USGS - science for a changing world

South Florida Information Access (SOFIA)

projects > across trophic level system simulation (atlss) > work plan

Project Work Plan

Department of the Interior USGS GE PES

Fiscal Year 2010 Study Work Plan

Project Title: Across Trophic Level System Simulation Program for the Greater Everglades
Project Start Date: 2004
Project End Date:
Web Site:,
Location (Subregions, Counties, Park or Refuge): Total System
Funding Source: USGS GE PES
Other Complementary Funding Source(s): CESI, NSF
Funding History: FY04, FY05, FY06, FY07, FY08, FY09
Principal Investigator(s): 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
Project Personnel:
Supporting Organizations: University of Florida, University of Tennessee
Associated/Linked Projects:

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, Tennessee 37996

Other Investigator(s): Dr. Steve Hartley
Email address:
Phone: 337-266-8543
Fax: 337-266-8616
Mail address: USGS-BRD National Wetland Research Center
700 Cajundome Road
Lafayette, Louisiana 70506

Other Investigator(s): Kenneth G. Rice, USGS; Frank J. Mazzotti, University of Florida
Email address:
Phone: 954-577-6305
Fax: 954-577-6347
Mail address: Institute of Food and Agricultural Sciences
University of Florida
3205 College Avenue
Fort Lauderdale, Florida 33314

Overview and Objectives: 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 noncontrolled 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 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.

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 (SFWMM) provides hydrology for ATLSS models at a 2-mile 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-m x 500-m resolution from the 2-mile 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, the American alligator, two species of crayfish, and the Florida panther.

A considerably more spatially explicit simulation model, ALFISH, 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 simulation modeling approach is being extended to crayfish.

Spatially explicit individual based (SEIB) models, which track the behavior, growth, and reproduction of individual organisms across the landscape, have been constructed for the Cape Sable Seaside Sparrow (SIMSPAR), the Snail Kite (EVERKITE), the Florida panther, the American crocodile (CROCMOD), 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 has been on the freshwater systems, with emphasis on the intermediate and upper trophic levels. ATLSS will be extended to estuarine and near-shore dynamic models once physical system models for these regions are completed. Modeling of the mangrove vegetative community and estuarine fish is now underway.

There are four tasks in this project. The first (DeAngelis) involves the coordination of the other tasks. The second task (Gross) involves the development and running of the ATLSS computer simulation models. The third task (Rice) involves developing restoration success indicators for the amphibian community. The fourth task (Johnston) involves upgrading of an ATLSS Data Visualization system.

Specific Relevance to Major Unanswered Questions and Information Needs Identified: 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 University 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. 

Recent Products:
Publications (2009):
Papers dealing with the fish community of the Everglades:
DeAngelis, D.L., Trexler, J.C., and Donalson, D.D., 2008. Food web dynamics in a seasonally varying wetland. Mathematical Biosciences and Engineering, 5:877–887.

DeAngelis, D.L., Trexler, J.C., and Donalson, D.D., 2009. Competition dynamics in a seasonally varying wetland, Chapter 1. In Cantrell, S., Cosner C., and Ruan, S., eds., Spatial Ecology. CRC Boca Raton, Florida: Chapman and Hall/CRC Press, 360 p.

Papers dealing with the distribution of nutrients between marsh and tree islands in the Everglades:
Ju, S. and DeAngelis, D.L., 2009. Nutrient fluxes at the landscape level and the R* rule. Ecological Modeling (currently on-line, hard copy will follow in 2009)

Ju, S. and DeAngelis, D.L., 2009. The R* rule and energy flux in a plant-nutrient ecosystem. Journal of Theoretical Biology, 256:326–332.

Other papers:
Feng, Z., Liu, R., DeAngelis, D.L., Bryant, J.P., Kielland, K., Chapin, F.S., III, and Swihart, R.K., 2009. Plant toxicity, adaptive herbivory, and plant community dynamics. Ecosystems, 12:534–547.

Zhang, J., Jiang, J., Liu, D, and DeAngelis, D.L., 2009. Vegetation coverage influence on rainfall-runoff relation based on wavelet analysis. Journal of American Science, 5:97–104.

Swihart, R.K., DeAngelis, D.L., Feng, Z., and Bryant, J.P., 2009. Troublesome toxins: Time to re-think plant-herbivore interactions in vertebrate ecology. BMC Commentary, 9:5.

Holland, J.N. and DeAngelis, D.L., 2009. Consumer-resource theory predicts dynamic transitions between outcomes of interspecific interactions. Ecology Letters, 12:1357–1366.

