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 18, Issue 4, 2020
The year 2020 is one we are unlikely to forget. At a time when a global pandemic and an economic collapse drove changing technologies and social and economic inequalities, extreme weather events across the country reminded us, especially here in California, that the effects of a warming earth are undeniable. A tumultuous presidency ended, leaving behind a science establishment uncertain about what lies ahead. Such disruptions add to the concern about the disappearance of journals from the Internet, and so it is only natural that readers might be interested in the status of SFEWS. Even as formidable challenges lie ahead, Editor-in-Chief, Sam Luoma, provides an editorial describing the stability and resilience of SFEWS as one sign of optimism to carry into 2021.
Getting Our Heads Above Water: Integrating Bird Conservation in Planning, Science, and Restoration for a More Resilient Sacramento–San Joaquin Delta
The Sacramento–San Joaquin Delta is an important region for bird conservation in California, particularly as part of a large, productive estuary on the Pacific Flyway. The Delta currently provides habitat to an abundant, diverse community of birds, but it is likely only a small fraction of what the Delta’s bird community once was. Meeting the goal of restoring a healthy Delta ecosystem is legislatively required to include providing habitat for birds among the conservation goals and strategies in the Delta Plan, yet birds and their habitat needs are often not addressed in science syntheses, conservation planning, and large-scale restoration initiatives in the Delta. In this essay, we provide an avian perspective on the Delta, synthesizing recent scientific work to describe factors that contribute to the Delta’s current importance for birds, and the conservation needs of the diverse array of bird species that call the Delta home. We also evaluate the potential for the Delta to become even more important for birds in the future, incorporating climate change effects, species range shifts, and changes to the composition and configuration of the Delta’s landscape. Finally, recognizing the uncertainties about the Delta’s future landscape and the complexity of this social-ecological system, we provide recommendations—aimed at a higher- level policy and planning audience—for integrating bird conservation with other goals in the Delta. To improve ecosystem integrity, conserve biodiversity, and provide benefits to local communities of people, we urge a focus on creating a more resilient Delta and employing a diversified portfolio of conservation strategies, both old and new.
Life cycle models (LCMs) provide a quantitative framework that allows evaluation of how management actions targeting specific life stages can have population-level impacts on a species. The LCM building process is also a powerful tool that can be used to identify data gaps existing in the knowledge of the target species, and that might strongly influence overall population dynamics. LCMs are particularly useful for species such as salmon that are highly migratory and use multiple aquatic ecosystems throughout their life. Furthermore, they are lacking for threatened Central Valley spring-run Chinook (Oncorhynchus tshawytscha; CVSC). Here, we developed a CVSC LCM to describe the dynamics of Mill, Deer and Butte Creek CVSC populations. We used model construction, calibration and a global sensitivity analysis to highlight important data gaps in the monitoring of those populations. In particular, we found strong model sensitivity and high uncertainty in various egg, juvenile and adult ocean life stages’ biological processes. We concluded that the current CVSC monitoring network is insufficient to support using a LCM to inform how future management actions (e.g., hydrology and habitat restoration) influence CVSC dynamics. We propose a series of monitoring recommendations, such as the development of an enhanced juvenile tracking monitoring program and the implementation of juvenile trapping efficiency methodology combined with genetic identification tools, to help fill highlighted data gaps. These additional data collection efforts will provide critical quantitative information about the status of this imperiled species at key life stages (e.g., CVSC juvenile abundance estimates), and create a more comprehensive monitoring framework fundamental for working on the recovery of the entire stock. Furthermore, additional data collection will strengthen the LCM parameterization and calibration process, and ultimately improve the model’s predictive performance.
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White Sturgeon (Acipenser transmontanus), a species of concern in the San Francisco Estuary, is in relatively low abundance due to a variety of factors. The purpose of our study was to identify the estuarine habitat used by White Sturgeon to aid in the conservation and management of the species locally and across its range. We seasonally sampled sub-adult and adult White Sturgeon in the central estuary using setlines across a habitat gradient representative of three primary structural elements: shallow wetland channels (mean sample depth = 2 m), shallow open-water shoal (mean sample depth = 2 m), and deep open-water channel (mean sample depth = 7 m). We found that the shallow open-water shoal and deep open-water channel habitats were consistently occupied by White Sturgeon in spring, summer, and fall across highly variable water quality conditions, whereas the shallow wetland channel habitat was essentially unoccupied. We conclude that sub-adult and adult White Sturgeon inhabit estuaries in at least spring, summer, and fall and that small, shallow wetland channels are relatively unoccupied.