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Project Work Plan

Greater Everglades Science Program: Place-Based Studies

Project Work Plan FY 2003


Project Title: Across Trophic Level System Simulation Program for the Everglade/Big Cypress Region
Project start date: January 1, 2003 Project end date: December 31, 2004
Project Funding: USGS and DOI's Critical Ecosystems Funding Initiative
Principal Investigator: Dr. Donald L. DeAngelis
Email address:
Phone: 305-284-3973 Fax: 305-284-3039
Mail address: Department of Biology, University of Miami, P. O. Box 249118, Coral Gables, Florida 33124

Other Investigator(s): Dr. Lou Gross
Email address:
Phone: 865-974-4295 Fax: 865-974-3067
Mail address: Department of Ecology and Evolutionary Biology, The University of Tennessee, Knoxville, TN 37996

Other Investigator(s): Dr. Jimmy Johnston
Email address:
Phone: 337-266-8556 Fax:
Mail address: USGS-BRD National Wetland Research Center, 700 Cajundome Road, Lafayette, Louisiana 70506

Other Investigator(s): Antonio Martucci
Email address:
Phone: 337-266-8556 Fax:
Mail address: USGS-BRD National Wetland Research Center, 700 Cajundome Road, Lafayette, Louisiana 70506

Other Investigator(s): Dr. Leonard Pearlstine
Email address:
Phone: Fax:
Mail address: University of Florida, IFAS, 3205 College Avenue, Fort Lauderdale, FL 33314-7799

Project Summary:

An essential component of restoration planning in South Florida has been the development and use of computer simulation models for the major physical processes driving the system, notably models of hydrology incorporating effects of alternative human control systems and non-controlled inputs such as rainfall. The USGS's ATLSS (Across Trophic Level System Simulation) Program utilizes the outputs of such physical system models as inputs to a variety of ecological models that compare the relative impacts of alternative hydrologic scenarios on the biotic components of South Florida. The immediate objective of ATLSS is to provide a rational, scientific basis for ranking the water management scenarios as part of to the planning process for Everglades restoration. The longer term goals of ATLSS are to help achieve a better understanding of components of the Everglades ecosystem, to provide an integrative tool for empirical studies, and to provide a framework monitoring and adaptive management schemes. The ATLSS Program coordinates and integrates the work of modelers and empirical ecologists at many universities and research centers.

There are three tasks in this project. The first (DeAngelis and Pearlstine) involves (1) the coordination of the other tasks, as well as other tasks supported through alternative funding and the development of decision support tools. The second task (Gross) involves the development and running of the ATLSS computer simulation models. The third task (Johnston) involves providing agencies the ability to view and analyze the model output.

Project Objectives and Strategy:

ATLSS (Across Trophic Level System Simulation) program addresses CERP's need for quantitative projections of effects of scenarios on biota of the Greater Everglades and can provide guidance to monitoring in an adaptive assessment framework. It does this through creating a suite of models for selected Everglades biota, which can translate the hydrologic scenarios into effects on habitat and demographic variables of populations.

ATLSS is constructed as a multimodel, meaning that it includes a collection of linked models for various physical and biotic systems components of the Greater Everglades. The ATLSS models are all linked through a common framework of vegetative, topographic, and land use maps that allow for the necessary interaction between spatially-explicit information on physical processes and the dynamics of organism response across the landscape. This landscape modeling approach is the work of USGS scientists and collaborators from several universities.

The South Florida Water Management Model provides hydrology for ATLSS models at a 2 x 2 mile spatial resolution. The ATLSS multimodeling approach starts with models that translate this coarse-scale hydrology output to a finer resolution appropriate for biotic components. This is achieved through use of GIS vegetation maps and empirical information relating hydroperiods with vegetation types, to develop an approximate hydrology at 500 x 500 m resolution from the 2 x 2 mile hydrology model.

