CALFED Science Fellows Class of 2005

January 01, 2005
Media Contact— Caitlin Coomber / / 858-534-0580

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.

Margaret Andrew

Margaret Andrew is a native of Athens, Ga., who earned a bachelor’s degree in biology from Stanford University in 2002. She is currently a doctoral student in the Graduate Group of Ecology at UC Davis and a graduate researcher at the Center for Spatial Technologies and Remote Sensing, also at Davis. Broadly, her research focuses on understanding the ways in which people modify and interact with landscapes and ecosystems. In particular, she is interested in biological invasions, factors controlling their spread and their ecological effects. She is currently analyzing remote sensing data from the San Francisco Bay/Sacramento-San Joaquin Delta region to map infestations of Lepidium latifolium (perennial pepperweed). This research will be extended to address traditional ecological questions. Upon completing her doctorate degree, she hopes to become a professor and continue studying biological invasions.

Progress Report Year 1 [AndrewYr1.pdf]

Progress Report Year 2 [AndrewYr2.pdf]

Final Report [Andrew_YR3.pdf]

Final Project Summary
Determining the Factors Controlling Site Invasibility to Lepidium latifolium. Andrew, M., R/SF-10 09.01.2005 - 12.31.2008. [R-SF_10_Andrew.pdf]

Project Abstract

Determining the Factors Controlling Site Invasibility to Perennial Pepperweed
Poject Number: R/SF-10
Project Dates: Sept. 05–Aug. 08
Margaret Andrew/UCD, (530) 753-5092

Perennial pepperweed is a noxious, nonnative weed infesting the San Francisco Bay-Delta. This project has used several years of airborne remote-sensing data to create detailed, accurate maps of perennial pepperweed in the region to, among other things, make inferences about the plant’s habitat requirements. The Solano Land Trust is using these maps to further their efforts to restore Rush Ranch and the Greater Jepson Prairie Ecosystem. In the last year, the CALFED Fellow has learned that the phenology of perennial pepperweed (i.e., the timing of its flowering) is highly variable in time and space. This pattern was evident in remote sensing data. Phenology is important because, among other things, it determines when the most conspicuous stages are present, which influences monitoring. The observed variability in phenology might also be ecologically important since it could explain the variety of conditions under which the weed thrives. The fellow is currently generating annual maps of perennial pepperweed at several sites in the delta, to quantify how fast the weed spreads and how far it is able to disperse, and to see how these population processes are affected by environmental conditions. At one site, she has documented a 50% increase in the infestation area in four years.


Annjanette Dodd

Annjanette Dodd holds two bachelor’s degrees from Humboldt State University (HSU), one in applied mathematics (1992), the other in environmental resource engineering (1997). While a master’s student in the Environmental Systems Program at HSU (1999), she began modeling river flows and sediment transport and decided to pursue a doctorate on this subject in the Department of Environmental Resources Engineering at Utah State University. As part of her thesis research, she is developing a computer model of river flows and sediment transport capable of simulating changes in the composition of riverbed materials and channel topography under different flow scenarios. Based on this work, she is currently a consultant on the design, documentation and testing of a model that simulates the movements of chinook salmon along the salmon-accessible portion of the Sacramento River, including the delta and San Francisco Bay. She is also a part-time faculty member at HSU, where she enjoys teaching undergraduate mathematics and engineering courses. She expects to earn her doctorate in the fall of 2005.

Progress Report Year 1 [DoddYr1.pdf]

Progress Report Year 2 [DoddYr2.pdf]

Final Report [DoddYr3.pdf]

Project Abstract

Development of a Simulation Model of Juvenile Salmon Movement in the Sacramento-San Joaquin Delta
Project Number: R/SF-7
Project Dates: Sept. 05–Aug. 08
Annjanette Dodd/HSU, 707.733.9462,

How do juvenile salmon move through the Sacramento-San Joaquin Delta? The goal of the project is to combine a hydrodynamic model of particle transport and a biological model of fish behavior to simulate the effects of water operations (e.g., reservoir release rates, pumping rates and other operations of the Delta Cross Channel gates) on juvenile salmon migration patterns. The strategy is to find the simplest model consistent with observational data, not to produce a “realistic” model of fish movement. The CALFED Fellow has used ultrasonic salmon tagging data to begin developing a particle-tracking model of fish movement through the delta. The observational data have shown that juveniles as small as 3 and 4 inches in length do not behave as passive particles. In 2008, she began modifying hydrodynamic models to include fish behavior. The results of the project will improve the ability to predict the effects of different flow regimes and water diversions on fish.

