The Science Fellows program is a project that brings together young scientists, CALFED agency scientists and senior research mentors in collaborative data analysis and research projects relevent to ecosystem management and water supply reliability questions.
The CALFED Science Fellows Program will put out a call annually for research proposals from junior scientists (with the backing of their research mentors) for analyses of the immense monitoring databases collected and maintained by the implementing agencies.
Lindsay Sullivan is postdoctoral fellow at the Romberg Tiburon Center at San Francisco State University. She is studying the trophic role of zooplankton and related questions surrounding their feeding, growth and reproductive behaviors. She earned a doctorate in oceanography from the University of Rhode Island in Kingston in 2006. Her doctoral research examined the feeding ecology of the ctenophore, Mnemiopsis leidyi. More recently, she began looking at the prey selection of larval and juvenile plankton-eating fish in the San Francisco Estuary and its relation to the population success of Delta smelt and other fishes.
Sullivan has received several awards in recognition of the achievement of female graduate students and is now active in supporting women in academia. She has twice won the Ann Durbin Award in biological oceanography, awarded in memory of Ann Durbin, a biological oceanography professor at the University of Rhode Island. Sullivan is also a member of P.E.O Sisterhood, an Iowa-based international organization promoting educational opportunities for women.
Progress Report Year 1 [SullivanYr1.pdf]
Progress Report Year 2 [SullivanYr2.pdf]
Final Report [SullivanFinal.pdf]
Prey Selection of Larval and Juvenile Planktivorous Fish in the San Francisco Estuary
R/SF-15 Jan. 07–Dec. 08
Lindsay Sullivan, SFSU, 415.435.7127,
In the last two decades, there has been an inexplicable shift in the species composition of zooplankton in the brackish waters of the San Francisco Estuary. Today, for reasons that are not understood, the most abundant copepod is the introduced Limnoithona tetraspina. Because this species is smaller than the historically dominant calanoid species Eurytemora affinis and Pseudodiaptomus forbesi, the apportioning of the total zooplankton biomass has changed, too. To look at what this means for plankton-eating fish, the CALFED Fellow conducted laboratory feeding-experiments with larval delta smelt and striped bass showing that both delta smelt and bass consume L. tetraspina. The peak abundance of the copepod, however, does not occur during either species’ larval stage. Information on prey-consumption patterns and the mechanisms that control them has direct implications for efforts to restore pelagic fish populations, particularly delta smelt.
Brian Sardella is a postdoctoral fellow in the department of animal science at UC Davis. He studies how fish adapt to environmental stress; his current research focuses on how sturgeon in the San Francisco Bay-Delta respond to changes in temperature and salinity. He earned a doctorate in zoology from the University of British Columbia in Vancouver in 2006. His doctoral research examined temperature and salinity tolerances of Mozambique tilapia in the Salton Sea in Riverside and Imperial counties.
Sardella comes to fisheries science with a background in general vertebrate physiology. He earned a master’s in biology from California State University, Chico in 2002. His thesis examined the effects of human activities on grebe nesting at Eagle Lake in Lassen, Calif. A native Californian, Sardella said the state’s waterways and native species are important to him on a personal level. He hopes his research will enhance restoration of the Bay-Delta and mitigate effects of global climate change.
Progress Report Year 1 [SardellaYr1.pdf]
Progress Report Year 2 [Sardella_YR2.pdf]
Temperature and Salinity Effects on the Physiology of White Sturgeon
R/SF-16 Jan. 07–Jan. 09
Brian Sardella, UCD, 604.822.3378,
This CALFED Fellow is conducting experiments on white and green sturgeon to better understand the effects of water temperature and salinity on the animals’ stress levels. In one experiment, the fellow calculated critical thermal maxima for green sturgeon at three different salinities and through this work showed that salinity does indeed influence the animal’s thermal tolerance, something that before has been speculated but not directly measured. In another experiment, he measured stress levels in fish exposed to a range of water temperatures and found that the animals have an amazingly robust thermal tolerance. Follow-up experiments have shown that fish respond to thermal and saline stress by increasing expression of a heat shock protein and the enzyme caspase, involved in apoptosis (programmed cell death), and can compensate for large disturbances in plasma ionic balance. In other words, sturgeons’ thermal tolerance and salinity acclimation are linked: fish respond to temperature based on salinity and to salinity based on temperature. The findings suggest that during the heat of summer variable salinity levels may result in species selecting otherwise suboptimal habitat areas or in high levels of fish unable to migrate. The CALFED Fellow says that these findings should be factored into management decisions.