The simplest ecological models in the ATLSS family are the Spatially-Explicit Species Index (SESI) models, which compute indices for breeding or foraging potential for key species. These models use the fine resolution hydrology output, combining several attributes of hydrology that are relevant to the well-being of particular species to derive an index value for every 500 x 500 spatial cell in the landscape. This can be done for hydrology data for any given year under any alternative water management scenario. SESI models have been constructed and applied during the Central and Southern Florida Comprehensive Review Study (Restudy) to the Cape Sable seaside sparrow, the snail kite, short- and long-legged wading birds, the white-tailed deer, and the American alligators.

A considerably more detailed model has been developed for the distribution of functional groups of fish across the freshwater landscape. This model considers the size distribution of large and small fish as important to the basic food chain that supports wading birds. It has been applied to assess the spatial and temporal distribution of availability of fish prey for wading birds. This modeling is being extended to crayfish.

Individual-based models, which track the behavior, growth and reproduction of individual organisms across the landscape, have been constructed for the Cape Sable seaside sparrow, the snail kite, The white-tailed deer, the Florida panther and various wading bird species. The models include great mechanistic detail on the behavioral and physiological aspects of these species. An advantage of these detailed models is that they link each individual animal to specific environmental conditions on the landscape. These conditions (e.g., water depth, food availability) can change dramatically through time and from one location to another, and determine when and where particular species will be able to survive and reproduce. ATLSS models have been developed and tested in close collaboration with field ecologists who have years of experience and data from working with the major animal species of South Florida.

The ATLSS integrated suite of models has been used extensively in Everglades Restoration planning. Restoration goals include recovery of unique Everglades species, including snail kites and Florida panthers. The quantity, quality, timing, and distribution of deliveries of water to the Greater Everglades are keys to the restoration of natural functions. The challenge is to provide the hydrologic conditions needed by communities of plants and animals, while maintaining water supplies and flood control for a large and expanding human population. The role of USGS's ATLSS Program is to predict the effects of changes in water management on Greater Everglades species and biological communities, as an aid to identifying and selecting those changes most effective for the restoration effort.

To date, the focus of ATLSS to date has been on the freshwater systems, with emphasis on the intermediate and upper trophic levels. ATLSS will be extended estuarine and near-shore dynamic models once physical system models for these regions are completed. Modeling of the mangrove vegetative community, estuarine fish, crocodiles, and roseate spoonbills is now underway.

An essential aspect of the ATLSS Program is making model output easily accessed and used by client agencies. For this purpose an ATLSS Data Viewer (ADV) has been developed. The ATLSS Data Visualization System was designed to make it simple to view and analyze SESI models. For example, it is possible to zero in on small areas to view detailed effects in parts of a species' range. It is possible sum indices over subregions and perform comparisons of model output with empirical data.

Based in part around the ADV, background work for a spatial decision support system (SDSS) is proposed in which the decision models are tightly integrated with, or directly generated from, geographic information systems (GIS) analyses and display. Spatially-explicit knowledge from which decisions made at specific sites are within the context of conditions proximate and regional to those sites are essential for intelligent ecological restoration and permitting. Examples include determination of areas suitable for viable and sustainable populations (habitat and risk assessment), areas of socioeconomic and environmental conflict, optimization of development footprints to protect natural systems, and hydrological and successional feedback dynamics that influence the landscape.

Potential Impacts and Major Products:

Many of the ATLSS models were used during scenario evaluation (1997-99). In this process, hydrology model output for scenarios was sent from the SFWMD to the U. of Tennessee. Hydrology output was used to drive the following ATLSS models: SESI models:Cape Sable seaside sparrow, snail kite, American alligator, long- and short-legged wading birds, white-tailed deer ). SEIB model: Cape Sable seaside sparrow (SIMSPAR). Spatially explicit number/biomass density model: Freshwater fish (ALFISH). ATLSS output was sent to the Alternative Evaluation Team (AET), composed of representatives of agencies in South Florida, and used extensively in its evaluations and recommendations.

