated with high intensity enclosure noises and vertical movements; however, limited replicate samples prohibited developing a statistical relation. Alarm behaviors did not directly contribute to injury or mortality of individual delta smelt; however, indirect or sublethal effects of alarm behaviors were not examined.

Use of the SmeltCam as an Efficient Fish-Sampling Alternative Within the San Francisco Estuary

University of California, Davis (UC Davis) | June 1st, 2021

Resource managers often rely on long-term monitoring surveys to detect trends in biological data. However, no survey gear is 100% efficient, and many sources of bias can

Resource managers often rely on long-term monitoring surveys to detect trends in biological data. However, no survey gear is 100% efficient, and many sources of bias can be responsible for detecting or not detecting biological trends. The SmeltCam is an imaging apparatus developed as a potential sampling alternative to long-term trawling gear surveys within the San Francisco Estuary, California, to reduce handling stress on sensitive species like the Delta Smelt (Hypomesus transpacificus). Although believed to be a reliable alternative to closed cod-end trawling surveys, no formal test of sampling efficiency has been implemented using the SmeltCam. We used a paired deployment of the SmeltCam and a conventional closed cod-end trawl within the Napa River and San Pablo Bay, a Bayesian binomial N-mixture model, and data simulations to determine the sampling efficiency of both deployed gear types to capture a Delta Smelt surrogate (Northern Anchovy, Engraulis mordax) and to test potential bias in our modeling framework. We found that retention efficiency—a component of detection efficiency that estimates the probability a fish is retained by the gear, conditional on gear contact—was slightly higher using the SmeltCam (mean = 0.58) than the conventional trawl (mean = 0.47, Probability SmeltCam retention efficiency > trawl retention efficiency = 94%). We also found turbidity did not affect the SmeltCam’s retention efficiency, although total fish density during an individual tow improved the trawl’s retention efficiency. Simulations also showed the binomial model was accurate when model assumptions were met. Collectively, our results suggest the SmeltCam to be a reliable alternative to sampling with conventional trawling gear, but future tests are needed to confirm whether the SmeltCam is as reliable when applied to taxa other than Northern Anchovy over a greater range of conditions.

Using the Distinct Population Segment concept to protect fishes with low levels of genomic differentiation: conservation of an endemic minnow (Hitch, Lavinia exilicauda)

American Fisheries Society (AFS) | December 23rd, 2018

In the United States, the Endangered Species Act (ESA) of 1973 was enacted to conserve species that are endangered or threatened throughout all or a portion of their rang

In the United States, the Endangered Species Act (ESA) of 1973 was enacted to conserve species that are endangered or threatened throughout all or a portion of their range. The definition of “species” includes subspecies and distinct population segments (DPSs). Among freshwater fishes, the use of DPS designations has largely been restricted to salmonids, although the DPS concept is increasingly applied to other fishes as well. As more taxa approach threatened status, the difficult question becomes what to do when genetic evidence does not strongly support formal taxonomic designations (full species or subspecies). We examine the potential application of the DPS concept to protect fishes by using the example of the Hitch Lavinia exilicauda, a cyprinid fish that is endemic to California. The Hitch is divided into three formally described, geographically separate subspecies (the Sacramento, Monterey, and Clear Lake Hitches). However, genomic studies (i.e., restriction site‐associated DNA sequencing), presented here with three independent analyses using a large data set, only weakly supported subspecies designations. Results suggested population structure but not subspecies structure. Nevertheless, conventional taxonomic methods, strong contemporary isolation, the importance of protecting genetic diversity, and high cultural value still qualify all three designated subspecies for DPS status and demonstrate how taxa such as the Clear Lake Hitch can warrant protection under the ESA.