Christine Whitcraft is a postdoctoral fellow at the Romberg Tiburon Center at San Francisco State University. She studies wetlands ecology and conservation and the effects of invasive, exotic plants on native wetland food webs. She earned a doctorate in biological oceanography from Scripps Institution of Oceanography in 2007. Her doctoral research examined the effects of invasive salt cedar trees (also known as tamarisk) on wetland plants, animals and the local food web. She also examined links between tidal flushing, sea grass abundance and local food webs.
“With hurricane Katrina and the Christmas tsunami in southern Asia, we saw that wetlands are important for our well being,” Whitcraft said, explaining her interest in wetlands conservation, “but we don’t quite know the mechanisms by which they function.” Her interest in wetlands and invasive species ecology began after college, while an intern with the Nature Conservancy in Delaware and the Smithsonian Environmental Research Center in Maryland in 1999.
Progress Report Year 1 [WhitcraftYr1.pdf]
Progress Report Year 2 [WhitcraftYr2.pdf]
Final Report [WhitcraftYr3.pdf]
Final Project Summary
Pepperweed's Ecosystem Impacts in Suisin Marsh: Methods for Control. Whitcraft, C., R/SF-17 05.01.2007 - 06.30.2009. [R-SF-17-Whitcraft.pdf]
Role of Exotics as Ecosystem Engineers Affecting Estuarine Food Webs in Suisan Marsh
R/SF-17 Feb. 07–Feb. 09
Christine Whitcraft, SFSU, 415.338.3704,
Invasive species are arguably one of the most formidable obstacles to restoring marsh habitats in the San Francisco Bay-Delta. To improve the chances of restoration success, this project is comparing the efficacies and nontarget impacts of multiple herbicides in eradicating perennial pepperweed in Suisun Marsh. The CALFED Fellow and partners at the Solano Land Trust report that both the type of herbicide and the timing of spraying are critical to success. The fellow has also been studying the ecological impacts of pepperweed in different habitats at the marsh. Among the findings of this component of the project: Plants growing in the transition zone between grassland and marsh have a profound impact on native plant and insect communities, potentially related to an observed increase in soil humidity; pepperweed poses much less of an environmental problem in areas of greater tidal inundation.
Christa Woodley is a doctoral fellow in ecology at the center for watershed sciences at UC Davis. She studies the emerging field of conservation physiology and is especially interested in understanding how global climate change, habitat loss, genetic “pollution,” invasive species and toxic chemicals threaten the environment. Her doctoral research looks at the physiological and behavioral responses of Sacramento perch to changing water quality—information she hopes will help managers protect and restore fishes in the San Francisco Bay-Delta.
Woodley earned a master’s of science from the College of Marine Sciences at the University of Southern Mississippi in 2001 for her research on the effects of habitat loss on the hormones, metabolism, growth and behavior of coastal marine fishes in Mississippi. She has been an assistant fisheries ecologist at the University of Southern Mississippi, a scientific leader for the university’s Southeast Area Monitoring and Assessment Program, and an assistant fisheries biologist at NOAA Fisheries in Miami.