ATLSS models will continue to be used for scenario evaluations for the Comprehensive Everglades Restoration Plan. Improved methods of viewing output data and utilizing it in a Decision Support System (DSS) will be developed. Two aspects of DSS development will be included in this proposal: (1) conceptual models of the DSS scope, analyses, data requirements, integration with agency needs, and limitations and (2) specific technical details and requirements of the DSS components, knowledge models to be created, and ecological models to be integrated. A functioning DSS is not part of this proposal. Rather, it supports the intensive groundwork necessary for successful implementation in later development stages.

Collaborators: Collaborators have included the following: Florida International University, Southwestern Louisiana University, University of Florida, University of Maryland, University of Miami, University of Tennessee, University of Washington, University of West Florida, National Wetland Research Center (USGS), Institute for Bird Populations, Everglades Research Group, Netherlands Institute of Ecology

Clients: National Park Service, U.S. Fish and Wildlife Service.



Title of Task 1: Coordination of the projects and tasks under ATLSS
Task Funding: Critical Ecosystems Studies Initiative, Department of Interior
Task Leaders: Donald L. DeAngelis
Phone: 305-284-1690 FAX:
Email address:
Task Status (proposed or active): Active
Task priority: High
Task Personnel: D. L. DeAngelis

Task Summary and Objectives: Coordinate all of the projects and tasks under ATLSS. Work with collaborators in planning their projects. Interact with agencies and interagency teams in South Florida to ascertain their needs for modeling and evaluation of restoration plans and determine how ATLSS can best meet those needs. Lay the groundwork for a decision support system.

Work to be undertaken during the proposal year and a description of the methods and procedures:

During the next two years there will be especially heavy need for working with the DOI agencies (National Park Service and Fish and Wildlife Service) to determine the needed ATLSS model simulations to be performed with respect to CERP. Also develop the capability at the University of Miami to test and modify these models where necessary, by working with DOI agencies and others in South Florida who have pertinent. There is now an urgent need to test a number of different water regulation scenarios in a short time, as well as to be able to make minor alterations in the models. This requires rapid turnaround of results (within a day or two). The leader of this task will work to achieve this goal both through interactions with Lou Gross of the University of Tennessee and Jimmy Johnston of the National Wetlands Research Center, as well as by improving the capabilities at the University of Miami.

In addition, the ATLSS Program will support a collaboration with Dr. Leonard Pearlstine to take steps towards the development of a Decision Support System. This is to go beyond ad-hoc policy formulation to an analytical and computer-supported platform for effective management and policy-making. Using available data to make informed decisions and recognizing research gaps to future study in a tractable manner is non-trivial. Support methodologies that help authorities involved in ecological restoration sort out all the decision variables and parameters, problem solving heuristics, and appreciate the impacts of potential policy actions is critical to successful planning and management (Kersten et al 2000).

Decision support systems (DSS) are broadly defined as computer-based systems used to aid decision makers using data and models to solve unstructured problems (Sprague and Carlson 1982). These model and knowledge-based system tools become necessary when complex geographic or domain interrelationships are considered. The development of a computerized DSS makes economic sense in integrated Everglades restoration efforts because of the large amount of data that must be collected and processed to produce and analyze decision alternatives, decision-making procedures that are applied to many cases within a domain or periodically repeated, many potential users, short time frames for making critical decisions, the expense of accessing top-level expertise, and the possibility of a large number of alternative decisions with significant and different implications.

Planned Outreach:

Title of Task 2: Development of Selected Model Components of an Across-Trophic-Level System Simulation (ATLSS) for the Wetland Systems of South Florida
Task Leaders: Louis J. Gross, University of Tennessee
Task Funding: USGS or DOI's Critical Ecosystems Studies Initiative
Phone: 865-974-4295
FAX: 865-974-3067
Task Status (proposed or active): Active
Task priority: High
Task Personnel: Louis J. Gross, Director, The Institute for Environmental Modeling, Univ. Tenn.; Staff of The Institute for Environmental Modeling including: Dr, Brian Beckage, Jon Cline, Jane Comiskey, Scott Duke-Sylvester, Dr. Holly Gaff, Mark Palmer, Michael Peek, Rene Salinas; Dr. Donald DeAngelis (USGS Program Manager) and numerous collaborators in USGS and a variety of South Florida agencies and universities