John Harrison

John Harrison holds a bachelor’s degree in biology from Brown University (1994) and a doctorate in geological and environmental sciences from Stanford (2003). He is currently a postdoctoral researcher in the Department of Land, Air and Water Resources at UC Davis and a visiting assistant research professor at the Institute of Marine and Coastal Sciences at Rutgers University. In addition, he cochairs an international UNESCO/UNEP-funded scientific working group known as Global NEWS, short for Global Nutrient Export from WaterSheds.

His research focuses on nutrient transport in rivers and ways in which natural and human factors control fluxes, fates and impacts of nutrients (e.g., nitrogen, phosphorus, carbon and silica) from land to sea. While a CALFED Fellow, Harrison will apply global nutrient export models to Central Valley river systems, and refine them as necessary. Using these new models, he will investigate river and coastal nutrient loading under a series of plausible future climate, population and land-use scenarios.

Progress Report Year 1 [HarrisonYr1.pdf]

Progress Report Year 2 [HarrisonYr2.pdf]

Final Report [Harrison_YR3.pdf]

Project Abstract

Modeling Nutrient and Organic Carbon Loads and Sources in Central Valley Watersheds: Taking Existing Monitoring Data to the Next Stage
Project Number: R/SF-8
Project Dates: Sept. 05–Aug. 08
John Harrison/WSU, (360) 546.9210

What are the relative contributions of various land-based sources of dissolved inorganic nitrogen and dissolved organic carbon to the Sacramento-San Joaquin river systems? How are river nitrogen and carbon concentrations, loads and sources likely to change in the coming decades? The CALFED Fellow has developed a model for predicting the effects of climate change, population growth, water demand and land use on nutrient loading in the region. Researchers are using the model to quantify the relative importance of various sources of nitrogen and carbon and how these might change. Once the model has been refined, scientists will input climate and land-use projections for 2030 to forecast changes in dissolved nutrient transport through Central Valley watersheds.

Walter Heady

Walter Heady holds a bachelor’s degree in biology from UC Santa Cruz (1996) and is currently a first-year doctoral student in the Ecology and Evolutionary Biology Department at UC Santa Cruz. Prior to entering graduate school, he was as a biological consultant for habitat conservation plans and environmental impact reports for sensitive species. Much of this work related to monitoring juvenile steelhead in Northern California watersheds. He has also been a watershed analyst for the San Lorenzo Valley Water District and currently participates in several monitoring programs in Monterey Bay National Marine Sanctuary, including a marine mammal project with the Center for Integrated Marine Technologies. His current research interests are in understanding the effects of stream flow, water temperature and food availability on juvenile steelhead growth, survival and movement in the Mokelumne and Consumes rivers.

Progress Report Year 1 [HeadyYr1.pdf]

Final Report [HeadyYr2.pdf]

Winning CALFED Fellow Studies Steelhead Survival - 12-05-08

Project Abstract

Effects of Water Temperature, Stream Flow and Flood Availability on the Growth, Survival and Movement of Central Valley Juvenile Steelhead (Oncorhynchus mykiss) with Implications for Water Management
Project Number: R/SF-11
Project Dates: Sept. 05–Aug. 08
Walter Heady/UCSC, (831) 459-5783

The CALFED Fellow has discovered that two constructed side channels on the lower Mokelumne River provide rearing habitat for juvenile chinook salmon and steelhead and enhance macro-invertebrate abundance and diversity. The fellow is now working in collaboration with the East Bay Municipal Utilities District and Cramer Fish Sciences on an acoustic telemetry project in the area. As of June 2008, 126 wild steelhead have been tracked along standardized transects using a handheld hydrophone. From the acoustic data, the fellow is looking at steelhead habitat associations, movement rates and their survival in different habitats. Some of the topics under investigation: Is in-stream wood important to fish, and when in their life history? Are there mortality hotspots on smolt migration routes? Where and how could this be rectified? In the coming year, the fellow will write up his research and make recommendations on how to integrate his findings into management decisions. Agencies that will receive the report include: CALFED, California Department of Fish and Game, East Bay Municipal Utility District, California Urban Water Association and U.S. Fish and Wildlife Service.