The Impacts of Global Climate Change on Delta Fishes: Predicting Fish Abundance, Distribution and Community Changes
R/SF-18 Jun. 07–May 10
Christa Woodley, UCD, 530.400.5871,
Global warming is predicted to reduce rainfall, raise sea level and enhance evaporation in the San Francisco-Sacramento region. This project looks at what this may mean to the distribution, foraging opportunities, growth and reproduction of the region’s native and invasive fishes. The CALFED Fellow is also studying the physiological responses of select fishes to various scenarios of future climate conditions. This research complements CALFED’s Computational Assessments of Scenarios of Change for the Delta Ecosystem project, the objective of which is to understand how the regional ecosystem might respond to a few plausible scenarios of climate change.
Robert Schroeter is a doctoral fellow in ecology in the department of wildlife, fish and conservation biology at UC Davis. He studies aquatic ecology and is especially interested in understanding the impact of exotic species on native fishes. His doctoral thesis examines the ways native fishes use brackish tidal marshes in the San Francisco Estuary and how non-native species and diminished water quality affect them.
He earned a master’s in biology from the University of Nevada in Reno in 1998. His research looked at the effects of an introduced brook trout on native cutthroat trout in mountain streams in eastern Nevada. Schroeter has taught courses at both UC Davis and the University of Nevada and hopes to become a science teacher. “I would like to open students’ eyes to the plight of native species and ecosystems,” he said.
Temporal and Spatial Patterns in Abundance and Production in Pelagic Organisms in the Low Salinity Zone (Suisan Marsh, Bay and Delta) of the San Francisco Estuary with Insight into Trophic Position and Impacts of Alien Invasive Species
R/SF-19 Dec. 06–Nov. 09
Robert Schroeter, UCD, 530.219.9693,
The goal of this project is to find answers to what has caused plummeting species abundances in the upper San Francisco Estuary. Taking advantage of multiple data sets, the CALFED Fellow is comparing habitats with extensive population declines (e.g., Suisun, Honker and Grizzly Bays and lower reaches of the Sacramento and San Joaquin Rivers) to those that have maintained relatively high numbers (e.g., Suisun Marsh) to identify environmental conditions and biological factors that may explain differences. As part of this investigation, the fellow will study the feeding ecology of several non-native invasive species (e.g., gelatinous zooplankton, caridean shrimp, various polychaetes and clams) that may be contributing to the observed decline of both estuary zooplankton and fishes.
Russell Perry is a doctoral fellow in the department of aquatic and fishery science at the University of Washington, Seattle. He studies salmon and is especially interested in understanding how individual salmon behaviors affect the survival rate of the entire population. Perry’s interest in salmon began while working a summer job with the U.S. Forest Service in Idaho, surveying and identifying endangered fish. “I saw these salmon that had migrated more than a thousand miles inland,” Perry said. “Their journey from egg to adult, to complete their life cycle, was amazing.”
Perry decided to study fisheries management at Utah State University, and after earning his bachelor’s degree in 1995 was hired as a fisheries technician at the U.S. Geological Survey’s Columbia River Research Laboratory in Cook, Washington. He went on to earn a master’s degree in resource and environmental management from Simon Fraser University in Canada in 2002. His thesis looked at the effects of suspended sediments on food webs supporting juvenile chinook salmon in the Yukon River.
Progress Report Year 1 [PerryYr1.pdf]
Final Report [PerryYr3.pdf]
Final Project Summary
Route-Specific Survival of Juvenile Salmon Migrating through the Sacramento-San Joaquin Delta.Perry, R., R/SF-20 11.01.2006 - 10.31.2009. [R-SF-20-Perry.pdf]
Estimating Route-specific Survival and Distribution of Juvenile Salmonids Migrating Through the Sacramento-San Joaquin River Delta
R/SF-20 Nov. 06–Oct. 09
Russell Perry, UW, 206.221.5455,
A model has been developed to predict the survival statistics for migrating salmon along different routes in the Sacramento-San Joaquin Delta. Based on the model, salmon have a 35 percent chance of being entrained into the interior delta when the Delta Cross Channel is open and a 9 percent chance during times when it is closed. Although standard errors were large, estimated fish mortality rates through the interior delta were higher than in the Sacramento River, consistent with previous research. The interior, however, was less important than other routes to total fish survival, due to the small number of fish braving the passage. To date few studies have combined simultaneous measurements of water and smolt movements. The Department of Water Resources will use the model to evaluate the effects of various water export options on salmon populations.
