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 5, Issue 1, 2007
Introduced Yellowfin Goby, Acanthogobius flavimanus: Diet and Habitat Use in the Lower Mokelumne River, California
The introduced yellowfin goby (YFG) is now common throughout the tidal portion of the Sacramento-San Joaquin River system. We investigated its habitat use, size and diet in the Mokelumne River, an eastern tributary to the system. Catch per unit effort (CPUE) by boat electrofishing was significantly higher in the fall than all other seasons sampled over four years. Habitat type, turbidity and dissolved oxygen were not significantly related to CPUE between years and seasons. Temperatures were negatively related to CPUE in fall sampling only. Delta outflow and CPUE showed a significant negative relationship. Fish captured ranged from 27 mm SL (standard length) (33 mm TL (total length)) to 155 mm SL (196 mm TL) (mean 113 mm SL (138 mm TL)), with largest fish captured during the fall. Seasonal and annual analysis showed a diet composed of a variety of macroinvertebrates, including chironomids, gammarids, aquatic isopods and ephemeropterans with no difference in composition among seasons or years. The YFG’s generalist diet gives it an advantage as a successful invader, but salinity requirements appear to limit its expansion potential.
The objective of this study was to evaluate the potential sources of pesticides to the Yolo Bypass, including those that could potentially impact critical life stages of resident fish. To assess direct inputs during inundation, pesticide concentrations were analyzed in water and suspended and bed sediment samples collected from source watersheds during high-flow events. To understand inputs from direct application on fields, pesticides were also measured in soils collected from several sites within the Bypass. Thirteen current-use pesticides were detected in water samples collected in 2004 with the highest pesticide concentrations observed at the input sites to the Bypass during high-flow. Hexazinone and simazine were detected at all sites and at some of the highest concentrations. In bed and suspended sediments collected in 2004 and 2005, thirteen current-use pesticides were detected along with DDT and its metabolites. Trifluralin, DDE, and DDT were highest in the bed sediments, whereas oxyfluorfen and thiobencarb were highest in the suspended sediments. With the exception of the three organochlorine insecticides, suspended sediments had higher pesticide concentrations compared to bed sediments, indicating the potential for pesticide transport especially during high-flow events. Soil samples were dominated by DDT and its degradates but also contained a variety of current-use pesticides typically at lower concentrations. The types of pesticides detected in water and sediments were correlated with agricultural application in each watershed.
Understanding the distribution of pesticides between the water and sediment is important in assessing their fate and transport within the Bypass, and in evaluating the exposure and potential effects to resident fish.
Climate over the watershed of the San Francisco Bay Delta estuary system varies on a wide range of space and time scales, and affects downstream estuarine ecosystems. The historical climate has included mild to severe droughts and torrential rains accompanied by flooding, providing important lessons for present-day resource managers. Paleoclimate records spanning the last 10,000 years, synthesized across the Estuary, watershed and key regions beyond, provide a basis for increased understanding of how variable California’s climate can be and how it affects the Bay Delta system.
This review of paleoclimate records reveals a gradual warming and drying in California from about 10,000 years to about 4,000 years before present. During this period, the current Bay and Delta were inundated by rising sea level so that by 4,000 years ago the Bay and Delta had taken on much of their present shape and extent. Between about 4,000 and 2,000 years ago, cooler and wetter conditions prevailed in the watershed, lowering salinity in the Estuary and altering local ecosystems. Those wetter conditions gave way to increasing aridity during the past 2,000 years, a general trend punctuated by occasional prolonged and severe droughts and occasional unusually wet, cool periods. California’s climate since A.D. 1850 has been unusually stable and benign, compared to climate variations during the previous 2,000 or more years. Thus, climate variations in California’s future may be even more (perhaps much more) challenging than those of the past 100 years. To improve our understanding of these past examples of climate variability in California, and of the linkages between watershed climate and estuarine responses, greater emphases on paleoclimate records in and around the Estuary, improved temporal resolutions in several record types, and linked watershed-estuary paleo-modeling capabilities are needed.
Framework for Assessing Viability of Threatened and Endangered Chinook Salmon and Steelhead in the Sacramento–San Joaquin Basin
Protected evolutionarily significant units (ESUs) of salmonids require objective and measurable criteria for guiding their recovery. In this report, we develop a method for assessing population viability and two ways to integrate these population-level assessments into an assessment of ESU viability. Population viability is assessed with quantitative extinction models or criteria relating to population size, population growth rate, the occurrence of catastrophic declines, and the degree of hatchery influence. ESU viability is assessed by examining the number and distribution of viable populations across the landscape and their proximity to sources of catastrophic disturbance.
Central Valley spring-run and winter-run Chinook salmon ESUs are not currently viable, according to the criteria-based assessment. In both ESUs, extant populations may be at low risk of extinction, but these populations represent a small portion of the historical ESUs, and are vulnerable to catastrophic disturbance. The winter-run Chinook salmon ESU, in the extreme case, is represented by a single population that spawns outside of its historical spawning range. We are unable to assess the status of the Central Valley steelhead ESU with our framework because almost all of its roughly 80 populations are classified as data deficient. The few exceptions are those populations with a closely associated hatchery, and the naturally-spawning fish in these streams are at high risk of extinction. Population monitoring in this ESU is urgently needed.
Global and regional climate change poses an additional risk to the survival of salmonids in the Central Valley. A literature review suggests that by 2100, mean summer temperatures in the Central Valley region may increase by 2-8°C, precipitation will likely shift to more rain and less snow, with significant declines in total precipitation possible, and hydrographs will likely change, especially the the southern Sierra Nevada mountains. Warming at the lower end of the predicted range may allow spring-run Chinook salmon to persist in some streams, while making some currently utilized habitat inhospitable. At the upper end of the range of predicted warming, very little spring-run Chinook salmon habitat is expected to remain suitable.
In spite of the precarious position of Central Valley salmonid ESUs, there are prospects for greatly improving their viability. Recovering Central Valley ESUs may require re-establishing populations where historical populations have been extirpated (e.g., upstream of major dams). Such major efforts should be focused on those watersheds that offer the best possibility of providing suitable habitat in a warmer future.