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.
Zooplankton, Anyone?
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 19, Issue 1, 2021
Research Article
Statistical Evaluation of Behavior and Population Dynamics Models Predicting Movement and Proportional Entrainment Loss of Adult Delta Smelt in the Sacramento–San Joaquin River Delta
There has been considerable debate about effects of entrainment of endangered Delta Smelt (Hypomesus transpacificus) at water export facilities located in the Sacramento–San Joaquin River Delta. In this paper we use a behavior-driven movement model (BMM) to simulate the movement of adult Delta Smelt, which, in conjunction with a population dynamics model, estimates the proportion of the population that is lost to entrainment, i.e., proportional entrainment loss (PEL). Parameters of the population model are estimated by maximum likelihood by comparing predictions to data from Fall Midwater Trawl (FMWT) and Spring Kodiak Trawl (SKT) surveys, as well as to daily salvage estimates. Our objectives are to evaluate different movement behavior hypotheses, to rank estimates of PEL based on how well predictions fit the data, and to sharpen our understanding of the data to inform future research and monitoring decisions.
We applied the modeling framework to data from water year 2002—a year when salvage was high—and tested 30 combinations of six behavior and five population dynamics models. More complex process and observation assumptions in the population model led to much improved fits in most cases, but did not appreciably influence PEL predictions, which were largely determined by movement predictions from the BMMs. Estimates of PEL varied considerably among behaviors (2% to 40%). The model with the highest predictive capability explained 98% of the variation in FMWT data across regions, 70% of the variation in SKT data across regions and surveys, and 28% and 43% of the daily variation in salvage at federal and state fish screening facilities, respectively. The PEL estimate from this model was 35%, more than double the original estimate from Kimmerer (2008) of 15%. While PEL estimates provided in this study should be considered preliminary, our framework for testing combined behavior-driven movement models and population dynamics models is an improvement compared to earlier efforts.
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Leveraging Delta Smelt Monitoring for Detecting Juvenile Chinook Salmon in the San Francisco Estuary
Monitoring is an essential component in ecosystem management, and leveraging existing data sources for multiple species of interest can be one effective way to enhance information for management agencies. Here, we analyzed juvenile Chinook Salmon (Oncorhynchus tshawytscha) bycatch data that has been collected by the recently established Enhanced Delta Smelt Monitoring program (EDSM), a survey designed to estimate the abundance and distribution of the San Francisco Estuary’s (estuary) endangered Delta Smelt (Hypomesus transpacificus). Two key aspects of the EDSM program distinguish it from other fish surveys in the estuary: a stratified random sampling design and the spatial scale of its sampling effort. We integrated the EDSM data set with other existing surveys in the estuary, and used an occupancy model to assess differences in the probability of detecting Delta Smelt across gear types. We saw no large-scale differences in size selectivity, and while detection probability varied among gear types, cumulative detection probability for EDSM was comparable to other surveys because of the program’s use of replicate tows. Based on our occupancy model and sampling effort in the estuary during spring of 2017 and 2018, we highlighted under-sampled regions that saw improvements in monitoring coverage from EDSM. Our analysis also revealed that each sampling method has its own benefits and constraints. Although the use of random sites with replicates, as conducted by EDSM, can provide more statistically robust abundance estimates relative to traditional methods, the use of fixed stations and simple methods such as beach seining may provide a more cost-effective way to monitor salmon occurrence in certain regions of the estuary. Leveraging the strengths of each survey’s method can enable stronger inferences on salmon abundance and distribution. Careful consideration of these trade-offs is crucial as the management agencies of the estuary continue to adapt and improve their monitoring programs.
