![[logo] US EPA](https://webarchive.library.unt.edu/eot2008/20081105194905im_/http://www.epa.gov/epafiles/images/logo_epaseal.gif){kind=logo}
Final Report: Spatial Patterns and Biodiversity
EPA Grant Number: R825433C055Subproject: this is subproject number 055 , established and managed by the Center Director under grant R825433
(EPA does not fund or establish subprojects; EPA awards and manages the overall grant for this center).
Center: EERC - Center for Ecological Health Research (Cal Davis)
Center Director: Rolston, Dennis E.
Title: Spatial Patterns and Biodiversity
Investigators: Quinn, James , Jassby, Alan D. , Moyle, Peter
Institution: University of California - Davis
EPA Project Officer: Levinson, Barbara
Project Period: October 1, 1996 through September 30, 2000
RFA: Exploratory Environmental Research Centers (1992)
Research Category: Center for Ecological Health Research , Targeted Research
Description:
Objective:The objective of this research project was to assemble and integrate a large variety of biodiversity databases and geographic information system (GIS) resources. This research project allowed for a number of unique analyses that can be coupled closely with other modeling and ecosystem projects to help determine such things as species composition, habitat availability, population estimates, risks of toxic substances to wildlife, and nonpoint source loading to rivers.
Summary/Accomplishments (Outputs/Outcomes):Our computer center, created de novo at the beginning of the grant, has developed into a national center for GIS and environmental database design and dissemination, and recently has been named the California Information Node (http://cain.nbii.gov/ ) of the National Biological Information Infrastructure (NBII) (one of NBII's five regional federal data centers established by Congress in 2000). Since the founding of the Center for Ecological Health Research (CEHR), a particular focus for computational activities was on biodiversity applications, including:
• Designing park and natural reserve systems to effectively capture and protect regional and global biodiversity.
• Assessing and predicting locations of, and suitable habitats for, rare and endangered species.
• Developing probabilistic models for viability of small populations, particularly long-lived species with complex age structures.
• Creating database tools for assessing potential impacts of environmental toxins on sensitive or indicator wildlife species.
• Producing maps and threat profiles for species in California that are important for conservation.
• Developing data structures, metadata and cataloging tools, controlled vocabularies, and information exchange standards to serve protected areas regionally, nationally, and globally.
• Developing an information framework for invasive species to support early detection and identification, early warning, rapid response, and international data exchange.
• Providing biodiversity Web resources to scientists, the agency community, and the interested public.
In addition to developing databases, models, and computational and Web services, this research project represented a major point of contact, integrating CEHR activities into state and regional programs for assessing and protecting biodiversity. Many of the resources begun under this project were adopted and further supported by various programs within the California Biodiversity Council process (representing 28 federal, state, and regional natural resource agencies, including U.S. Environmental Protection Agency [EPA] Region 9). Investigators and graduate students supported by this research project represented the University of California–Davis at many functions; served on interagency technical, advisory, and standards committees; and took a core role in assembling and integrating a body of biodiversity information for California. Most of the projects received substantial matching funding from partner agencies, and many involved agency collaborators working on campus.
The following activities were accomplished:
• With additional Park Service support, the national databases for
species occurrences in national parks (http://ice.ucdavis.edu/nps/ 
), NPFlora
and NPFauna, largely were completed, and since have been taken over by National
Park Service. Expanded international versions were developed for Man and the
Biosphere Program biosphere reserves, World Heritage sites, and other globally
important parks and natural preserves (see http://ice.ucdavis.edu/mab ). This
resource now has data for vertebrates and vascular plants from thousands of
sites in more than 160 countries, making it perhaps the most geographically
extensive international biodiversity database now in existence. It has provided
a testing ground for methods of taxonomic and metadata integration among diverse
international data resources, and is one of the first ecological data sources
being supported by the United States for inclusion in the recently established
Global Biodiversity Information Facility. California-specific versions were
developed for California State parks and some private holdings, along with
Observe; software to enter and manage reports of occurrences of individual
sightings or collections of species. These have become the main information
systems used by the California Parks System to manage biodiversity information.
