SFEWS Vol. 20, Issue 2 | June 2022
#ChinookSalmon #SacramentoSplittail #tidalmarsh #floodplain #openwater #drought #flood #juvenileproductionestimate #JPE #lifehistory #raceidentification #springrun #SacramentoRiver #CADelta #quantile #regressionforest #Steelhead #machinelearning #entrainmentloss #SanFrancisco #estuary #SFE #BayDelta #gillnet #gearselectivity #Drainage #waterquality #agriculturaldrainage #returnflow #diversions #Delta #island #groundwater #nitrogen #phosphorous #metals
Considerations for the Development of a Juvenile Production Estimate for Central Valley Spring-Run Chinook Salmon
Effective species management depends on accurate estimates of population size. There are, however, no estimates of annual juvenile production for Central Valley spring-run Chinook Salmon (“spring run”), a highly imperiled species in California, making it difficult to evaluate population status and effectively manage key issues such as entrainment of this species at water diversions. In recognition of this critical information gap, we initiated an effort to develop a juvenile production estimate (JPE) for spring run, defined here as an annual forecast of the number of juvenile Central Valley spring-run Chinook Salmon that enter the Sacramento–San Joaquin Delta (“Delta”) from the Sacramento Valley.
Machine Learning Forecasts to Reduce Risk of Entrainment Loss of Endangered Salmonids at Large-Scale Water Diversions in the Sacramento–San Joaquin Delta, California
Incidental entrainment of fishes at large-scale state and federal water diversion facilities in the Sacramento-San Joaquin Delta, California, can trigger protective management actions when limits imposed by environmental regulations are approached or exceeded. These actions can result in substantial economic costs, and likewise they can affect the status of vulnerable species. Here, we examine data relevant to water management actions during January–June; the period when juvenile salmonids are present in the Delta.
Gill Net Selectivity for Fifteen Fish Species of the Upper San Francisco Estuary
Gill-net size selectivity for 15 fish species occurring in the upper San Francisco Estuary was estimated from a data set compiled from multiple studies which together contained 7,096 individual fish observations from 882 gill net sets. The gill nets considered in this study closely resembled the American Fisheries Society’s recommended standardized experimental gill nets for sampling inland waters. Relationships between gill-net mesh sizes and the sizes for each fish species retained in them were estimated indirectly using generalized linear modeling and maximum likelihood.
Nutrient and Trace Element Contributions from Drained Islands in the Sacramento–San Joaquin Delta, California
Inventorying nutrient and trace element sources in the Sacramento-San Joaquin Delta (the Delta) is critical to understanding how changes—including alterations to point source inputs such as upgrades to the Sacramento Regional Wastewater Treatment Plant (SRWTP) and landscape-scale changes related to wetland restoration—may alter the Delta’s water quality. While island drains are a ubiquitous feature of the Delta, limited data exist to evaluate island drainage mass fluxes in this system. To better constrain inputs from island drains, we measured monthly discharge along with nutrient and trace element concentrations in island drainage on three Delta islands and surrounding rivers from June 2017 to September 2018.
Climate Change Impacts on San Francisco Estuary Aquatic Ecosystems: A Review ample header
In the San Francisco Estuary, signals of climate change are apparent in the long-term monitoring record. Here we synthesize current and potential future climate change effects on three main ecosystems (floodplain, tidal marsh, and open water) in the upper estuary and two representative native fishes that commonly occur in these ecosystems (anadromous Chinook Salmon, Oncorhynchus tshawytscha and estuarine resident Sacramento Splittail, Pogonichthys macrolepidotus).
Volume 6, Issue 2, 2008
Studies that assess the success of riparian restoration projects seldom focus on wildlife. More generally, vegetation characteristics are studied, with the assumption that animal populations will recover once adequate habitats are established. On the Sacramento River, millions of dollars have been spent on habitat restoration, yet few studies of wildlife response have been published. Here we present the major findings of a suite of studies that assessed responses of four taxonomic groups (insects, birds, bats, and rodents). Study designs fell primarily into two broad categories: comparisons of restoration sites of different ages, and comparisons of restoration sites with agricultural and remnant riparian sites.
Older restoration sites showed increased abundances of many species of landbirds and bats relative to younger sites, and the same trend was observed for the Valley elderberry longhorn beetle (Desmocerus californicus dimorphus), a federally threatened species. Species richness of landbirds and ground-dwelling beetles appeared to increase as restoration sites matured. Young restoration sites provided benefits to species that utilize early successional riparian habitats, and after about 10 years, the sites appeared to provide many of the complex structural habitat elements that are characteristic of remnant forest patches. Eleven-year old sites were occupied by both cavity-nesting birds and special-status crevice-roosting bats. Restored sites also supported a wide diversity of bee species, and had richness similar to remnant sites. Remnant sites had species compositions of beetles and rodents more similar to older sites than to younger sites.
Because study durations were short for all but landbirds, results should be viewed as preliminary. Nonetheless, in aggregate, they provide convincing evidence that restoration along the Sacramento River has been successful in restoring riparian habitats for a broad suite of faunal species. Not only did the restoration projects provide benefits for special-status species, but they also appeared effective in restoring the larger native riparian community. Increases in bird abundance through time were observed both at restoration sites and in remnant habitats, suggesting that restoration efforts may be having positive spill-over effects, although observed increases may have been caused by other factors.
Although positive overall, these studies yielded some disconcerting results. The Lazuli Bunting (Passerina amoena) declined at restoration sites and remnant habitats alike, and certain exotic invasive species, such as black rats, appeared to increase as restoration sites matured.