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Modeling Delta Smelt Distribution for Hypothesized Swimming Behaviors
Delta Smelt, Hypomesus transpacificus, is an endangered pelagic fish native to the San Francisco Estuary. The distribution of Delta Smelt in the estuary shifts landward from low-salinity habitat to freshwater habitat before spawning. This spawning migration often coincides with the first substantial freshwater inflow to the estuary during winter. To accomplish this landward shift in distribution, Delta Smelt are believed to use the tides by swimming to faster-moving currents during flood tides and then repositioning themselves to slower-moving currents to reduce seaward movement on ebb tides. Studies have hypothesized that the swimming behavior of Delta Smelt during this period is influenced by environmental conditions such as salinity and turbidity. The details of these swimming behaviors—including the extent to which flows, salinity, and turbidity affect behaviors and distributions—are uncertain. The spawning migration is of management interest because an increase in observed counts of Delta Smelt at the South Delta water-export facilities has coincided roughly with the spawning migration in many years. In this study, we investigated a range of hypothesized swimming behaviors using a three-dimensional particle-tracking model for water year 2002 during the spawning migration, and compared the predicted distributions of Delta Smelt to distributions inferred from catch data. Our goal was to improve understanding of the influence of Delta Smelt swimming on distribution, and, ultimately, to develop a modeling tool to help management agencies identify conditions associated with entrainment losses. Predictions of Delta Smelt distributions and entrainment varied greatly among behaviors. Without swimming, Delta Smelt would be rapidly transported seaward of Suisun Bay, while continuous tidal migration would move them deep into the interior Delta. These behaviors and a simple turbidity-driven behavior model predicted distributions inconsistent with observations, while more complex behavior rules allowed improved predictions.
Evaluating the Role of Boat Electrofishing in Fish Monitoring of the Sacramento–San Joaquin Delta
The San Francisco Estuary is an incredibly diverse ecosystem with a mosaic of aquatic habitats inhabited by a number of economically, culturally, and ecologically important fish species. To monitor the temporal and spatial trends of this rich fish community, long-term fish monitoring programs within the estuary use a variety of gear types to capture fish species across life stages and habitats. However, concerns have been raised that current sampling gears may fail to detect certain species—or life stages—that inhabit areas that are not accessible by current gear types (e.g., riprap banks, shallow vegetated areas). Boat electrofishing is one sampling method that has been proposed to supplement current long-term fish monitoring in the upper estuary. In this study, we used fish catch data from past boat electrofishing studies, a long-term beach seine survey, and a couple of long-running trawl surveys to compare the relative probability of detecting various fishes across these sampling gears. Overall, we found that boat electrofishing led to notable improvements in the detection rates for many native and non-native fishes we examined. Boat electrofishing gear was better at detecting the majority of species in the spring (20 out of 38 species, 53%) and fall-winter (24 out of 34 species, 70%) sampling periods. Based on these findings, we recommend that resource managers consider the implementation of a long-term boat electrofishing survey to help them in their long-term conservation planning for fishes within the upper estuary.
- 4 supplemental PDFs
Re-Examining Factors That Affect Delta Smelt (Hypomesus transpacificus) Entrainment at the State Water Project and Central Valley Project in the Sacramento–San Joaquin Delta
Managing endangered species is challenging when increased rarity leads to an inability to detect their responses to environmental conditions. In the San Francisco Estuary, the state and federally listed Delta Smelt (Hypomesus transpacificus) has declined to record low numbers, elevating concern over entrainment at the State Water Project (SWP) and Central Valley Project (CVP) water export facilities. The objective of this study was to: (1) revisit previous work on factors that affect adult Delta Smelt collected at the SWP and CVP fish collection facilities using updated conceptual models and a new statistical approach; and (2) to determine factors that affect salvage at time-scales of interest to management. Boosted Regression Tree (BRT) models were applied to salvage data at the SWP and CVP, aggregated into two response categories: a “first flush” response that represented daily salvage from the start of the entrainment window to the 50% midpoint of observed salvage, and a “seasonal” response that included daily salvage from the entire entrainment window. Precipitation, sub-adult abundance, Yolo Bypass flow, and exports best explained first flush salvage at both the SWP and CVP. The seasonal models included a similar set of influential variables, but the relative influence of precipitation was lower compared to the first flush models., Yolo Bypass flow was more influential for seasonal salvage at the SWP, compared to the CVP; Old and Middle River flow was more influential for seasonal salvage at the CVP. Although the rank of variable importance that explains salvage differed slightly between first flush and seasonal time-scales, this study suggests that salvage is most influenced by hydrodynamics, water quality, and population abundance. The application of BRT models to predict salvage is limited, because salvage has been low since federal protections were implemented in 2008. Forecast models that integrate real-time variables with fish behavior models may improve Delta Smelt management.