• Graduate student Paul Randall created the first online representation
of California fish diversity (http://ice.ucdavis.edu/aquadiv/ ). Dr. Randall's
thesis used these data to test models of fish distributions in poorly surveyed
areas, mostly those separated from major river systems by barriers such as
waterfalls or dams. The maps, particularly of invasive species, have been used
widely by the U.S. EPA and other water agencies to assess the condition of
watersheds and to set priorities for restoration activities.
• Forest Service biologist and graduate student Carlos Davidson mapped
native and current distributions of amphibians in the Central Valley and Sierra
Nevada (http://ice.ucdavis.edu/aquadiv/amphib/amphib.html ) to assess the extent
and causes of amphibian declines in the region. The results suggest that a
combination of exposure to agricultural chemicals and stocking of waterways
by predatory fish explains most of the pattern (Davidson, et al., 2001).
• Graduate student Kimberly Keating developed and tested statistical methods to assess the number of rare species probably missed by biological surveys using different methods and intensities of sampling. With U.S. Geological Survey (USGS) funding, he also reconstructed an 800-year fire history of Glacier National Park and assessed its impact on the distributions of rare plants and beetles.
• With matching support from the California Environmental Protection
Agency, CEHR researchers developed an analytical framework and software for
estimating impacts of particular toxins on particular species of wildlife.
The result is the widely used, online Cal/Ecotox database (http://www.oehha.org/cal_ecotox/default.htm ;
see Donahoe, 2000).
• Working with the California Native Plant Society, CEHR researchers,
especially Carrie Shaw, James Thorne, and Jeff Kennedy, helped develop the
consensus classification of California vegetation that now is being incorporated
into the National Vegetation Mapping Project, and also developed the online
version of the resulting manual (http://www.ice.ucdavis.edu/cnps/ ). With the
same partners, our biodiversity group also maintains a catalog of California
vegetation maps and related resources (http://icemaps.des.ucdavis.edu/vegmap/ ).
• Project researchers have been active in invasive species informatics nationally and internationally. Drs. Quinn and Meese organized international workshops on invasive species data, metadata, and interoperability standards (National Center for Ecological Analysis and Synthesis, Santa Barbara, 1999; Denver, 2000; and two in Davis in 2001 and 2002, all cosponsored by the International Office at USGS-Biological Research Development). As part of these workshops, we authored the U.S. proposal for international data sharing presented and adopted at Inter-American Biodiversity Information Network (Summit of the Americas) meetings in Brasilia in 1999, and authored software used to implement large parts of it with World Bank support in 2000. Dr. Quinn also collaborated with informatics experts at the Commission for Environmental Cooperation (North American Free Trade Agreement) on extending this work into aquatic species and modeling invasion risks, as part of the North American Biodiversity Information Network (NABIN), and served for 3 years on NABIN's technical advisory committee. These efforts now are being integrated into a global initiative, the Global Invasive Species Information Network, with Dr. Quinn as a coorganizer.
• Data, analysis, and software development created by our decision support group have supported decisions by the California Resources Agency. California has never had a comprehensive species distribution and protection system. Projects undertaken by our decision support group have provided a crucial step in that direction, and state parks are the first of many governmental consumers to use the products for land acquisition decisions. The California Resources Agency is using these data. In addition, a graduate student, Mike Byrne, hired from the Institution of Civil Engineers (ICE) after his graduation, will use these data to begin a more comprehensive California species conservation strategy.
• This research project’s advancement of new techniques in plant community and habitat classification mapping has led to improved procedures by local and state government in creating general plans and infrastructure improvements. Three California counties, Napa, Lake, and Mendocino, now are using techniques developed during this research project, and 12 more counties actively are considering this approach to land classification and conservation information management. This development has influenced the U.S. Forest Service, the California Department of Forestry and Fire Protection, and the historic mapping agencies for California to begin modifications of their own systems to comply with this direction.
