Showing papers in "San Francisco Estuary and Watershed Science in 2012"

Contemporaneous Subsidence and Levee Overtopping Potential, Sacramento-San Joaquin Delta, California

Abstract: The levee system in California's Sacramento-San Joaquin Delta helps protect freshwater quality in a critical estuarine ecosystem that hosts substan- tial agricultural infrastructure and a large human population. We use space-based synthetic aperture radar interferometry (InSAR) to provide synoptic vertical land motion measurements of the Delta and levee system from 1995 to 2000. We find that Delta ground motion reflects seasonal hydrologic signals superimposed on average subsidence trends of 3 to 20 mm yr -1 . Because the measurements are insensi- tive to subsidence associated with peat thickness variations over Delta-island length scales, it is most likely that InSAR rates reflect underlying Quaternary sedimentary column compaction. We combine InSAR rates with sea-level rise scenarios to quantify 21st century levee overtopping potential. If left unmitigat- ed, it is likely that 50 to 100 years from now much of the levee system will subside below design thresholds.

Conceptual Model of Sedimentation in the Sacramento- San Joaquin River Delta

Abstract: Sedimentation in the Sacramento–San Joaquin River Delta builds the Delta landscape, creates benthic and pelagic habitat, and transports sediment-associated contaminants. Here we present a conceptual model of sedimentation that includes submodels for river supply from the watershed to the Delta, regional transport within the Delta and seaward exchange, and local sedimentation in open water and marsh habitats. The model demonstrates feedback loops that affect the Delta ecosystem. Submerged and emergent marsh vegetation act as ecosystem engineers that can create a positive feedback loop by decreasing suspended sediment, increasing water column light, which in turn enables more vegetation. Sea-level rise in open water is partially countered by a negative feedback loop that increases deposition if there is a net decrease in hydrodynamic energy. Manipulation of regional sediment transport is probably the most feasible method to control

Pre-Screen Loss and Fish Facility Efficiency for Delta Smelt at the South Delta's State Water Project, California

Abstract: Water exports have been implicated in the decline of fish populations in the upper San Francisco Estuary, California. We evaluated the relation between delta smelt salvage at the John E. Skinner Delta Fish Protective Facility (SFF) and underlying entrainment losses at the State Water Project

Tidal Wetland Vegetation in the San Francisco Bay-Delta Estuary

Abstract: We analyzed tidal wetland vegetation patterns in the San Francisco Bay–Delta estuary (Bay–Delta) and discuss their significance for future conservation. Our objective was to conduct a balanced, random sample of six historic “remnant” tidal wetlands along a salinity gradient that ranged from southern San Pablo Bay to the lower Delta. We also wanted to compare diversity among these sites at five different scales, ranging from small subplots to total species per site. We randomly established twenty 0.1-ha plots at each site, and sampled ten 7-m2 circular subplots (subplot scale) in each plot for species presence and cover. We calculated total species per plot (plot scale) and total species per site (site scale) based on these subplot data. We calculated importance values for each species found in subplots based on frequency of occurrence and proportion of total cover at each site. In addition, we recorded species found within the 0.1-ha plot but not sampled in subplots (plot_all scale), and calculated the total species for each site based on these plot_all data (site_all scale). Thus, richness at each site was evaluated at five different scales that ranged from 7 m2 to 20,000 m2. We conducted a one-way ANOVA that compared mean richness among three scales with continuous data: subplot, plot, and plot_all. At lower estuary (San Pablo Bay) sites, richness values at these three scales were significantly lower than upper estuary (Suisun–Delta) sites. In Suisun–Delta sites, significant differences in richness varied, depending on sampling scale. Rush Ranch, a brackish wetland, had the highest average number of species per plot, whereas Sand Mound Slough, a freshwater wetland, had the highest average number of species at the subplot scale and the most total species at the site_all scale. Sand Mound Slough also had the highest number of unique species (22) compared to the other sites. We found a strong negative correlation (r2 = 0.99) between total species number and salinity (the most in the Delta at the lowest salinity, and the least at China Camp with the greatest salinity). Our analysis suggests the following conservation recommendations: (1) restore habitat for freshwater plant species diversity in the Delta; (2) restore transitional brackish wetland habitat in salt marshes of the San Pablo Bay and San Francisco Bay; and (3) focus on control of pepperweed (Lepidium latifolium) in brackish marshes.