Task Summary and Objectives: The ongoing goals in this project have been to produce models capable of projecting and comparing the effects of alternative hydrologic scenarios on various trophic components of the Everglades. The methodology involves: 1) a landscape structure; 2) a high resolution topography to estimate high resolution water depth across the landscape; 3) models to calculate spatially explicit species indices (SESI) for breeding and foraging success measures across the landscape; 4) spatially explicit individual-based (SEIB) computer simulation models of selected species populations; and 5) a variety of visualization and evaluation tools to aid model development, validation, and comparison to field data. Included in this are numerous sub-projects for different species, vegetation succession, analysis of alternative approaches to developing high resolution, models which deal with estuarine systems, methods to allow users from a variety of agencies to access and run the models, and methods to enhance the computational efficiency of the simulations. The continuing general objective is to provide a flexible, efficient collection of methods, utilizing the best current science, to evaluate the relative impacts of alternative hydrologic plans on the biotic systems of South Florida. This is done in a spatially-explicit manner which allows different stakeholders to evaluate the impacts based upon their own criteria for the locations and biotic systems under consideration.

Work to be undertaken during the proposal year and a description of the methods and procedures:

The proposed work has numerous sub-tasks, with a variety of connections between them. The following list provides a summary of activities to be undertaken over the next two years of this ongoing set of modeling projects.

Modification of High Resolution Topography

In mid or late 2002 the SFWMD will be releasing a revised calibration/validation simulation of the SFWMM that will include hydrologic conditions through 2000. The current version stops after 1995. This will allow an updated ATLSS High Resolution Topography to be computed and verified in combination with the High Accuracy Elevation Data that is being provided by the USGS, as well as utilizing the most current FGAP vegetation map from the Florida Gap analysis project. This will provide an updated, current basis for evaluation of all the ATLSS models utilizing recent hydrology.

Modification of High Resolution Hydrology

In combination with the modification of the ATLSS High Resolution Topography is an associated modification of the methods by which water is distributed across the landscape according to the High Resolution Hydrology model. This revised hydrology will be utilized in all the ATLSS model evaluation runs as well as linked with the estuarine hydrology being developed by the SICS model in USGS.

Development of ATLSS Vegetation Succession Models

Two reports have been developed by TIEM which detail the hydrologic conditions associated with each of the vegetation alliance types included in the Florida Gap map, and provide estimates of the transition rate from one alliance to another based upon hydrologic condition dynamics and disturbance time. The major objective for this task now is to implement the results of these reports into a dynamic model for succession, taking account of the spatial correlations in alliances. This dynamic succession model will then be evaluated and utilized in all the ATLSS models.

SESI Model Evaluation

The vast majority of spatially-explicit species data that are appropriate to use to evaluate the SESI model performance is from post-1995. The major task is to develop standardized statistically-valid procedures to compare spatial data that are often sparse to the output of the SESI models, utilizing the most recent hydrologic data from the calibration/validation of the SFWMM, then modify the model calibration as appropriate.. The objective is to determine the effectiveness of these models in projecting the relative impacts of different plans on the quantities measured by the SESI models.

New SESI Model Development

A variety of new SESI models are underdevelopment, including a roseate spoonbill model, a crocodile model, and a freshwater fish model (for small fish). These models are being developed in collaboration with several field biologists including Jerry Lorenz, Frank Mazzotti and Joel Trexler. In addition, models for the apple snail and two crayfish species, though now developed, need additional effort to be spent on evaluation

Structured Population Model Development

ALFISHES has been constructed to simulate estuarine fish levels driven by a hydrologic model from USGS (SICS), but this now needs to be coupled to the freshwater fish model and has not been driven by the SFWMM. These models will be linked and evaluated. Additionally, the new structured alligator model needs to be effectively linked to the ATLSS High Resolution Hydrology and vegetation succession models. These activities will be ongoing through the two years of the proposed effort.

