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 11, Issue 3, 2013
There is a large and complex literature that addresses the question of optimally employing science in environmental policy. That literature mostly focuses on the challenges of efficient and effective interactions: it is probably fair to say it is long on identifying problems and short on answers. As a complement to the existing literature as well as the BDCP and the DSC's science plan, we invited nine experts each to write a 2,000-word essay to address the statement that science will guide policies concerning water supply reliability and ecosystem restoration in the Bay-Delta.
- 1 supplemental file
Successes, Failures and Suggested Future Directions for Ecosystem Restoration of the Middle Sacramento River, California
Large-scale ecosystem restoration projects seldom undergo comprehensive evaluation to determine project effectiveness. Consequently, there are missed opportunities for learning and strategy refinement. Before our study, monitoring information from California’s middle Sacramento River had not been synthesized, despite restoration having been ongoing since 1989. Our assessment was based on the development and application of 36 quantitative ecological indicators. These indicators were used to characterize the status of terrestrial and floodplain resources (e.g., flora and fauna), channel dynamics (e.g., planform, geomorphology), and the flow regime. Indicators were also associated with specific goal statements of the CALFED Ecosystem Restoration Program. A collective weight of evidence approach was used to assess restoration success. Our synthesis demonstrates good progress in the restoration of riparian habitats, birds and other wildlife, but not in restoration of streamflows and geomorphic processes. For example, from 1999 to 2007, there was a > 600% increase in forest patch core size, and a 43% increase in the area of the river bordered by natural habitat > 500 m wide. Species richness of landbirds and beetles increased at restoration sites, as did detections of bats. However, degraded post-Shasta Dam streamflow conditions continued. Relative to pre-dam conditions, the average number of years that pass between flows that are sufficient to mobilize the bed, and those that are of sufficient magnitude to inundate the floodplain, increased by over 100%. Trends in geomorphic processes were strongly negative, with increases in the amount of bank hardened with riprap, and decreases in the area of floodplain reworked. Overall the channel simplified, becoming less sinuous with reduced overall channel length. Our progress assessment presents a compelling case for what needs to be done to further advance the ecological restoration of the river. The most important actions to be taken relate to promoting river meander and floodplain connectivity, and restoring components of the natural flow regime.
- 1 supplemental ZIP
Eastward Migration or Marshward Dispersal: Exercising Survey Data to Elicit an Understanding of Seasonal Movement of Delta Smelt
Differing and confounding understandings of the seasonal movements of the delta smelt (Hypomesus transpacificus) in the San Francisco Estuary persist nearly 2 decades after its listing as threatened under the federal and state endangered species acts. The U.S. Fish and Wildlife Service and the U.S. Bureau of Reclamation have characterized the delta smelt as a species that migrates extensive distances from Suisun Bay and the Sacramento and San Joaquin rivers confluence in the fall and winter, eastward and upstream to the central and east Sacramento–San Joaquin Delta to spawn, with the next generation returning to downstream rearing areas in the following spring (OCAP Technical Support Team unpublished; USBR 2012). This description of inter-seasonal movements of delta smelt stands in contrast to findings drawn from previous studies, which describe movements by pre-spawner delta smelt from open waters in bays and channels to proximate marshlands and freshwater inlets (e.g., Moyle et al. 1992; Bennett 2005). In an effort to resolve this disagreement over the movements of delta smelt, we use publicly available data on its distribution drawn from trawl surveys to generate maps from which we infer seasonal patterns of dispersal. In the fall, before spawning, delta smelt are most abundant in Suisun Bay, the Sacramento and San Joaquin rivers confluence, the lower Sacramento River, and the Cache Slough complex. By March and April, the period of peak detection of spawning adults, relative densities in Suisun Bay and the rivers’ confluence have diminished in favor of higher concentrations of delta smelt in Montezuma Slough and the Cache Slough complex. A relatively small percentage of fish are observed in areas of the Sacramento River above Cache Slough. We conclude that inter-seasonal dispersal of delta smelt is more circumscribed than has been previously reported. This conclusion has real-world implications for efforts to conserve delta smelt. Our findings support a conservation strategy for delta smelt that focuses on habitat restoration and management efforts for tidal marsh and other wetlands in north Delta shoreline areas directly adjacent to open waters that have been documented to support higher concentrations of the fish.