Alexander Parker is a postdoctoral fellow at the Romberg Tiburon Center at San Francisco State University. He studies microbial biogeochemistry and is particularly interested in identifying the degree to which bacteria are part of the base of the marine food web. He has measured carbon cycling by bacteria in the perpetually cold Arctic Ocean and recently participated in a National Science Foundation “Biocomplexity in the Environment” program to explain the relatively low primary productivity in parts of the equatorial Pacific Ocean.
He earned a doctorate in oceanography from the University of Delaware in Newark in 2004. His doctoral research examined the flow of carbon and nitrogen through bacteria and phytoplankton at different times and places in the Delaware Estuary. A central theme of his research is the use of radioactive and stable isotope tracers for measuring carbon and nitrogen fluxes. He plans to continue to develop and apply novel approaches to studying microbes to better understand their role in controlling carbon and nitrogen cycles in the San Francisco Bay-Delta.
Progress Report Year 1 [ParkerYr1.pdf]
Final Report [ParkerYr2.pdf]
Heterotrophic Bacteria and the Food Web of the Low Salinity Zone and Salt Marsh Habitats of the San Francisco Estuary
R/SF-21 Nov. 06–Oct. 08
Alexander Parker, SFSU, 415.338.3746,
This project is based on the premise that the declines in phytoplankton abundance in the less salty areas of the San Francisco Estuary have likely increased the relative importance of bacterial carbon as a food source for higher trophic levels. To examine whether this is indeed true, the CALFED Fellow has been collecting field data that will allow him to compare phytoplankton and bacteria production and their contributions to supporting the local food web. In the project’s second year, the fellow mapped the spatial and temporal patterns in phytoplankton and bacteria activity and abundance, and investigated factors influencing these patterns in restored vs. natural salt marshes. In coming months, he will investigate the flux of inorganic nutrients and dissolved and particulate organic matter in restored and “natural” areas of Suisun Marsh, and the bioavailability of this organic matter.
Allison Luengen is a postdoctoral fellow working jointly at the U.S. Geological Survey in Sacramento and State University of New York at Stony Brook. She studies the pathways by which toxic metals enter the marine food chain and the processes that control their accumulation in the food chain.
She earned a doctorate in environmental toxicology from UC Santa Cruz in 2007. Her doctoral research identified heavy metals preferentially accumulated by phytoplankton in San Francisco Bay. She earned a master’s in environmental toxicology from UC Santa Cruz in 2001. Her master’s thesis showed that chronic heavy metal pollution in San Francisco Bay alters the immune responses of marine mussels, potentially making these mollusks vulnerable to other types of environmental degradation. Luengen was raised on Puget Sound in Washington and is, naturally, an avid sailor and swimmer. “I’ve lived and worked on the water my whole life,” she said. “I want to know what is going on in an environment I love.”
Progress Report Year 1 [LuengenYr1.pdf]
Progress Report Year 2 [LuengenYr2.pdf]
Final Report [LuengenYr3.pdf]
Mercury Interactions with Algae: Effects on Mercury Bioavailability in the San Francisco Bay Delta
R/SF-22 Jan. 07–Dec. 09
Allison Luengen, UCSC, 631.632.3128,
The CALFED Fellow will develop a biogeochemical model for predicting the bioavailability of mercury in the San Francisco Bay-Delta. She is particularly interested in the extent to which dissolved organic matter limits the uptake of mercury by phytoplankton – the entry point for mercury contamination in the marine food web. Initial findings show that higher levels of dissolved organic matter reduce mercury uptake in phytoplankton. The model under development should be of great benefit to the Regional Water Quality Control Boards in evaluating the potential for the high levels of mercury in the Bay-Delta to enter the food chain.