Individual-level and Population-level Historical Prey Demand of San Francisco Estuary Striped Bass Using a Bioenergetics Model

Abstract: Striped bass are both a major predator of native fishes and support a recreational fishery in the San Francisco Estuary (the estuary). Quantifying their demands on their prey is important for understanding long-term trends of fish in the estuary. In this study, we: (i) applied a bioenergetics model of sub-adult (age 1 and age 2) and adult (age 3+) striped bass (Morone saxatilis) to quantify long-term consumption patterns from 1969 through 2004 in the estuary; (ii) developed a method to estimate the abundances of sub-adult striped bass; (iii) evaluated how consumption varied by age and gender; and (iv) identified factors that affect the resulting consumption estimates. On a ‘per capita’ basis, modeled individual prey fish consumption increased after 1990, and individual total and prey fish consumption by age-2 striped bass increased after 1994. Conversely, individual total and prey fish consumption by adult striped bass decreased over the period analyzed. This decline in individual consumption over the study period was related to a decline in mean length at age of adults. As expected, long-term trends in population consumption (total and prey fish) by all ages of striped bass (ages 1 through 6) closely followed their respective population- abundance trends. Population total consumption and prey fish-specific consumption by sub-adult striped bass was found to be similar to the population consumption by adult striped bass, largely because of the high abundance of sub-adults. Unlike adult striped bass that may emigrate and forage in the Pacific Ocean, the majority of sub-adult striped bass reside within the estuary; hence, consumption by the relatively abundant sub-adult population may have significant effects upon their estuarine prey species.

Juvenile Chinook Salmon (Oncorhynchus tshawytscha) in and Around the San Francisco Estuary

Abstract: Author(s): Williams, John G. | Abstract: Central Valley Chinook must pass through the San Francisco Estuary as juveniles and again as maturing adults. Much attention has been given to the effects on Chinook of management of the freshwater part of the estuary, and the Sacramento–San Joaquin Delta, and especially to the effects on Chinook of diversions of water from the Delta. Here, I review available information on juvenile Chinook in and around the estuary that seems most relevant to management of the estuary and of Chinook. Most naturally produced juvenile fall Chinook enter the estuary as small fish (l50 mm) that typically use tidal habitats, and anthropogenic changes in the Delta and around the bays have sharply reduced that habitat. Nevertheless, there is evidence that many surviving naturally produced fall Chinook leave fresh water at l55 mm length. Juvenile Chinook from other runs are older and larger when they enter the estuary, and probably pass through it more rapidly. Presumably, these have been less directly affected by loss of tidal habitat, but are also affected by degradation of the estuarine ecosystem. The effects of Delta diversions on Chinook vary strongly by run and river of origin; surprisingly few Sacramento River fall Chinook have been recovered at the diversions. Central Valley Chinook, especially fall Chinook, are strongly affected by hatchery culture that reduces juvenile life-history diversity, probably results in density-dependent mortality in the estuary, and presumably reduces fitness for natural reproduction. Hatchery culture diverts juvenile fall Chinook away from, and precludes for selection for, the life history trajectories followed by most naturally produced fish, to which more attention should be given.