• The methods for the integration of multiscalar, thematically diverse spatial and tabular data developed during this research project have created major opportunities for governmental units to improve the quality and timing of their environmental decision processes. The most notable adoption of these techniques to date has been the California Department of Transportation, which provided ICE with a large award to operationalize these techniques specifically for the very early detection of potentially significant environmental impacts related to highway projects. It is the estimate of the Department of Transportation that the techniques developed will save them millions of dollars per project, and will cut months and even years off of the total project planning and development cycle.
Supplemental Keywords:ecosystem, ecosystem protection, environmental exposure and risk, geographic area, international cooperation, water, terrestrial ecosystems, aquatic ecosystem, aquatic ecosystem restoration, aquatic ecosystems and estuarine research, biochemistry, ecological effects, ecological indicators, ecological monitoring, ecology and ecosystems, environmental chemistry, restoration, state, water and watershed, watershed, watershed development, watershed land use, watershed management, watershed modeling, watershed restoration, watershed sustainability, agricultural watershed, exploratory research environmental biology, California, CA, Clear Lake, Lake Tahoe, anthropogenic effects, aquatic habitat, biogeochemical cycling, ecological assessment, ecology assessment models, ecosystem monitoring, ecosystem response, ecosystem stress, environmental stress, environmental stress indicators, fish habitat, hydrologic modeling, hydrology, integrated watershed model, lake ecosystems, lakes, land use, nutrient dynamics, nutrient flux, water management options, water quality, wetlands. , Ecosystem Protection/Environmental Exposure & Risk, Water, INTERNATIONAL COOPERATION, Scientific Discipline, RFA, ECOSYSTEMS, Water & Watershed, Restoration, Aquatic Ecosystem Restoration, Aquatic Ecosystems & Estuarine Research, Terrestrial Ecosystems, Aquatic Ecosystem, computing technology, Biochemistry, Environmental Microbiology, Fate & Transport, Watersheds, Monitoring/Modeling, ecological impact, contaminant transport models, computer simulation modeling, aquatic, fate and transport, watershed management, watershed restoration, database, computer science, data management, decision support systems, ecological research, ecology assessment models, aquatic modeling, alternative mechanistic models, hydrological transport model, analytical models, material transport, GIS, ambient particle properties, aquatic ecosystems, data analysis, ecosystem assessment, environmental stress, sediment transport, watershed sustainablility, hydrology, modeling, watershed influences, restoration strategies, ecosystem stress, ecological models, biodiversity, habitat, integrated watershed model
Relevant Websites:
http://cain.nbii.gov/
http://ice.ucdavis.edu/nps
http://www.ice.ucdavis.edu/mab
http://ice.ucdavis.edu/aquadiv/
http://ice.ucdavis.edu/aquadiv/amphib/amphib.html
http://www.oehha.org/cal_ecotox/default.htm
http://www.ice.ucdavis.edu/cnps/
http://icemaps.des.ucdavis.edu/vegmap/
http://www.iabin-us.org/meetings/iabin_tech_brasilia_4-99/tech_full_eng.htm
http://ice.ucdavis.edu/cehr/
Progress and Final Reports:
1999 Progress Report
2000 Progress Report
Original Abstract
Main Center Abstract and Reports:
R825433 EERC - Center for Ecological Health Research (Cal Davis)
Subprojects under this Center:
(EPA does not fund or establish subprojects; EPA awards and manages the overall grant for this center).
