San Francisco Estuary and Watershed Science

Zooplankton provide critical food for threatened and endangered fish species in the San Francisco Estuary (estuary). Reduced food supply has been implicated in the Pelagic Organism Decline of the early 2000s, and further changes in zooplankton abundance, seasonality, and distribution may continue to threaten declining fishes. While we have a wealth of monitoring data, we know little about the abundance trends of many estuary zooplankton species. To fill these gaps, we reviewed past research and then examined trends in seasonality and abundance from 1972 to the present of three key but understudied zooplankton species (Bosmina longirostris, Acanthocyclops spp., and Acartiella sinensis) that play important roles in the estuary food web. We fit Bayesian generalized additive mixed models of each taxon’s relationship with salinity, seasonality, year, and geography on an integrated database of zooplankton monitoring in the upper estuary. We found marked changes in the seasonality and overall abundance of each study species. Bosmina longirostris no longer peaks in abundance in the fall months, Acanthocyclops spp. precipitously declined in all months and lost its strong relationship with salinity, and A. sinensis adult abundance has become more strongly related to salinity while juveniles have developed wider seasonal abundance peaks. Through these analyses, we have documented the relationship of each species with salinity and seasonality since the beginning of monitoring or their introduction, thus increasing our understanding of their ecology and importance in the estuary. These results can inform food-web models, be paired with fish data to model the contributions of these species toward fish abundance trends and be mirrored to elucidate other species’ trends in future studies.

For many imperiled species, comparisons between wild and cultured populations are invaluable for informing conservation measures, though opportunities to do so may be rare. In this study, we asked whether spawning between and among wild and cultured Delta Smelt varies in terms of behavior or resulting egg fertilization success. We conducted two laboratory experiments in which we allowed wild females to spawn with wild males (wild × wild) and cultured females to spawn with wild males (cultured × wild). Due to small sample sizes, we qualitatively compared our results to published studies of all cultured Delta Smelt (cultured × cultured). Across all three groups, Delta Smelt exhibited spawns that were similar in sequence and manner, varied widely in diel timing, and occurred predominantly between a single female and one or two males. Egg fertilization success was higher in wild × wild trials than in cultured × wild ones, but both fell within the wide range observed among cultured × cultured fish. Thus, spawning was generally similar between cultured and wild Delta Smelt, whether they were in same- or mixed-origin groups. These findings provide rare insight into the spawning behavior of wild Delta Smelt and inform ongoing conservation efforts.

The escapement objective used to manage fisheries for Sacramento River Fall Chinook (SRFC) Salmon was established in 1984. Despite substantial changes to the system and multiple calls to re-evaluate the objective, data and analytical limitations have slowed progress. Synthesizing the available information is further complicated by the different measurement scales employed by relevant studies. Here, I offer a modeling framework for integrating consideration of established hatchery spawning goals, natural-area production or habitat capacities measured at varying spatial scales, and policy decisions about what fraction of potential natural production is desired along with risk tolerance. The model allows evaluating how likely a potential escapement goal (measured at the currently-used scale of fall-run adults returning to both hatcheries and natural areas throughout the Sacramento River basin) is both to meet hatchery goals and to produce at least a specified fraction of potential natural production. The framework also incorporates consideration of forecasting and ocean harvest planning error into identifying a pre-season planning target and its probability of resulting in escapement at least as high as the goal. The model indicates that the low end of the current escapement goal range of 122,000 to 180,000 adults, if achieved, would be more likely than not to achieve hatchery goals while achieving around 50% of potential natural production. Realized escapement equal to the high end is modeled to be very likely to achieve hatchery goals, and likely to achieve around 75% of potential basin-wide natural production or around 60% of upper Sacramento River potential production. The model indicates diminishing returns from total adult SRFC escapements higher than about 300,000 adults. However, past performance of forecast and harvest-planning models suggest that a pre-season target higher than the ultimate escapement goal is needed to have even a 50% chance of achieving the escapement goal.

Conserving bird populations is a key goal for management of the Sacramento–San Joaquin Delta ecosystem and is likely to have effects well beyond its boundaries. To inform bird- conservation strategies, we identified Priority Bird Conservation Areas for riparian landbirds and waterbirds in the Delta, defined as the most valuable 5% of the landscape for each group. We synthesized data from 2,547 surveys for riparian landbirds and 7,820 surveys for waterbirds to develop predictive distribution models, which then informed spatial prioritization analyses. We identified a total of 26,019 ha that are a high priority for conserving riparian landbirds, waterbirds, or both, representing the most important places in the Delta to protect and manage, as well as strategic areas where adjacent restoration could expand valuable habitat. These Priority Bird Conservation Areas include the Yolo Bypass Wildlife Area, Cosumnes River Preserve, Stone Lakes National Wildlife Refuge, and bufferlands that surround the Sacramento County Regional Sanitation District. However, we also found that over 60% of the Priority Bird Conservation Areas are not currently protected, indicating a vulnerability to changes in land cover or land use. We recommend advancing strategies for bird conservation in the Delta by developing more specific objectives and priorities, extending these analyses to include other bird species, and planning to mitigate the loss of Priority Bird Conservation Areas where they are most vulnerable to land cover change. The predictive models and analysis framework we developed represent the current state of the science on areas important to bird conservation, while also providing a foundation for an evolving bird-conservation strategy that reflects the Delta’s continuously evolving knowledge base and landscape.