Fish Assemblages in Reference and Restored Tidal Freshwater Marshes of the San Francisco Estuary - eScholarship

Abstract: We examined the spatial and temporal distributions of fishes at a reference and three restored marshes between April 1998 and July 1999 in the Sacramento–San Joaquin Delta, California, to determine the factors that influence fish assemblages in space and time. Shallow-water fishes were sampled using beach seines with and without block-net enclosures in open-water shoals and submerged aquatic vegetation (SAV). Purse seining was used to sample fishes in deep water, including offshore, tidal slough, and marsh-edge habitats. Overall, fish assemblages in reference and restored marshes were dominated by introduced species. One-way analysis of similarity (ANOSIM) did not reveal study site differences in fish assemblages in either data set. However, nonmetric multi-dimensional scaling (NMS) and ANOSIM tests of the shallow-water collections revealed differences in fish assemblages using habitats with and without SAV. Introduced fishes, including predatory centrarchid fishes, were abundant in SAV. NMS and ANOSIM tests of the deep-water collections revealed differences in fish assemblages between offshore and nearshore (marsh-edge and tidal slough) habitats. Notably, native fishes were abundant in tidal sloughs. Temporal analyses revealed a suite of species more common in winter and spring, versus another group of introduced species that were more common in summer and fall. Our study findings indicate that newly restored habitats in the Sacramento–San Joaquin Delta will be invaded by introduced fishes. To promote native fish habitat, restoration planning should focus on areas and regions of the Delta where tidal marshes can be restored with little intervention, and where invasive SAV is less likely to colonize.

Managing California’s Water: Insights from Interviews with Water Policy Experts

Abstract: This paper presents insights from interviews with over 100 California water policy experts, who answered open-ended questions regarding California’s long-term water policy challenges and potential solutions. Interviews were conducted in the spring and summer of 2010, and interviewees were selected from a range of sectors and regions within California. Top long-term policy problems cited include management of the Sacramento–San Joaquin Delta, dysfunctional institutions and water governance, unsustainable water supplies and flood management, poor environmental protection, and problems with water rights and valuing water. In addition to a range of specific management solutions, respondents emphasized the importance of public education, incentivized cooperation, more holistic water management, local innovation, and removal of regulatory obstacles as primary solutions to California’s long-term water challenges. There was little emphasis on new surface storage projects, except from politicians. Other respondents preferred local and regional approaches to improve water supply, such as conservation, groundwater banking, recycling, or stormwater management. Despite differences in opinion on the problems with implementation of the Endangered Species Act, there was broad agreement that environmental management approaches need to shift away from single-species, piecemeal approaches toward ecosystem-based, multi-species approaches.

Tidal Marsh Vegetation of China Camp, San Pablo Bay, California

Abstract: China Camp (Marin County, California) preserves extensive relict stands of salt marsh vegetation developed on a prehistoric salt marsh platform with a complex sinuous tidal creek network. The low salt marsh along tidal creeks supports extensive native stands of Pacific cordgrass (Spartina foliosa). The outer salt marsh accreted following hydraulic gold mining sedimentation. It consists of a wave-scarped pickleweed-dominated (Sarcocornia pacifica) high salt marsh terrace with a broad fringing low marsh dominated by S. foliosa, including intermittent, variable stands of alkali-bulrush (Bolboschoenus maritimus). Most of the extensive prehistoric salt marsh plains within the tidal creek network also support mixed assemblages of S. pacifica, but high marsh zones along tidal creek banks support nearly continuous linear stands of gumplant (Grindelia stricta) and saltgrass (Distichlis spicata) with more diverse salt marsh forb assemblages. Salt pans with submerged wigeongrass (Ruppia maritima) are scarce, local, and small. The landward edge of the tidal marsh forms rare examples of ecotones with adjacent terrestrial vegetation, including those of alluvial valleys (riparian scrub and woodland, freshwater marsh, sedge-rush meadows) and hillslope grassland and oak woodland vegetation. Narrow high tidal marsh ecotones bordering terrestrial grasslands are locally dominated by creeping wildrye (Elymus triticoides) and Baltic rush (Juncus balticus), mostly on south-facing slopes. Brackish tidal marsh ecotones above ordinary high tides are associated with freshwater discharges from groundwater and surface flows. Brackish marsh ecotones support large clonal stands of sedge, bulrush, and rush vegetation (Carex praegracilis, C. barbarae, Bolboschoenus maritimus, Juncus phaeocephalus, Schoenoplectus acutus), intergrading with terrestrial freshwater wetlands and salt marsh. The terrestrial ecotone assemblages at China Camp are comparable with those of other prehistoric tidal marshes in the San Francisco Estuary, but China Camp lacks most native clonal perennial Asteraceae and halophytic annual forbs of the region’s remnant high tidal marsh ecotones. Few globally rare salt marsh plant populations have been reported from China Camp within the National Estuarine Research Reserve and State Park boundaries, but some species regionally uncommon in San Francisco Bay tidal marshes occur. To date, non-native tidal marsh plant invasions have been relatively minor and localized within China Camp.