James Hobbs

James Hobbs holds a bachelor’s degree in marine biology (1997) and a doctorate in ecology from UC Davis (2004). He is currently a postdoctoral researcher at the Bodega Marine Laboratory and John Muir Institute for the Environment at UC Davis but during his CALFED Fellowship will be at working in the geography department at UC Berkeley. Concerned by the decline in fish populations worldwide, his research looks at, among other things, the links between degradation of fish nursery habitats and declines, or changes, in recruitment. To do this, he studies the chemical signatures in ear stones in fish, the patterns of larval dispersal and migratory histories of species. He currently has a project in the San Francisco Bay-Delta studying the effects of climate change and human activities (such as water diversions and habitat destruction) on the delta smelt, longfin smelt and Sacramento splittail. Another project in Bodega and Tomales bays focuses on the role of sea grass habitats and ocean circulation on the recruitment of rockfish.

Progress Report Year 1 [HobbsYr1.pdf]

Progress Report Year 2 [HobbsYr2.pdf]

Final Report [HobbsYr3.pdf]

Final Project Summary
Otolith Growth and Microchemistry to Determine Variability in Recruitment Success of Delta Smelt. Hobbs, J., R/SF-9 09.01.2005 - 08.31.2008. [R-SF-9-Hobbs.pdf]

Project Abstract

The Application of Otolith Geochemistry to Determine Stock Structure, Survival and the Relative Impact of Water Exports on the “Threatened” Delta Smelt
Project Number: R/SF-9
Project Dates: Sept. 05–Aug. 08
James Hobbs/UCD, (707) 875-1973

The delta smelt is a small fish found in only one ecosystem in the world: the brackish waters of the San Francisco Estuary. Unfortunately for its survival, about two-thirds of the state’s fresh water is pumped from this same habitat. As a result, untold numbers of smelt larvae are sent through the extensive pumping systems of state and federal water projects. By studying the otolith geochemistry of adult smelt collected during a monitoring survey, the CALFED Fellow has shown that a majority of recruiting delta smelt reside in the North and Central West Delta, rather than the South Delta, where freshwater exports occur. Another important finding has been that the low-salinity habitats in Suisun Bay provide critical nursery areas for juvenile smelt during wet years. During these years, smelt are confined to the delta’s confluence, where they are susceptible to “export.” It also appears that several contingents (life history patterns) exist in the population: those that are spawned in freshwater and then early in life move to low-salinity waters; those that move late to low-salinity waters, and those that reside permanently in freshwater. These contingents likely have evolved to adapt to varying estuarine conditions and have different growth and survival rates. The project’s findings have had a direct impact on the region’s freshwater pumping schedules and have also invigorated interest in restoring the Cache slough area in the North Delta.

Suzanne Langridge

Suzanne Langridge holds bachelor’s degree from Smith College and is currently a doctoral student in environmental studies at UC Santa Cruz. Her thesis examines fundamental ecological interactions between restored riparian habitats in the Sacramento River and neighboring farms. In particular, she is interested in understanding how the movement of organisms between farmed and restored areas (including agricultural pests and enemies of these pests) affects the success of habitat restoration projects. In the future, she plans to use her findings to further restoration and conservation goals in watersheds, focusing on the potential to incorporate agricultural lands and communities into watershed planning and restoration. She has a longtime passion for ornithology and has conducted research, and otherwise assisted in conservation and restoration efforts, of peregrine falcons, bald eagles, endemic Hawaiian birds and southwestern willow flycatchers. She is currently program director of the Santa Cruz bird club and is a founding member of UC Santa Cruz's Campus Food Systems Committee, which seeks to incorporate locally grown organic and socially responsible food products into campus dining facilities

Progress Report Year 1 [LangridgeYr1.pdf]

Progress Report Year 2 [LangridgeYr2.pdf]

Final Report [LangridgeYr3.pdf]

Final Project Summary
Addressing Stakeholder Concerns: Pests and Pest Control in the Sacramento River Conservation Area. Langridge, S., R/SF-12 09.01.2005 - 06.30.2010. [R-SF-12-Langridge.pdf]

Project Abstract

Addressing Stakeholder Concerns: Pests and Pest Control in the Sacramento River Conservation Area
Project Number: R/SF-12
Project Dates: Sept. 05–Aug. 08
Suzanne Langridge/UCSC, (831) 459-3902

Could habitat restoration in the Sacramento River Valley increase the presence of agricultural pests, particularly birds and/or insects that might feed on nearby walnut orchards? The preliminary answer is, “No.” To date, it has been shown that the abundance of agricultural-pest birds (i.e., American crow, Brewer’s blackbird and European starling) can decrease by increasing riparian habitat along the Sacramento River. The fellow reports that two major pests in walnuts, the navel orangeworm and codling moth, were less abundant at orchards surrounded by riparian habitat. There was also a greater density of pest-eating birds, more species of these birds and more attacks on insects by birds near riparian habitat. These findings and others have been incorporated into a report to the Colusa Subreach Planning Committee and have been presented to the Sacramento River Conservation Area Forum Technical Advisory Committee. Members of these committees have various levels of support for and concerns about the effects of restoring former farmland.