Nat Seavy is a postdoctoral fellow at the U.S. Geological Survey in Hawaii. An ornithologist, he studies how habitat changes—particularly those due to human activities—influence bird population dynamics and survival rates. He is currently creating a manual for monitoring seabirds at national wildlife refuges on the U.S. Pacific Islands.
He earned a doctorate in zoology at University of Florida in Gainesville in 2006 for his research on the effects of forest fire management on bird communities in southern Oregon and northern California. Prior to this, he spent 18 months in the foothills of the Ruwenzori Mountains in Uganda, studying the comparative energetics—the energy used to maintain body temperatures— in East African sunbirds. This research formed the basis of a master’s degree, also earned at the University of Florida.
Progress Report Year 1 [Seavy_YR1.pdf]
Progress Report Year 2 [Seavy_YR2.pdf]
Final Report [Seavy_YR3.pdf]
Measuring and Predicting the Success of Riparian Restoration for Wildlife Populations
R/SF-23 Nov. 06–Oct. 09
Nathaniel Seavy, PRBOCS/UCD, 415.868.0655 x311,
How do bird populations respond to riparian habitat restoration and what can be done to improve bird conservation in restored areas?
What kind of information on bird populations, within the context of riparian habitat restoration, would be most useful to managers? To answer this, the CALFED Fellow distributed a questionnaire to riparian habitat managers and posted the results of the survey online. The fellow has also engaged in dialogs with River Partners, the Sonoma Ecology Center, The Nature Conservancy and the California Department of Fish and Game, as well as researchers at UC Davis, to develop a better understanding of managers’ perspectives and needs. In response to what he has learned, he is developing seasonal fecundity models that can, among other things, enable evaluations of the relative effects of nest predators and brood parasites on bird reproduction. He is also analyzing recapture rates of tagged and released birds to calculate population growth rates in restored areas. In 2008, he used LiDAR scanning data to map bird habitats in the Cosumnes River Preserve in southeastern Sacramento County.
Anthony Clemento is a doctoral fellow in ocean sciences at UC Santa Cruz and the NOAA Southwest Fisheries Science Center in Santa Cruz. He studies molecular genetics and its application to salmon and steelhead conservation. In particular, he would like to identify genes responsible for key life history variations (e.g., size, growth rates, and age at sexual maturity) in salmon and trout.
Clemento was a pre-med major in college who decided to switch to natural resource ecology after completing a field studies program in Nepal, run through the Wildlands Study Program at San Francisco State University. His interest turned to salmon biology during his time with the AmeriCorps Watershed Stewards Project, working with a fisheries biologist at the California Department of Fish and Game in Willits. Clemento went on to pursue a master’s degree in fisheries biology at Humboldt State University. His research used genetic markers to determine the sub-population structure of steelhead trout on the Middle Fork of the Eel River in Northern California. He also helped Caltrans identify highway culverts blocking salmon and trout migrations.
Progress Report Year 1 [Clemento_Year1.pdf]
Progress Report Year 2 [ClementoYr2.pdf]
Final Report [ClementoYr3.pdf]
Validation of a New Method for Population Assessment of Pacific Salmonids Using Genetic Markers
R/SF-24 Nov. 06–Oct. 09
Anthony Clemento, UCSC, 831.420.3906,
The CALFED Fellow is developing a method for tracing the parentage of Central Valley chinook. If successful, this virtual-tagging method will be a powerful new tool for monitoring the effects of hatchery practices, water policy, climate change and fisheries management on salmon populations. To date, the fellow has developed 10 single nucleotide polymorphism markers for chinook that have been included in a Pacific Salmon Commission-funded project to identify genetic stocks of West Coast and Alaska salmon. In collaboration with California Department of Fish and Game, he has sampled fin clips from the entire 2006 and 2007 spring-run broodstock from the Feather River Hatchery. DNA has been extracted from almost 4,000 individuals, and he is now genotyping the broodstock with the most informative nucleotide markers.