SEIB Visualization and Modeling

The Pantrack visualization tool has combined all available information on radio locations for the panther, and has allowed for new views of panther ecology to be developed. The tool needs to be ported to a Windows environment to allow a variety of panther biologists easy access to it. It also is being used to evaluate behavioral rules for panthers that will be included in a new SEIB model of the panther (linked to deer and hogs). This model will be quite different from the previously constructed SEIB for panther due to a greatly enhanced understanding of panther behavior (summarized in a paper to appear in the journal Conservation Ecology) that has been made possible through the use of Pantrack. An additional SEIB model that has been undergoing modification is SIMSPAR which is to be expanded to additional spatial regions, and this can be done given additional high resolution topographic data.

Delivery of Models to Client Agencies

All ATLSS SESI models have been made available to ENP staff members, but use of these has been limited due to computer constraints (ATLSS models are developed to run on a Sun Microsystems platform rather than a Windows platform). A major task will be to develop methods to allow either agency representatives to readily and rapidly make model runs they desire on a remote system of Sun machines, or to move the codes to be platform independent. Efforts in both these directions are planned but will likely take more than the first year of the proposed effort to complete. The initial objective will be to ensure the capability for USGS staff at University of Miami to run all the ATLSS codes, and then to develop methods to allow remote users to carry out runs.

ATLSS DataViewer and Database

ATLSS SESI model output is currently being used within the ATLSS DataViewer (a product of the NWRC staff of USGS) to allow ease of visualization of the basic yearly spatially-explicit indices produced by these models. Modifications to allow the output of other ATLSS models within this are underway, though the only effort to date has been with the ALFISH freshwater fish model. Yet to be developed are standards for visualizing the outputs of SEIB models, and that task will be ongoing during year one of the project. An additional task will be to include outputs from the ALFISHES estuarine fish model. A separate task concerns the development of a database structure for all ATLSS model output. Although a formal metadata structure has been established and utilized within the ATLSS models, there has not been any formal database constructed to maintain the results of ATLSS runs. With the decreasing cost of storage, it is now feasible to construct such a database (using Oracle), and allow web access to it from within the DataViewer to allow users to visualize alternative ATLSS model runs without having the files shipped to them on a CD. This database establishment effort will be ongoing throughout the two years of the project.

 Planned Outreach:

The outreach activities associated with this project fall into three major categories. First, there is outreach to the user community for the ATLSS models. This includes developing efficient methods for users to run and evaluate various model results. These efforts are mentioned above under the Delivery and DataViewer descriptions of the project. In addition, ATLSS staff regularly make presentations of the results of the project to groups in South Florida. A second component of outreach concerns publication of the results of the effort, collaboration on the uses of these approaches in similar regional management projects, and collaboration with various scientists (including geographers and computer experts) to expand ATLSS capabilities and to illustrate the utility of these approaches to other scientists. We have an extensive record of such collaborations and will continue these as funding is available. Ongoing publication of the results of ATLSS modeling is continuing, and we have an excellent record of successful publication in peer-reviewed journals (see for a listing). The third outreach component involves the use of ATLSS results in an educational context. We have proposed efforts to expand the use of ATLSS within the BioQUEST collection (this is one of the major projects in undergraduate biology education ongoing in the US), beyond the current use of the SEIB wading Bird model, to include additional SEIB models and SESI models.

Title of Task 3: Development of an Internet Based GIS to Visualize ATLSS Datasets For Resource Managers
Task Funding: Critical Ecosystems Studies Initiative, Department of Interior
Task Leaders: James B. Johnston
Phone: 337-266-8556 Fax:
Task Status (proposed or active): Active
Task priority: High
Task Personnel: James B. Johnston and Antonio Martucci

Task Summary and Objectives:

The Across Trophic Level System Simulation (ATLSS) Program attempts to predict the responses of a suite of higher trophic level species to different alterations in the Everglades/Big Cypress region of South Florida to represent the biotic community and various factors that affect this community. A tremendous amount of digital data have resulted from running these scenarios. To make these data available to resource managers and scientists, the USGS-National Wetlands Research Center has developed the ATLSS Data Viewer System (ADV). It is a spatial query and visualization GIS tool that provides the capability of retrieving, displaying, and analyzing ATLSS model data by using a user-friendly graphical interface and project-oriented procedures: The project has