J. Toby Minear

J. Toby Minear graduated cum laude with distinction from Colorado College in 1998 with a bachelor's degree in biology and later earned a master's in landscape architecture from UC Berkeley in 2003. His master's thesis looked at southern steelhead habitat and sediment dynamics in Matilija Creek, Southern California. He is now a doctoral student in the school of Landscape Architecture & Environmental Planning at UC Berkeley. His current research examines the long-term effects of dam operations on the physical characteristics of downstream river channels in the Central Valley, California.

He has been a research assistant for various geomorphology projects in the Western United States. In one of these projects, he studied thermal microhabitat use by salmonids. In another, he examined the dynamics of large woody debris in old-growth forests. In his free time, he spends time relaxing in a kayak or raft on the rivers in the Western United States.

Progress Report Year 1 [MinearYr1.pdf]

Final Report [MinearYr2.pdf]

Project Abstract

Long-term Geomorphic Effects of Dams on Rivers in the Central Valley of California: A Comprehensive and Comparative Approach
Project Number: R/SF-13
Project Dates: Sept. 05–Aug. 08
Toby Minear/UCB, (510) 847-4454

Not all dams impact water flows and sediment transport equally. Results from this project have shown that in the Central Valley some dams (e.g., Monticello Dam on Putah Creek and Friant Dam on the San Joaquin River) greatly reduced flows downstream and as a result have effectively frozen sediment transport downstream. Other dams (e.g., Oroville Dam on the Feather River, Folsom Dam on the American River and Shasta Dam on the Sacramento River) continue to release flood flows, down-cutting riverbeds. Recent laboratory experiments have shown that ecologically significant bars are often the first river features to adjust to a reduction in sediment. The bars adjust by down cutting at the toes, leaving the bed relatively flat and with relatively little ecological value. A real-life example of this process is observed on the Trinity River downstream of Lewiston Dam. Findings from this project can be used to evaluate the pros and cons of environmental flows in one watershed vs. another and to more effectively restore habitats downstream of dams.

John Stella

John Stella graduated cum laude in architecture from Yale University in 1988 and earned a master’s degree in Environmental Science, Policy and Management from UC Berkeley in 1998. He is currently a doctoral student in the department of Environmental Science, Policy and Management at UC Berkeley, studying the effects of water policies and human activity on restored cottonwood and willow forests in the San Joaquin Valley. More broadly, he is interested in understanding the biological and physical processes that structure riparian ecosystems. His goal is to pioneer innovative, feasible and scientifically sound methods for restoring ecological functioning of rivers impacted by dams and other human activities.

John has worked extensively as a biological consultant in the private sector and is currently a consultant at Stillwater Sciences, an environmental consulting firm specializing in watershed and riverine science and management applications. He is also a part-time advisor on several field studies and manipulation experiments investigating the links between riparian vegetation and river hydrology. He ultimately aspires to promote ecologically sound land and water use within a university or public resources agency.

Project Abstract

Restoring Non-Equilibrium Riparian Communities in Disturbance-Altered Ecosystems: Implications for River Management and Climate Change
Project Number: R/SF-14
Project Dates: Jan. 06–Dec. 08
John Stella, SUNY/ESF, (315) 470.4902

The Fremont cottonwood stabilizes riverbanks, fixes carbon, produces woody debris and creates complex floodplain habitat for at-risk species of fish and wildlife. The objective of this project is to better understand the ecological factors influencing the health, growth and sustainability of cottonwood forests. The major discovery so far: Along naturally meandering rivers, periodic channel cutoff events create safe zones within which recruitment of cottonwoods is likely to occur. Field data are now being used to develop a conceptual model for how these safe zones arise and evolve, and their importance in sustaining cottonwood forests. Habitat loss and changes in the region’s hydrology have reduced the extent and heath of cottonwood forests. This research may help reverse the decline by identifying optimal floodplain elevations and physical characteristics for native vegetation.

About California Sea Grant

NOAA’s California Sea Grant College Program funds marine research, education and outreach throughout California. Our headquarters is at Scripps Institution of Oceanography, University of California, San Diego; we are one of 33 Sea Grant programs in the National Oceanic and Atmospheric Administration (NOAA), U.S. Department of Commerce.