SFEWS: Volume 19, Issue 2
Welcome to the June issue of San Francisco Estuary and Watershed Science. At midyear in 2021, research surrounding the San Francisco Estuary looks forward. Here, six articles in four categories offer advances in science using new technologies and a re-examination of past efforts.
Photo: CA Dept. of Water Resources, public domain.
In Honor of Dr. Larry R. Brown
Herbold et al. remember Dr. Larry R. Brown, who died suddenly in February of 2021. This note captures how important his scientific work was in the San Francisco Estuary and why he will be intensely missed by many of his colleagues.
Photo: Canva stock image
Preparing Scientists, Policymakers, and Managers for a Fast-Forward Future
To accelerate forward-looking science, policy, and management in the Delta, Norgaard et al. propose that the State of California create a Delta Science Visioning Process to fully and openly assess the challenges of more rapid change to science, policy, and management and offer appropriate solutions, including legislation.
Photo: CA Dept. of Water Resources, public domain
Ecological Effects of Climate-Driven Salinity Variation in the San Francisco Estuary: Can We Anticipate and Manage the Coming Changes?
Ghalambor et al. review and summarize the presentations and discussions that arose during the symposium “Ecological and Physiological Impacts of Salinization of Aquatic Systems from Human Activities,” which brought together an interdisciplinary group of scientists, managers, and policy-makers to answer the central question: can we use existing knowledge and future projections to predict and manage anticipated ecological impacts?
Photo: Canva stock image
Effects of Tidally Varying River Flow on Entrainment of Juvenile Salmon into Sutter and Steamboat Slough
Previous studies suggest that fish generally “go with the flow”—however, complex tidal hydrodynamics at sub-daily time-scales may be decoupled from net flow. To further examine entrainment of acoustically tagged juvenile Chinook Salmon into Sutter and Steamboat sloughs, Romine et al. modeled routing of acoustic tagged juvenile salmon as a function of tidally varying hydrodynamic data. Results indicate that discharge, the proportion of flow that entered the slough, and the rate of change of flow were good predictors of the probability of an individual fish being entrained.
Photo: John Burau
Examining Retention-at-Length of Pelagic Fishes Caught in the Fall Midwater Trawl Survey
A study was conducted in 2014-2015 to investigate and quantify the efficiency of the Fall Midwater Trawl for catching the endangered fish species Delta Smelt (Hypomesus transpacificus). Mitchell and Baxter revisit the same gear efficiency study and further utilize the data set by fitting selectivity curves for three additional pelagic fish species: Threadfin Shad (Dorosoma petenense), American Shad (Alosa sapidissima), and Mississippi Silverside (Menidia beryllina), and by applying more statistically sensitive approaches.
Photo: Lara Mitchell
Use of the SmeltCam as an Efficient Fish Sampling Alternative Within the San Francisco Estuary
Resource managers often rely on long-term monitoring surveys to detect trends in biological data. However, no survey gear is 100% efficient, and many sources of bias can both detect or miss biological trends. Huntsman et al. evaulate the SmeltCam, an imaging apparatus developed as a sampling alternative to long-term trawling gear surveys within the San Francisco Estuary, with the potential to reduce handling stress on sensitive species like the Delta Smelt (Hypomesus transpacificus).
Photo: Ken Newman
Volume 16, Issue 2, 2018
[Abstracts are not presented for essays. -The SFEWS Editors.]
The salt marsh harvest mouse (SMHM, Reithrodontomys raviventris) is an endangered species, endemic to the San Francisco Estuary. Despite being protected for almost half a century and being included in a large number of recovery, restoration, and management plans, significant data gaps hinder conservation and management of the species, a challenge further complicated by developing threats such as climate change. In this review, we present the current state of knowledge; highlight research gaps on habitat requirements and distribution, taxonomic status and genetic structure, physiology, reproduction and demographics, population dynamics, and behavior and community interactions; and present an overview of threats to the species. Our review indicates that substantial data gaps exist; although some aspects of SMHM ecology, such as habitat use, have been addressed extensively, others, such as the effects of environmental contamination, are largely unaddressed. We suggest that conservation and restoration-planning processes consider experimental approaches within restoration designs to address these deficiencies. Continued investment in basic and applied SMHM ecology to collect baseline and long-term data will also be beneficial. Additionally, further coordination among managers and researchers can facilitate more effective responses to uncertainties and emerging threats, especially climate change, which threatens the SMHM and its habitat throughout its range.