  • Designed a customized graphical user interface that makes the system user-friendly
  • Displayed the ATLSS SESI output data, performed analyses, and generated outputs that allow resource managers and decision makers to make informed decisions
  • Provided training courses for users.
This project concerns the development of a customized spatial query and visualization tool that provide capabilities of loading ATLSS models data and showing, in the Everglades/Big Cypress area, alternative water management changes and their effects on numerous species modeled in ATLSS (i.e. Cape Sable seaside sparrow, Snail Kite, wading birds, white-tailed deer, American alligator, Florida panther), as opposed to one species, and compare numerous scenarios for one species. The overall goal is to provide an easy-to-use tool capable to access the vast amounts of data produced by the ATLSS models, display and integrate spatial and non-spatial information from different sources, interactively extract statistics for user-specified areas, allowing the users to produce easy-to-read outputs in form of maps, time series graphs, summarized tables, reports and metadata. Particular attention is being devoted in:
  • implementing procedures that meet final users expectations
  • designing a graphical user interface that:
  • keeps the system easy-to-use
  • gives the user enough flexibility to perform advanced analysis
  • limits or warns the users from using the ATLSS data improperly

Continuous feedback will be requested to ATLSS models developers and potential final users to release a finished product that fulfills the initial planning tasks. This project will be used as prototype server application for an Internet based visualization tool.

Work to be undertaken during the proposal year and a description of the methods and procedures:

The above goals have largely been completed. However, several tasks remain and the following will be accomplished under the requested funding.

1. Add new base maps into the ATLSS DVS, such as Elevation Data from USGS, official version of GAP data, project boundaries for different projects within CERP, current satellite images.

2. Add to the DVS flow graphs and brief descriptions on SESI and other models.

3. Use the DVS to visualize and analyze data from other ATLSS models like individual-based and dynamic models (in particular, ALFISH, SIMSPAR, and EVERKITE) will be added to the ATLSS DVS.

Additional DVS's functionality and/or upgrading of DVS's code and interface will be necessary.

4. Develop DVS's capability to input user's empirical data in order to determine the degree of correlation between models output and empirical data. Additional code will be necessary to allow users to import into the DVS a set of locations (UTM, decimal degrees, or degree, minute, second coordinates), extract ATLSS model values, and display the result or export it to external applications like MS Excel or the ATLSS Model Validation tool.

5. Simplify DVS's capability of extracting mean index values based on user-defined areas.

6. Develop interface and functionality and upgrade code as needed to allow agencies capable of independently running ATLSS models (SFWMD and ENP) to read and display their runs into the ATLSS DVS.

7. Improve the DVS user's Guide based on user's comments and suggestions

8. The capability to display and analyze the output of the ATLSS simulation models

Planned Outreach

1. Develop a WEB-based ATLSS DVS user's Support Center. This site will contain an overview of ATLSS models and the DVS's graphical user interface and capability. It will also provide users with downloadable files of project and data, and information about installing and using the DVS. Contacts will be provided to allow users to submit questions, suggestions, and ideas on the DVS and the data included in it. A "Frequently Asked Questions" list will be created and constantly updated based on user-submitted comments.

2. Develop a WEB-based GIS tool using ESRI-ArcIms technology, which allows users to retrieve, display, and analyze ATLSS model outputs and related vector and raster data sets "on-line" by using an Internet browser like MS IExplorer or Netscape Navigator.

3. Organize task-oriented DVSs tutorial exercises and provide additional training sessions for "primary" ATLSS DVS users.

Development of ATLSS DVS 2.0

1. Develop an ESRI-ArcGis 8.x-based version of the ATLSS Data Visualization System. The entire DVS will be rewritten to benefit of the capability provided by the newest desktop GIS released by ESRI.

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