SFEWS: Volume 19, Issue 3
In our September issue new research and commentary provide insights on several topics: how to integrate zooplankton science to inform estuary management; how simulated fishing can avoid missed fish and detect gear bias in the water; why juvenile Chinook Salmon length-at-date criteria don't match genetic run assignments; whether declines in breeding waterfowl population relate to wetland habitat and salinity; and what kinds of food web support can be achieved by use of a managed flow pulse.
Photo: Forster’s Terns at Crown Beach, public domain. Attribution: © Ingrid Taylar, Creative Commons 2.0 Generic license.
Catch as Catch Can
"Catchability" refers to the relationship between catch rate and the true population. Ecological monitoring programs use catch per unit of effort (CPUE) to standardize catch and monitor changes in fish populations; however, CPUE is proportional to the portion of the population that is vulnerable to the type of gear used in sampling, which is not necessarily the entire population. Tobais' simulation combines a module for sampling conditions with a module for individual fish behavior to estimate the proportion of available fish that would escape from the sample. The method is applied to the case study of the well monitored fish species Delta Smelt (Hypomesus transpacificus) in the San Francisco Estuary, where it has been hypothesized that changing water clarity may affect catchability for long-term monitoring studies.
Waterfowl Reproductive Success Depends on High Water, Low Salt
Availability of wetlands with low salinities during the breeding season can influence waterfowl reproductive success and population recruitment. Salinities as low as 2 ppt (3.6 mS/cm) can impair duckling growth and influence behavior, with mortality occurring above 9 ppt (14.8 mS/cm). Schacter et al. used satellite imagery to quantify the amount of available water, and sampled surface water salinity at Grizzly Island, in the brackish Suisun Marsh, at three time-periods during waterfowl breeding (April, May, July) over 4 years (2016–2019). Among their findings was during peak duckling production in May, 81%–95% of available water had salinity above 2 ppt, and 5%–21% was above 9 ppt. Local waterfowl populations would benefit from management practices that provide fresher water during peak duckling production in May and retain more water through July.
Deep Dives Among Waterbird Populations in South SF Bay
In south San Francisco Bay, former salt ponds now managed as wildlife habitat support large populations of breeding waterbirds. In 2006, the South Bay Salt Pond Restoration Project began the process of converting 50% to 90% of these managed pond habitats into tidal marsh. Hartman et al. compared waterbird populations in south San Francisco Bay before (2001) and after (2019) approximately 1,300 ha of managed ponds were breached to tidal action to begin tidal marsh restoration. Study results showed average annual nest abundance declined during 2017–2019 by 53%, 71%, and 36%, for American Avocets, Back-necked Stilts, and Forster’s Terns, respectively. All three species established nesting colonies on newly constructed islands within remaining managed ponds; however, these new colonies did not make up for the steep declines observed at other historical nesting sites. For future wetland restoration, retaining more managed ponds that contain islands suitable for nesting may help to limit further declines in breeding waterbird populations.
Managed Pulse Flows as Food Web Support
While freshwater inflow has been a major focus of resource management in estuaries, including the upper San Francisco Estuary, there is a growing interest in using focused flow actions to maximize benefits for specific regions, habitats, and species. To test this concept, in summer 2016, Frantzich et al. used a managed flow pulse to target an ecologically important region: a freshwater tidal slough called the Cache Slough Complex. Their goal was to improve estuarine habitat by increasing net flows through CSC to enhance downstream transport of lower trophic-level resources, an important driver for fishes such as the endangered Delta Smelt. Simulations using a 3-D hydrodynamic model (UnTRIM) indicated that the managed flow pulse had a large effect on the net flow of water through Yolo Bypass, and between the CSC and further downstream. The managed flow pulse resulted in increased densities of zooplankton (copepods, cladocerans) demonstrating potential advection from upper floodplain channels into the target CSC and Sacramento River regions. Though conducted during a single year, this study may provide an instructive example of how a relatively modest change in net flows can generate measurable changes in ecologically relevant metrics, and how an adaptive management action can help inform resource management.
Length-at-Date Criteria and Genetic Run Assignments
Four distinct runs of Central Valley Chinook Salmon are named after their primary adult return times: fall, late-fall, winter, and spring run. Estimating the run-specific composition of juveniles entering and leaving the Sacramento–San Joaquin Delta is crucial for assessing population status and processes that affect juvenile survival through the Delta. Historically, the run of juvenile Chinook Salmon captured in the field has been determined using a length-at-date criteria (LDC); however, LDC run assignments may be inaccurate if there is high overlap in the run-specific timing and size of juveniles entering and leaving the Delta. In this study, Brandes et al. use genetic run assignments to assess the accuracy of LDC at two trawl locations in the Sacramento River (Delta entry) and at Chipps Island (Delta exit).Across years, there was extensive overlap among the distributions of run-specific fork lengths of genetically identified juveniles, indicating that run compositions based on LDC assignments would tend to underestimate fall-run and especially late-fall-run compositions at both trawl locations, and greatly overestimate spring-run compositions (both locations) and winter-run compositions (Chipps Island). We therefore strongly support ongoing efforts to include tissue sampling and genetic run identification of juvenile Chinook Salmon at key monitoring locations in the Sacramento–San Joaquin River system.
Pelagic fish in the San Francisco Estuary are harder to catch in recent decades. Over the past thirty years, Delta Smelt catch in the Fall Midwater Trawl Survey has declined by 99%, Longfin Smelt catch has declined by over 95%, and even the notoriously hardy Striped Bass have declined by over 75%. To manage the system and reverse these declines, we need a better understanding of the “bottom-up” processes that exert control on these populations—we need to study fish food. In other words, in addition to studying fish directly, we need to increase our understanding of what pelagic fish eat: zooplankton. In this essay, Hartman et al. break down not only what fish eat (zooplankton) and why they are important drivers of species abundance in higher trophic areas of the food web, but also how scientists and natural resources managers can communicate better to understand which zooplankton data can inform and develop management-relevant questions.
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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