- 1 supplemental PDF
California’s salmonids are at the southern limits of their individual species’ ranges, and display a wide diversity of strategies to survive in California’s highly variable climate. Land use changes after statehood in 1850 eliminated important habitats, or blocked access to them, and reduced the abundance, productivity, and distribution of California’s salmon. Habitat simplification, fishing, hatchery impacts, and other stressors led to the loss of genetic and phenotypic (life history, morphological, behavioral, and physiological) diversity in salmonids. Limited diversity and habitat loss left California salmon with reduced capacity to cope with a variable and changing climate. Since 1976, California has experienced frequent droughts, as were common in the paleo-climatological record, but rare in the peak dam-building era of 1936–1976. Increasing temperatures and decreasing snowpacks have produced harsher conditions for California’s salmon in their current habitats than they experienced historically. The most likely way to promote salmon productivity and persistence in California is to restore habitat diversity, reconnect migratory corridors to spawning and rearing habitats, and refocus management to replenish the genetic and phenotypic diversity of these southernmost populations.
While our knowledge of the range of survival that outmigrating juvenile Chinook Salmon experience in different routes of the Sacramento–San Joaquin Delta has increased in recent years, few studies have focused on their survival during outmigration in the Yolo Bypass, the Delta’s primary floodplain. The Yolo Bypass floodplain provides valuable rearing habitat and growth benefits to juvenile fish in flood years, and efforts are underway to improve access to the Yolo Bypass and the Toe Drain, its perennial navigation channel, under a broader range of flows and river stages than is currently possible. We compared variation in transit time, and estimated survival between different release groups of fish outmigrating through the Yolo Bypass or through migratory routes in the lower Sacramento River. Tagged late-fall-run juvenile Chinook Salmon were released in both systems in 2012 and 2013. There was no significant difference between the estimated cumulative probability of survival in the Yolo Bypass system and combined routes of the lower Sacramento River in either year (0.312–0.629 vs. 0.342–0.599, 95% credible interval in 2012; and 0.111–0.408 vs. 0.240–0.407, 95% credible interval in 2013, respectively). The Yolo Bypass had a higher coefficient of variation (CV) in travel time relative to the lower Sacramento River routes in both years (0.34 vs. 0.29 in 2012, and 0.44 vs. 0.34 in 2013). This work suggests that in relatively low water years, the estimated survival of outmigrating juvenile Chinook Salmon in the Toe Drain is directly comparable to routes in the lower Sacramento River, and that metrics of behavioral diversity in movement behavior can and should be incorporated into future telemetry studies.
The Effect of Submersed Aquatic Vegetation on Invertebrates Important in Diets of Juvenile Largemouth Bass Micropterus salmoides
A suite of submersed aquatic vegetation (SAV) species, and especially Brazilian Waterweed (Egeria densa), has proliferated rapidly in California’s Sacramento–San Joaquin Delta. This expansion is concurrent with population declines in native fish species and increases in many non-native fish species, including Largemouth Bass Micropterus salmoides. In this study, we investigated the effect of SAV species composition and E. densa specifically on macroinvertebrate communities and juvenile Largemouth Bass diets. Invertebrate communities differed across sites in the Delta, driven primarily by changes in abundance of the amphipod Hyalella sp., oligochaetes, ostracods, and insect larvae of the family Chironomidae. Juvenile Largemouth Bass consistently consumed SAV-associated invertebrates, and preferentially consumed larger taxa, when available. Gut fullness of juvenile Largemouth Bass was lowest in sites dominated by E. densa, although there was no clear mechanism for this difference. However, SAV species composition had little effect on abundance of Hyalella sp., chironomid larvae, or damselfly naiads, prey items commonly consumed by juvenile Largemouth Bass. Our results suggest that E. densa does not provide a qualitative increase in macroinvertebrate food for fishes compared to other SAV species.
- 3 supplemental PDFs
Evaluation of the Delta Simulation Model-2 in Computing Tidally Driven Flows in the Sacramento-San Joaquin Delta
We investigate the fidelity of the Delta Simulation Model-2 (DSM2), a one-dimensional branched network hydrodynamics solver, which is used to model water quality and ecology in the Sacramento–San Joaquin Delta estuary. We find that while DSM2 reproduces the total flows well, it does not accurately represent the harmonic components of the tides and tidal modulation of subtidal flow. The inaccurate representation of tidal dynamics affects prediction of subtidal flows, flow splits at key junctions, and salinity. These deviations are the result of coarse spatial and temporal representation of tides as well as unrepresented estuarine physical processes. We propose and evaluate two types of schemes intended to improve fidelity: modifying the model domain and specifying fine grid and boundary conditions, and incorporating and parameterizing more complex physical processes into the 1-D model. We also develop a comprehensive protocol to evaluate the model in which we assess the fidelity of model results. In this protocol, we also include a decomposition of the model error into a systematic component because of model representation, and an unsystematic component, which includes errors from both unmodeled physical processes and data precision. Our analysis reveals that these recommendations would be effective provided they can be incorporated with model recalibration. Both our proposed schemes and the model evaluation process will be useful in analyzing models of networked surface water systems such as the Delta in which the distribution of observations is spatially inhomogeneous.
- 1 supplemental PDF