Downscaling Future Climate Projections to the Watershed Scale: A North San Francisco Bay Case Study

Abstract: We modeled the hydrology of basins draining into the northern portion of the San Francisco Bay Estuary (North San Pablo Bay) using a regional water balance model (Basin Characterization Model; BCM) to estimate potential effects of climate change at the watershed scale. The BCM calculates water balance components, including runoff, recharge, evapotranspiration, soil moisture, and stream flow, based on climate, topography, soils and underlying geology, and the solar-driven energy balance. We downscaled historical and projected precipitation and air temperature values derived from weather stations and global General Circulation Models (GCMs) to a spatial scale of 270 m. We then used the BCM to estimate hydrologic response to climate change for four scenarios spanning this century (2000–2100). Historical climate patterns show that Marin’s coastal regions are typically on the order of 2 °C cooler and receive five percent more precipitation compared to the inland valleys of Sonoma and Napa because of marine influences and local topography. By the last 30 years of this century, North Bay scenarios project average minimum temperatures to increase by 1.0 °C to 3.1 °C and average maximum temperatures to increase by 2.1 °C to 3.4 °C (in comparison to conditions experienced over the last 30 years, 1981–2010). Precipitation projections for the 21st century vary between GCMs (ranging from 2 to 15% wetter than the 20th-century average). Temperature forcing increases the variability of modeled runoff, recharge, and stream discharge, and shifts hydrologic cycle timing. For both high- and low-rainfall scenarios, by the close of this century warming is projected to amplify late-season climatic water deficit (a measure of drought stress on soils) by 8% to 21%. Hydrologic variability within a single river basin demonstrated at the scale of subwatersheds may prove an important consideration for water managers in the face of climate change. Our results suggest that in arid environments characterized by high topo-climatic variability, land and water managers need indicators of local watershed hydrology response to complement regional temperature and precipitation estimates. Our results also suggest that temperature forcing may generate greater drought stress affecting soils and stream flows than can be estimated by variability in precipitation alone.

A Conceptual Model for Floodplains in the Sacramento-San Joaquin Delta

Abstract: Floodplains are among the most biologically productive and diverse ecosystems on Earth and they provide significant benefits to society such as attenuation of floodwaters, groundwater recharge, filtration of nutrients and sediments, carbon sequestration, fisheries productivity and recreation. However, floodplains are also among the most converted and threatened ecosystems. Floodplain habitats in the Sacramento-San Joaquin Delta, and throughout California’s Central Valley, have been greatly reduced from their historic extent and key processes that create and maintain floodplains, such as flood flows and meander migration, have been greatly altered. These widespread alterations to habitats and processes have lead to declines in many species’ populations in California’s Central Valley and Delta, creating challenges for both environmental and water management. To address these challenges numerous entities and programs are now focused on restoring floodplains and other Delta habitats. This paper provides a conceptual model for floodplains that characterizes the key features and identifies the critical processes, drivers, and linkages that allow floodplains to produce a variety of functional outputs of management importance. These outputs include: (1) the floodplain habitat mosaic, including riparian vegetation and its associated wildlife; (2) spawning and rearing habitat for native fish; and (3) food-web productivity that can support native fish on the floodplain as well as be exported to downstream ecosystems. The model emphasizes that the production of these outputs from floodplains requires vertical and lateral hydrological connectivity across a broad range of flow conditions. For example, long-duration flooding in the spring promotes native fish spawning and food-web productivity that benefits native species.