Losses of Sacramento River Chinook Salmon and Delta Smelt to Entrainment in Water Diversions in the Sacramento–San Joaquin Delta
Pumping at the water export facilities in the southern Sacramento-San Joaquin Delta kills fish at and near the associated fish-salvage facilities. Correlative analyses of salvage counts with population indices have failed to provide quantitative estimates of the magnitude of this mortality. I estimated the proportional losses of Sacramento River Chinook salmon (Oncorhynchus tshawytscha) and delta smelt (Hypomesus transpacificus) to place these losses in a population context. The estimate for salmon was based on recoveries of tagged smolts released in the upper Sacramento River basin, and recovered at the fish-salvage facilities in the south Delta and in a trawling program in the western Delta. The proportion of fish salvaged increased with export flow, with a mean value around 10% at the highest export flows recorded. Mortality was around 10% if pre-salvage losses were about 80%, but this value is nearly unconstrained. Losses of adult delta smelt in winter and young delta smelt in spring were estimated from salvage data (adults) corrected for estimated pre-salvage survival, or from trawl data in the southern Delta (young). These losses were divided by population size and accumulated over the respective seasons. Losses of adult delta smelt were 1–50% (median 15%) although the highest value may have been biased upward. Daily losses of larvae and juveniles were 0–8%, and seasonal losses accumulated were 0–25% (median 13%). The effect of these losses on population abundance was obscured by subsequent 50-fold variability in survival from summer to fall.
Habitat Associations and Behavior of Adult and Juvenile Splittail (Cyprinidae: Pogonichthys macrolepidotus) in a Managed Seasonal Floodplain Wetland
Although there is substantial information about the benefits of managed seasonal wetlands to wildlife, little is known about whether this habitat can help support “at risk” native fishes. The Sacramento splittail Pogonichthys macrolepidotus, a California Species of Special Concern, does not produce strong year classes unless it has access to floodplain wetlands of the San Francisco Estuary and its tributaries. Our study examined the potential use of managed inundation to support spawning and rearing of splittail in years when the availability of seasonal habitat is limited. Wild adult splittail were captured during their spawning migration and transferred to a 3.8-ha engineered wetland, where they successfully spawned shortly after introduction. Radio telemetry studies suggested that post-spawning adults were relatively sedentary over the study period. Adult splittail were primarily located in habitats with open water or light vegetation, and in the deepest portions of the wetland. Snorkel surveys showed that early stages (mean 21-mm fork length [FL]) of young splittail produced in the wetland were strongly associated with shallow areas with shoreline emergent terrestrial vegetation and submerged aquatic vegetation, but moved offshore to deeper areas with tules and submerged terrestrial vegetation at night. Larger juveniles (mean 41-mm FL) primarily used deeper, offshore habitats during day and night. At night, schools of both younger and older juveniles dispersed, and individuals were associated with the bottom of the water column. These observations have important implications for the construction of managed and restored wetlands for the benefit of native fishes.
A Note on the Effect of Wind Waves on Vertical Mixing in Franks Tract, Sacramento–San Joaquin Delta, California
A one-dimensional numerical model that simulates the effects of whitecapping waves was used to investigate the importance of whitecapping waves to vertical mixing at a 3-meter-deep site in Franks Tract in the Sacramento-San Joaquin Delta over an 11-day period. Locally-generated waves of mean period approximately 2 s were generated under strong wind conditions; significant wave heights ranged from 0 to 0.3 m. A surface turbulent kinetic energy flux was used to model whitecapping waves during periods when wind speeds > 5 m s-1 (62% of observations). The surface was modeled as a wind stress log-layer for the remaining 38% of the observations. The model results demonstrated that under moderate wind conditions (5–8 m s-1 at 10 m above water level), and hence moderate wave heights, whitecapping waves provided the dominant source of turbulent kinetic energy to only the top 10% of the water column. Under stronger wind (> 8 m s-1), and hence larger wave conditions, whitecapping waves provided the dominant source of turbulent kinetic energy over a larger portion of the water column; however, this region extended to the bottom half of the water column for only 7% of the observation period. The model results indicated that phytoplankton concentrations close to the bed were unlikely to be affected by the whitecapping of waves, and that the formation of concentration boundary layers due to benthic grazing was unlikely to be disrupted by whitecapping waves. Furthermore, vertical mixing of suspended sediment was unlikely to be affected by whitecapping waves under the conditions experienced during the 11-day experiment. Instead, the bed stress provided by tidal currents was the dominant source of turbulent kinetic energy over the bottom half of the water column for the majority of the 11-day period.
Policy and Program Analysis
Current projections of climate change present a number of challenges to scientists and decision-makers. The projections predict a twenty-first-century climate in which many climate variables are likely to trend across broad geographical areas and at rates that are rapid by historical standards. The projections of change are likely to remain uncertain for many years to come, and complete surprises are possible. Responses to these changes will have to span large areas and many variables, and impacts will interact in complex ways. In the face of these challenges, we offer recommendations as to strategic approaches that the CALFED Science Program—which serves here as an important and illustrative example from among the many current scientific resource- and ecosystem-management programs—and the scientific and public-policy communities in central California, in general, may need to pursue. Recommended strategies include emphasis on long-term eco- and resource-system adaptability—rather than historical verisimilitude—in its restoration targets; major commitments to long-term monitoring of restoration and impacts; even more integration across scientific disciplines, observations, models, and across the study area; increased use of manipulative experiments; and recognition that climate-change issues must be addressed in all efforts undertaken by the program.