Viability assessment for Pacific salmon and steelhead listed under the Endangered Species Act

National Marine Fisheries Service (NMFS) | July 25th, 2016

The Endangered Species Act (ESA) requires that the National Marine Fisheries Service (NMFS) review the status of listed species under its authority at least every five ye

The Endangered Species Act (ESA) requires that the National Marine Fisheries Service (NMFS) review the status of listed species under its authority at least every five years and determine whether any species should be removed from the list or have its listing status changed. Assessments of the viability of ESA-listed Pacific salmonids were conducted by the Southwest Fisheries Science Center and the Northwest Fisheries Science Center. The information from these assessments is incorporated into the West Coast Region’s status review, and the NMFS West Coast Region will make final determinations about any proposed changes in listing status, taking into account not only biological information (viability assessments) but also threats to the species and ongoing or planned protective efforts. This report from the Southwest Fisheries Science Center covers 10 ESA-listed Evolutionarily Significant Units (ESUs) and Distinct Population Segments (DPSs) that lie wholly or partially in California. In this review, we consider 1) new information relevant to the delineation of ESU/DPS boundaries, and 2) new information on status and trends in abundance, productivity, spatial structure and diversity specifically addressed by viability criteria previously developed by Technical Recovery Teams (TRTs). These viability assessments summarize current information (through the 2014–2015 spawning year where available) with respect to the viability criteria developed by the TRTs.  Consequently, the current assessments consider not only changes in populations that have occurred since the 2010 assessments but also the status of populations and ESUs/DPSs in relation to the viability criteria developed by the TRTs. For eight of the ESUs/DPSs (Southern Oregon/Northern California Coho Salmon, Central California Coast Coho Salmon, California Coastal Chinook Salmon, Northern California Steelhead, Central California Coast Steelhead, South-central California Steelhead, Southern California Steelhead, and California Central Valley Steelhead) the new information suggests that there has been no change in extinction risk since 2010 viability assessments. For two ESUs (Central Valley Spring-run Chinook Salmon, and Sacramento River Winter-run Chinook Salmon) the new information suggests a change in extinction risk. The viability of Central Valley Spring-run Chinook salmon appears to have improved since the 2010 assessment, but this ESU is far from being viable and is still facing relatively high extinction risk. The viability of Sacramento River Winter-run Chinook Salmon has been reduced and the ESU faces greater extinction risk since the 2010 assessment.

Visual, spectral, and microchemical quantification of crystalline anomalies in otoliths of wild and cultured delta smelt

Nature Portfolio (Springer Nature) | December 1st, 2022

Developmental abnormalities in otoliths can impact growth and survival in teleost fishes. Here, we quantified the frequency and severity of developmental anomalies in oto

Developmental abnormalities in otoliths can impact growth and survival in teleost fishes. Here, we quantified the frequency and severity of developmental anomalies in otoliths of delta smelt (Hypomesus transpacificus), a critically endangered estuarine fish that is endemic to the San Francisco Estuary. Left–right asymmetry and anomalous crystalline polymorphs (i.e., vaterite) were quantified and compared between wild and cultured populations using digital image analysis. Visual estimates of vaterite were validated using X-ray diffraction, Raman spectroscopy, laser ablation ICPMS, and electron probe microanalysis. Results indicated that cultured delta smelt were 80 times more likely to contain a vateritic otolith and 18 times more likely to contain relatively large (≥ 15%) amounts of vaterite. Similarly, cultured fish exhibited 30% greater asymmetry than wild fish. These results indicate that cultured delta smelt exhibit a significantly higher frequency of vestibular abnormalities which are known to reduce fitness and survival. Such hatchery effects on otolith development could have important implications for captive culture practices and the supplementation of wild fish populations with cultured individuals.

Water storage decisions will determine the distribution and persistence of imperiled river fishes

Ecological Society of America (Wiley) | December 17th, 2020

Managing the world’s freshwater supply to meet societal and environmental needs in a changing climate is one of the biggest challenges for the 21st century. Dams provid

Managing the world’s freshwater supply to meet societal and environmental needs in a changing climate is one of the biggest challenges for the 21st century. Dams provide water security; however, the allocation of dwindling water supply among reservoirs could exacerbate or ameliorate the effects of climate change on aquatic communities. Here, we show that the relative sensitivity of river thermal regimes to direct impacts of climate change and societal decisions concerning water storage vary substantially throughout a river basin. In the absence of interspecific interactions, future Colorado River temperatures would appear to benefit both endemic and nonnative fish species. However, endemic species are already declining or extirpated in locations where their ranges overlap with warmwater nonnatives and changes in water storage may lead to warming in some of the coolest portions of the river basin, facilitating further nonnative expansion. Integrating environmental considerations into ongoing water storage negotiations may lead to better resource outcomes than mitigating nonnative species impacts after the fact.