Using Conceptual Models in Ecosystem Restoration Decision Making: An Example from the Sacramento-San Joaquin River Delta, California

Abstract: The Sacramento–San Joaquin Delta (the Delta) is located on the western edge of California’s Central Valley and is of critical ecological and economic importance. However, ecosystem alterations for human uses changed many of the Delta’s natural processes, and it is now considered in need of restoration. An approach was developed to evaluate and rank restoration actions in the Delta under the Ecosystem Restoration Program’s Delta Regional Ecosystem Restoration Implementation Plan (DRERIP). The DRERIP approach provides an explicit framework for evaluating restoration actions, using linked conceptual models, an action evaluation procedure, and a decision-support tool. Conceptual models allow scientists and managers to synthesize scientific information and make qualitative predictions about ecosystem function and restoration outcomes to guideand focus restoration efforts. The action evaluation procedure is a structured assessment of restoration actions. The procedure clearly describes actions to be evaluated, assesses the magnitude (importance and scale) and certainty of anticipated ecological outcomes, estimates degrees of worth (achieving intended outcomes) and risk (causing adverse consequences), evaluates the reversibility of the action, and identifies opportunities for learning. The values for worthiness, risk, reversibility, and learning opportunity are used in the decision- support tool to determine the fate of a proposed action. The decision-support tool is a structured decision tree that determines the disposition of an action: whether a restoration project should be discarded, revised with a different approach and re-evaluated, or implemented; and, if implemented, at what scale (targeted research, pilot project, or full implementation). The DRERIP approach provides managers with a valuable tool for restoration planning, and a foundation for integration with quantitative methods for a comprehensive ecosystem restoration plan.

Fish Assemblages in Reference and Restored Tidal Freshwater Marshes of the San Francisco Estuary

Abstract: We examined the spatial and temporal distributions of fishes at a reference and three restored marshes between April 1998 and July 1999 in the Sacramento–San Joaquin Delta, California, to determine the factors that influence fish assemblages in space and time. Shallow-water fishes were sampled using beach seines with and without block-net enclosures in open-water shoals and submerged aquatic vegetation (SAV). Purse seining was used to sample fishes in deep water, including offshore, tidal slough, and marsh-edge habitats. Overall, fish assemblages in reference and restored marshes were dominated by introduced species. One-way analysis of similarity (ANOSIM) did not reveal study site differences in fish assemblages in either data set. However, nonmetric multi-dimensional scaling (NMS) and ANOSIM tests of the shallow-water collections revealed differences in fish assemblages using habitats with and without SAV. Introduced fishes, including predatory centrarchid fishes, were abundant in SAV. NMS and ANOSIM tests of the deep-water collections revealed differences in fish assemblages between offshore and nearshore (marsh-edge and tidal slough) habitats. Notably, native fishes were abundant in tidal sloughs. Temporal analyses revealed a suite of species more common in winter and spring, versus another group of introduced species that were more common in summer and fall. Our study findings indicate that newly restored habitats in the Sacramento–San Joaquin Delta will be invaded by introduced fishes. To promote native fish habitat, restoration planning should focus on areas and regions of the Delta where tidal marshes can be restored with little intervention, and where invasive SAV is less likely to colonize.