R825433C001 Potential for Long-Term Degradation of Wetland Water Quality Due to Natural Discharge of Polluted Groundwater
R825433C002 Sacramento River Watershed
R825433C003 Endocrine Disruption in Fish and Birds
R825433C004 Biomarkers of Exposure and Deleterious Effect: A Laboratory and Field Investigation
R825433C005 Fish Developmental Toxicity/Recruitment
R825433C006 Resolving Multiple Stressors by Biochemical Indicator Patterns and their Linkages to Adverse Effects on Benthic Invertebrate Patterns
R825433C007 Environmental Chemistry of Bioavailability in Sediments and Water Column
R825433C008 Reproduction of Birds and mammals in a terrestrial-aquatic interface
R825433C009 Modeling Ecosystems Under Combined Stress
R825433C010 Mercury Uptake by Fish
R825433C011 Clear Lake Watershed
R825433C012 The Role of Fishes as Transporters of Mercury
R825433C013 Wetlands Restoration
R825433C014 Wildlife Bioaccumulation and Effects
R825433C015 Microbiology of Mercury Methylation in Sediments
R825433C016 Hg and Fe Biogeochemistry
R825433C017 Water Motions and Material Transport
R825433C018 Economic Impacts of Multiple Stresses
R825433C019 The History of Anthropogenic Effects
R825433C020 Wetland Restoration
R825433C021 Sierra Nevada Watershed Project
R825433C022 Regional Transport of Air Pollutants and Exposure of Sierra Nevada Forests to Ozone
R825433C023 Biomarkers of Ozone Damage to Sierra Nevada Vegetation
R825433C024 Effects of Air Pollution on Water Quality: Emission of MTBE and Other Pollutants From Motorized Watercraft
R825433C025 Regional Movement of Toxics
R825433C026 Effect of Photochemical Reactions in Fog Drops and Aerosol Particles on the Fate of Atmospheric Chemicals in the Central Valley
R825433C027 Source Load Modeling for Sediment in Mountainous Watersheds
R825433C028 Stress of Increased Sediment Loading on Lake and Stream Function
R825433C029 Watershed Response to Natural and Anthropogenic Stress: Lake Tahoe Nutrient Budget
R825433C030 Mercury Distribution and Cycling in Sierra Nevada Waterbodies
R825433C031 Pre-contact Forest Structure
R825433C032 Identification and distribution of pest complexes in relation to late seral/old growth forest structure in the Lake Tahoe watershed
R825433C033 Subalpine Marsh Plant Communities as Early Indicators of Ecosystem Stress
R825433C034 Regional Hydrogeology and Contaminant Transport in a Sierra Nevada Ecosystem
R825433C035 Border Rivers Watershed
R825433C036 Toxicity Studies
R825433C037 Watershed Assessment
R825433C038 Microbiological Processes in Sediments
R825433C039 Analytical and Biomarkers Core
R825433C040 Organic Analysis
R825433C041 Inorganic Analysis
R825433C042 Immunoassay and Serum Markers
R825433C043 Sensitive Biomarkers to Detect Biochemical Changes Indicating Multiple Stresses Including Chemically Induced Stresses
R825433C044 Molecular, Cellular and Animal Biomarkers of Exposure and Effect
R825433C045 Microbial Community Assays
R825433C046 Cumulative and Integrative Biochemical Indicators
R825433C047 Mercury and Iron Biogeochemistry
R825433C048 Transport and Fate Core
R825433C049 Role of Hydrogeologic Processes in Alpine Ecosystem Health
R825433C050 Regional Hydrologic Modeling With Emphasis on Watershed-Scale Environmental Stresses
R825433C051 Development of Pollutant Fate and Transport Models for Use in Terrestrial Ecosystem Exposure Assessment
R825433C052 Pesticide Transport in Subsurface and Surface Water Systems
R825433C053 Currents in Clear Lake
R825433C054 Data Integration and Decision Support Core
R825433C055 Spatial Patterns and Biodiversity
R825433C056 Modeling Transport in Aquatic Systems
R825433C057 Spatial and Temporal Trends in Water Quality
R825433C058 Time Series Analysis and Modeling Ecological Risk
R825433C059 WWW/Outreach
R825433C060 Economic Effects of Multiple Stresses
R825433C061 Effects of Nutrients on Algal Growth
R825433C062 Nutrient Loading
R825433C063 Subalpine Wetlands as Early Indicators of Ecosystem Stress
R825433C064 Chlorinated Hydrocarbons
R825433C065 Sierra Ozone Studies
R825433C066 Assessment of Multiple Stresses on Soil Microbial Communities
R825433C067 Terrestrial - Agriculture
R825433C069 Molecular Epidemiology Core
R825433C070 Serum Markers of Environmental Stress
R825433C071 Development of Sensitive Biomarkers Based on Chemically Induced Changes in Expressions of Oncogenes
R825433C072 Molecular Monitoring of Microbial Populations
R825433C073 Aquatic - Rivers and Estuaries
R825433C074 Border Rivers - Toxicity Studies