SFEWS: Volume 19, Issue 2
Welcome to the June issue of San Francisco Estuary and Watershed Science. At midyear in 2021, research surrounding the San Francisco Estuary looks forward. Here, six articles in four categories offer advances in science using new technologies and a re-examination of past efforts.
Photo: CA Dept. of Water Resources, public domain.
In Honor of Dr. Larry R. Brown
Herbold et al. remember Dr. Larry R. Brown, who died suddenly in February of 2021. This note captures how important his scientific work was in the San Francisco Estuary and why he will be intensely missed by many of his colleagues.
Photo: Canva stock image
Preparing Scientists, Policymakers, and Managers for a Fast-Forward Future
To accelerate forward-looking science, policy, and management in the Delta, Norgaard et al. propose that the State of California create a Delta Science Visioning Process to fully and openly assess the challenges of more rapid change to science, policy, and management and offer appropriate solutions, including legislation.
Photo: CA Dept. of Water Resources, public domain
Ecological Effects of Climate-Driven Salinity Variation in the San Francisco Estuary: Can We Anticipate and Manage the Coming Changes?
Ghalambor et al. review and summarize the presentations and discussions that arose during the symposium “Ecological and Physiological Impacts of Salinization of Aquatic Systems from Human Activities,” which brought together an interdisciplinary group of scientists, managers, and policy-makers to answer the central question: can we use existing knowledge and future projections to predict and manage anticipated ecological impacts?
Photo: Canva stock image
Effects of Tidally Varying River Flow on Entrainment of Juvenile Salmon into Sutter and Steamboat Slough
Previous studies suggest that fish generally “go with the flow”—however, complex tidal hydrodynamics at sub-daily time-scales may be decoupled from net flow. To further examine entrainment of acoustically tagged juvenile Chinook Salmon into Sutter and Steamboat sloughs, Romine et al. modeled routing of acoustic tagged juvenile salmon as a function of tidally varying hydrodynamic data. Results indicate that discharge, the proportion of flow that entered the slough, and the rate of change of flow were good predictors of the probability of an individual fish being entrained.
Photo: John Burau
Examining Retention-at-Length of Pelagic Fishes Caught in the Fall Midwater Trawl Survey
A study was conducted in 2014-2015 to investigate and quantify the efficiency of the Fall Midwater Trawl for catching the endangered fish species Delta Smelt (Hypomesus transpacificus). Mitchell and Baxter revisit the same gear efficiency study and further utilize the data set by fitting selectivity curves for three additional pelagic fish species: Threadfin Shad (Dorosoma petenense), American Shad (Alosa sapidissima), and Mississippi Silverside (Menidia beryllina), and by applying more statistically sensitive approaches.
Photo: Lara Mitchell
Use of the SmeltCam as an Efficient Fish Sampling Alternative Within the San Francisco Estuary
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 both detect or miss biological trends. Huntsman et al. evaulate the SmeltCam, an imaging apparatus developed as a sampling alternative to long-term trawling gear surveys within the San Francisco Estuary, with the potential to reduce handling stress on sensitive species like the Delta Smelt (Hypomesus transpacificus).
Photo: Ken Newman
Volume 17, Issue 1, 2019
Clarifying Effects of Environmental Protections on Freshwater Flows to—and Water Exports from—the San Francisco Bay Estuary
Understanding and resolving conflicts over management of scarce natural resources requires access to information that helps characterize the problem. Where information is lacking, perceived differently by stakeholders, or provided without relevant context, these conflicts can become intractable. We studied water management practices and constraints that affect the flow of water into and through the San Francisco Bay estuary — home to six endangered fish species and two water export facilities owned by the state and federal governments that serve millions of people and large expanses of agricultural land in California. Media reports reflect widely held beliefs that environmental regulations, and particularly protections for endangered fish species, frequently limit water diversions and substantially increase freshwater flow to San Francisco Bay. We analyzed long-term trends in freshwater flow to San Francisco Bay relative to annual runoff from its Central Valley watershed, and the frequency and magnitude of specific regulatory and physical constraints that govern operations of the water export facilities. We found that the percentage of Central Valley runoff that reached San Francisco Bay during the ecologically sensitive winter-spring period declined over the past several decades, such that the estuary experienced drought conditions in most years. During a 9-year period that included a severe natural drought, exports were constrained to maintain salinity control as often as to protect endangered fish populations. Salinity-control and system-capacity constraints were responsible for Delta outflow volumes that dwarfed those related to protection of fish and wildlife populations, endangered or otherwise. These results run counter to common media narratives. We recommend rapid synthesis and easily accessible presentation of data on Central Valley water diversions and constraints on them; such data should be contextualized via comparison to regional hydrology and water management system capacity.