Delta Flow Factors Influencing Stray Rate of Escaping Adult San Joaquin River Fall-Run Chinook Salmon ()

Abstract: Adult salmon that stray when they escape into non-natal streams to spawn is a natural phenomenon that promotes population growth and genetic diversity, but excessive stray rates impede adult abundance restoration efforts. Adult San Joaquin River (SJR) Basin fall-run Chinook salmon (Oncorhynchus tshawytscha) that return to freshwater to spawn migrate through the San Francisco Bay and Sacramento–San Joaquin River Delta (Delta). The Delta has been heavily affected by land development and water diversion. During the fall time-period for the years 1979 to 2007 Delta pumping facilities diverted on average 340% of the total inflow volume that entered the Delta from the SJR. The hypothesis tested in this paper is that river flow and Delta exports are not significantly correlated with SJR salmon stray rates. Adult coded-wire-tagged salmon recoveries from Central Valley rivers were used to estimate the percentage of SJR Basin salmon that strayed to the Sacramento River Basin. SJR salmon stray rates were negatively correlated (P = 0.05) with the average magnitude of pulse flows (e.g., 10 d) in mid- to late-October and positively correlated (P = 0.10) with mean Delta export rates. It was not possible to differentiate between the effects of pulse flows in October and mean flows in October and November on stray rates because of the co-linearity between these two variables. Whether SJR-reduced pulse flow or elevated exports causes increased stray rates is unclear. Statistically speaking the results indicate that flow is the primary factor. However empirical data indicates that little if any pulse flow leaves the Delta when south Delta exports are elevated, so exports in combination with pulse flows may explain the elevated stray rates. For management purposes, we developed two statistical models that predict SJR salmon stray rate: (1) flow and export as co-independent variables; and (2) south Delta Export (E) and SJR inflow (I) in the form of an E:I ratio.

Abundance, Species Richness, and Reproductive Success of Tidal Marsh Birds at China Camp State Park, Marin County, California

Abstract: Extensive habitat loss and degradation have resulted in decreases in populations of tidal marsh breeding birds in the San Francisco Estuary in the past 150 years. We conducted point count surveys and nest monitoring in tidal marsh habitat at China Camp State Park from 1996 through 2007 to assess bird abundance, species richness and reproductive success over time. We found overall species richness at China Camp to be significantly lower than that of other San Pablo Bay tidal marshes, but also to be increasing during the study period. We present relative density indices and confirm breeding for three focal species that are of conservation concern: San Pablo song sparrow (Melospiza melodia samuelis), California black rail (Laterallus jamaicensis coturniculus), and California clapper rail (Rallus longirostris obsoletus). Song sparrows were observed at higher densities at China Camp than at other San Pablo Bay sites. There was no apparent trend in song sparrow density during the study period at China Camp, in contrast with the rest of San Pablo Bay, which displayed a significant decline. We determined song sparrow nest survival probability using the method described by Mayfield (1975) and found that nest survival at China Camp varied markedly among years, from >30% in 1996 to 6% in 2006, with no discernible trend. The main causes of nest failure were predation and tidal flooding. Song sparrow nests were found predominantly in gumplant (Grindelia stricta) and pickleweed (Sarcocornia pacifica) and less commonly in saltgrass (Distichlis spicata). Clapper rails nested exclusively in pickleweed and black rail nests were found mainly in gumplant and less commonly in saltgrass. China Camp’s expansive ancient marsh supports endemic and bird species of conservation concern, while serving as a reference site for tidal marsh studies in San Francisco Bay. The long-term monitoring of tidal marsh bird breeding parameters at China Camp has the potential to provide early detection of declining population trends before local populations become imperiled.

Delta Flow Factors Influencing Stray Rate of Escaping Adult San Joaquin River Fall-Run Chinook Salmon (Oncorhynchus tshawytscha)

Abstract: Adult salmon that stray when they escape into non-natal streams to spawn is a natural phenomenon that promotes population growth and genetic diversity, but excessive stray rates impede adult abundance restoration efforts. Adult San Joaquin River (SJR) Basin fall-run Chinook salmon (Oncorhynchus tshawytscha) that return to freshwater to spawn migrate through the San Francisco Bay and Sacramento–San Joaquin River Delta (Delta). The Delta has been heavily affected by land development and water diversion. During the fall time-period for the years 1979 to 2007 Delta pumping facilities diverted on average 340% of the total inflow volume that entered the Delta from the SJR. The hypothesis tested in this paper is that river flow and Delta exports are not significantly correlated with SJR salmon stray rates. Adult coded-wire-tagged salmon recoveries from Central Valley rivers were used to estimate the percentage of SJR Basin salmon that strayed to the Sacramento River Basin. SJR salmon stray rates were negatively correlated (P = 0.05) with the average magnitude of pulse flows (e.g., 10 d) in mid- to late-October and positively correlated (P = 0.10) with mean Delta export rates. It was not possible to differentiate between the effects of pulse flows in October and mean flows in October and November on stray rates because of the co-linearity between these two variables. Whether SJR-reduced pulse flow or elevated exports causes increased stray rates is unclear. Statistically speaking the results indicate that flow is the primary factor. However empirical data indicates that little if any pulse flow leaves the Delta when south Delta exports are elevated, so exports in combination with pulse flows may explain the elevated stray rates. For management purposes, we developed two statistical models that predict SJR salmon stray rate: (1) flow and export as co-independent variables; and (2) south Delta Export (E) and SJR inflow (I) in the form of an E:I ratio.

Embryonic and Larval Development of Sacramento Splittail Pogonichthys macrolepidotus

Abstract: Embryonic and larval development of Sacramento splittail (Pogonichthys macrolepidotus) was char- acterized from zygote to metamorphosis in labora- tory conditions. Fertilized eggs were obtained from induced and natural tank spawning of adults caught in the Yolo Bypass of the Sacramento River. Splittail produced transparent adhesive eggs with a moder- ate perivitelline space. Duration of embryonic devel- opment from fertilization to hatching was 100 h at 18 ± 0.5 °C. Newly hatched larvae were 5.2 to 6.0 mm total length with no mouth opening. Yolk- sac larvae were demersal and absorbed the yolk within 10 days post-hatch. Exogenous feeding started at 6 days post-hatch, concomitant with swim bladder inflation and swim-up movement. Fin differentia- tion began at approximately 10 d post-hatch (ca. 8.3 to 8.85 mm total length) and was completed at 50 d post-hatch (ca. 19.6 to 20.85 mm total length) when larval finfold was fully resorbed and the adult com- plement of fin rays was present in all fins, but scales were still lacking.

Population Studies of Tidal Marsh Breeding Birds at Rush Ranch: A Synthesis

Abstract: Rush Ranch, with the largest contiguous area of fully-tidal marsh remaining in northern Suisun Bay, is critical habitat for a number of endemic bird species that breed in brackish tidal marsh. Despite the abundance of non-native invasive plants (particularly perennial pepperweed, Lepidium latifolium) and altered hydrology, it is the best remaining representative in Solano County of the tidal marsh that once covered more than 27,000 ha (67,000 acres) in Suisun Bay. This paper presents a synthesis of bird population studies conducted at Rush Ranch since the late 1970s, concentrating on California clapper rail (Rallus longirostris obsoletus), California black rail (Laterallus jamaicensis coturniculus), Suisun song sparrow (Melospiza melodia maxillaris), common yellowthroat (Geothlypis trichas), and marsh wren (Cistothorus palustris). These studies indicate declines in clapper rail abundance, when we compared the past 8 years to surveys conducted 10 to 25 years ago. However, black rails appear to be increasing at Rush Ranch, and overall in Suisun Bay. Nest monitoring of reproductive attempts by song sparrows conducted between 1996 and 2005 indicates low overall nest survival rates, mainly from high predation rates, but also great year-to-year variability. Low nest survival rates of tidal marsh song sparrows observed at Rush Ranch appear to be too low to sustain populations, and such low rates are consistent with the apparent population declines observed for this subspecies at Rush Ranch. Nest survival and other components of reproductive success of tidal marsh birds should be monitored in the future to provide information on ecosystem condition and population health, as well as the response of these species to management, including control of non-native plant species.