The Relative Importance of Agricultural and Wetland Habitats to Waterbirds in the Sacramento–San Joaquin River Delta of California
Biodiversity loss from agricultural intensification underscores the urgent need for science-based conservation strategies to enhance the value of agro-ecosystems for birds and other wildlife. California’s Central Valley, which has lost over 90% of its historical wetlands and currently is dominated by agriculture, still supports waterbird populations of continental importance. A better understanding of how waterbirds use available habitat is particularly needed in the Sacramento–San Joaquin Delta, an ecosystem under threat. From 2013 to 2015, we studied waterbird habitat associations in the Delta during fall migration and winter by conducting diurnal counts at random locations in key waterbird habitats throughout the Delta. Waterbird use of cover types (agricultural crops and managed wetlands) varied substantially among waterbird groups, by season, and among geographic sub-regions of the Delta. Overall, wetlands were particularly important to waterbirds in fall. In winter, wetlands and flooded rice and corn were important to many waterbird groups, and non-flooded corn and irrigated pasture to geese and cranes. The factors that influenced waterbird abundance and distribution also varied substantially among groups and differed at various geographic scales. In both seasons, most groups had a positive association at the field level with flooded ground and open water, and a negative association with vegetation. Given the great uncertainty in the future extent and pace of habitat loss and degradation in the Delta, prioritizing the conservation actions needed to maintain robust waterbird populations in this region is urgent. For the Delta to retain its importance to waterbirds, a mosaic of wetlands and wildlife-friendly crops that accounts for the value of the surrounding landscape must be maintained. This includes restoring additional wetlands and maintaining corn, rice, alfalfa, and irrigated pasture, and ensuring that a substantial portion of corn and rice is flooded in winter.
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Largemouth Bass (Micropterus salmoides) were introduced into the Sacramento-San Joaquin Delta (the Delta) over 100 years ago. In the last 2 decades, the abundance of centrarchids (including Largemouth Bass) in the littoral zone has increased, while some native fish and fish that were previously abundant in the pelagic zone have declined. Largemouth Bass are now one of the most abundant piscivores in the Delta. Understanding the ecology of this top predator — including a comprehensive understanding of what prey are important in Largemouth Bass diets — is important to understanding how this species may affect the Delta fish community. To address this need, we conducted electrofishing surveys of Largemouth Bass at 33 sites every 2 months from 2008 to 2010, measuring fish fork lengths and collecting stomachs contents at each site. We characterized diets using Percent Index of Relative Importance for 3,004 Largemouth Bass, with samples that spanned all seasons. Amphipods dominated the diets of Largemouth Bass ≤175 mm FL year-round, with dipterans, odonates, and copepods and cladocerans representing other important diet items. Non-native red swamp crayfish (Procambarus clarkii) were the most important prey for Largemouth Bass >175 mm FL. Non-native centrarchids (including Largemouth Bass) and amphipods were important prey items as well. Prickly Sculpin (Cottus asper) were the most frequently consumed native fish. Other native fish and pelagic fish species rarely occurred in Largemouth Bass diets, and we discuss trends in how the frequency of co-occurrence of these fishes with Largemouth Bass in the electrofishing surveys was associated with their frequency in Largemouth Bass diets. The Largemouth Bass in the Delta appear to be sustained largely on a diet of other non-natives that reside in the littoral zone.
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Evaluation of Long-Term Mark-Recapture Data for Estimating Abundance of Juvenile Fall-Run Chinook Salmon on the Stanislaus River from 1996 to 2017
Conservation and management of culturally and economically important species rely on monitoring programs to provide accurate and robust estimates of population size. Rotary screw traps (RSTs) are often used to monitor populations of anadromous fish, including fall-run Chinook Salmon (Oncorhynchus tshawytscha) in California’s Central Valley. Abundance estimates from RST data depend on estimating a trap's efficiency via mark-recapture releases. Because efficiency estimates are highly variable and influenced by many factors, abundance estimates can be highly uncertain. An additional complication is the multiple accepted methods for how to apply a limited number of trap efficiency estimates, each from discrete time-periods, to a population’s downstream migration, which can span months. Yet, few studies have evaluated these different methods, particularly with long-term monitoring programs. We used 21 years of mark-recapture data and RST catch of juvenile fall-run Chinook Salmon on the Stanislaus River, California, to investigate factors associated with trap efficiency variability across years and mark-recapture releases. We compared annual abundance estimates across five methods that differed in treatment of trap efficiency (stratified versus modeled) and statistical approach (frequentist versus Bayesian) to assess the variability of estimates across methods, and to evaluate whether method affected trends in estimated abundance. Consistent with short-term studies, we observed negative associations between estimated trap efficiency and river discharge as well as fish size. Abundance estimates were robust across all methods, frequently having overlapping confidence intervals. Abundance trends, for the number of increases and decreases from year to year, did not differ across methods. Estimated juvenile abundances were significantly related to adult escapement counts, and the relationship did not depend on estimation method. Understanding the sources of uncertainty related to abundance estimates is necessary to ensure that high-quality estimates are used in life cycle and stock-recruitment modeling.
Long-term fish survey monitoring programs use a variety of fishing gears to catch fish, and the resulting catches are the basis for status and trends reports on the condition of different fish stocks. These catches can also be part of the data used to set stock assessment models, which establish harvest regulations, and to fit population dynamics models, which are used to analyze population viability. However, most fishing gears are size-selective, and fish size — among other possible covariates, such as environmental conditions — affects the probability that a fish will be caught in the path the gear sweeps. Failing to properly account for selectivity can adversely affect the ability to interpret and use status and trends measures, stock-assessment models, and population-dynamics models. Our side-by-side gear comparison study evaluated the selectivity of multiple open-water trawl surveys that have provided decades worth of information on the imperiled fish species Delta Smelt (Hypomesus transpacificus). We used data from the study to estimate gear selectivity curves for multiple trawls using two methods. The first method examines the total number of fish-at-length caught across all gears, and does not directly use or estimate fish length distribution in the population. The second method examines the total number of fish caught by each gear separately, and explicitly estimates fish length distribution in the population. The results from the two methods were similar, and we found that one trawl was highly efficient at catching larger Delta Smelt. This is the first formal multi-gear evaluation of how well survey gear used to monitor Delta Smelt in the San Francisco Estuary selects fish by size, and we plan to incorporate the results into Delta Smelt population models.
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