Embryonic and Larval Development of Sacramento Splittail

Abstract: Embryonic and larval development of Sacramento splittail (Pogonichthys macrolepidotus) was characterized from zygote to metamorphosis in laboratory conditions. Fertilized eggs were obtained from induced and natural tank spawning of adults caught in the Yolo Bypass of the Sacramento River. Splittail produced transparent adhesive eggs with a moderate perivitelline space. Duration of embryonic development from fertilization to hatching was 100 h at 18 ± 0.5 °C. Newly hatched larvae were 5.2 to 6.0 mm total length with no mouth opening. Yolk-sac larvae were demersal and absorbed the yolk within 10 days post-hatch. Exogenous feeding started at 6 days post-hatch, concomitant with swim bladder inflation and swim-up movement. Fin differentiation began at approximately 10 d post-hatch (ca. 8.3 to 8.85 mm total length) and was completed at 50 d post-hatch (ca. 19.6 to 20.85 mm total length) when larval finfold was fully resorbed and the adult complement of fin rays was present in all fins, but scales were still lacking.

San Francisco Estuary and Watershed Science 2012: Participating in the Journey

Abstract: SFEWS has reached a number of milestones during the year 2012. In September, we received the 100,000th request for an article; an illustration of the sustained interest in the papers we are publishing. Views and downloads in the last four months are tied for the highest ever for such a period. For the first time SFEWS published four issues in 2012 (instead of the usual three) thanks to the financial support of the Delta Stewardship Council and a dedicated team working with the Managing Editor. We feel we can maintain this rate of publication. Finally we continue our work toward expanding the visibility of SFEWS via websites, search engines, better tracking of our readership, participation in science conferences, and inexpensive advertising. As always, however, our major focus for the future is sustaining the integrity and high quality of our articles through a strong peer review process. We thank you for your support of SFEWS and wish the best to all for 2013.

Juvenile Chinook Salmon () in and Around the San Francisco Estuary

Abstract: Central Valley Chinook must pass through the San Francisco Estuary as juveniles and again as maturing adults. Much attention has been given to the effects on Chinook of management of the freshwater part of the estuary, and the Sacramento–San Joaquin Delta, and especially to the effects on Chinook of diversions of water from the Delta. Here, I review available information on juvenile Chinook in and around the estuary that seems most relevant to management of the estuary and of Chinook. Most naturally produced juvenile fall Chinook enter the estuary as small fish (<50 mm) that typically use tidal habitats, and anthropogenic changes in the Delta and around the bays have sharply reduced that habitat. Nevertheless, there is evidence that many surviving naturally produced fall Chinook leave fresh water at <55 mm length. Juvenile Chinook from other runs are older and larger when they enter the estuary, and probably pass through it more rapidly. Presumably, these have been less directly affected by loss of tidal habitat, but are also affected by degradation of the estuarine ecosystem. The effects of Delta diversions on Chinook vary strongly by run and river of origin; surprisingly few Sacramento River fall Chinook have been recovered at the diversions. Central Valley Chinook, especially fall Chinook, are strongly affected by hatchery culture that reduces juvenile life-history diversity, probably results in density-dependent mortality in the estuary, and presumably reduces fitness for natural reproduction. Hatchery culture diverts juvenile fall Chinook away from, and precludes for selection for, the life history trajectories followed by most naturally produced fish, to which more attention should be given.

Mammals of China Camp State Park and Rush Ranch Open Space Preserve

Abstract: China Camp State Park is primarily a forested area with a fringing saline marsh while the Rush Ranch Open Space Preserve has large brackish marshes backed by grass-covered hills. The emphasis of this chapter is on small mammals common to both areas, i.e. endangered salt marsh harvest mice and several rare shrews. Both China Camp and Rush Ranch contain significant stretches of intact marsh–upland ecotone that provide refuge for small mammals during periods of high water. This refuge habitat will become even more important as accelerating sea level rise increases marsh inundation and reduces other available cover. Future efforts to conserve populations of salt marsh harvest mice and shrews around San Francisco Bay should focus on protection and expansion of the marsh–upland ecotone.