Presentations (2009):
Fernandes, Miguel V., DeAngelis, Donald, and Gaines, Michael S., 2009. The effects of tree island size and water depth on population patterns of the cotton rat (Sigmodon hispidus) and marsh rice rat (Oryzomys palustris) in the Florida Everglades. Poster: San Jose, California, Ecological Society of America Annual Meeting.

Planned Products: See tasks below.
Collaborators: Collaborators during the project 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, and the 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: USGS Priority Ecosystem Science
Task Leaders: Donald L. DeAngelis
Phone: 305-284-1690
Task Status (proposed or active): Active
Task priority: High
Time Frame for Task 1: 10/01/2004–9/31/2007
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 year there will be especially heavy need for working with the DOI agencies (National Park Service and Fish and Wildlife Service) to perform the needed ATLSS model simulations for CERP evaluations. Part of this work will involve making ATLSS models more directly accessible to agencies. A meeting with agency representatives on September 22, 2005, indicated that 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 is working to achieve this goal both through interactions with Lou Gross of the University of Tennessee as well as by improving the capabilities at the Joint Ecological Modeling (JEM) Center. Currently the USGS's Across Trophic Level System Simulation (ATLSS ) models are run at the University of Tennessee using 2-mile x 2-mile hydrology provided by the South Florida Water Management Model (SFWMM).

The task leader will also coordinate with other modeling research in order to incorporate new models in the ATLSS framework. 

The task leader is also engaged in other projects related to Everglades research and restoration.

  1. Working with a Ph.D. student at the University of Miami (Shu Ju) to create a nutrient cycling model for tree islands in the Everglades to understand the differences in productivity, tree communities, and other properties between and within tree islands. Two papers have been published this year.
  2. Working with Prof. Joel Trexler of FIU to create a simple, more flexible version of ALFISH, called GEFISH, that can be used to predict fish biomasses on subregions of the Everglades. Two papers on this model have been published this year and a third is in revision.
  3. The snail kite individual-based model (EVERKITE) has been upgraded by a post-doc working with me at the University of Miami. I have contributed to developing a dynamic apple snail model to determine the effects of hydrology on the population dynamics of this key prey of the snail kite.
  4. Working with Dr. Michael Gaines of the University of Miami to complete the report on 11 years of study of effects of tree island size and hydroperiod on abundance, survival, reproduction, and movement of rice rats and cotton rats. A poster was presented at the 2007 Ecological Society of America meeting on this work. The graduate student working on this project, Miguel Fernandes, has given presentations on the work in south Florida.


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 Funding: USGS Priority Ecosystem Science FY07
Task Leaders: Louis J. Gross, University of Tennessee
Phone: 865-974-4295
FAX: 865-974-3067
Task Status (proposed or active): Active
Task priority: High
Time Frame for Task 2: 2004–2011
Task Personnel: Louis J. Gross, Director, The Institute for Environmental Modeling, University of Tennessee. Staff of The Institute for Environmental Modeling including: Jane Comiskey and Eric Carr.

Task Summary and Objective(s): 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 index (SESI) models on the landscape; 4) spatially explicit individual-based (SEIB) computer simulation models of selected species populations; 5) spatially explicit structured population dyanmics models for key biotic resources in the system; and 6) a variety of visualization tools to aid model development, validation, and comparison to field data.

INFORMATION NEEDS AND USES. It was identified early in the planning for the Everglades restoration that models would have to play a key role in the process of choosing a restoration plan and evaluating its success. The ATLSS models have done and are doing this in the following ways:

There are several tasks ongoing as part of the ATLSS project components at the University of Tennessee. Several of these have previously been funded by National Science Foundation awards, the National Park Service and funds from the University of Tennessee, and those components are not addressed here. Rather, we include here only the tasks directly related to the planned funding for this project. The tasks included are therefore limited due to the greatly reduced magnitude of the funding available

This project has had the goal of developing models for key components of the Everglades landscape as part of the overall Across Trophic Level System Simulation Program. A major component of this effort has been the development of the ATLSS Spatially Explicit Species Index (SESI) Models. The principle tasks have included developing the models, parameterizing the models, linking the models to various inputs, including hydrology and habitat spatially-explicit information, applying the models to evaluate numerous hydrologic scenarios, assessing the impacts of uncertainty in the inputs and parameters of the model on model performance, and constructing an interface for these models to the ATLSS Dataviewer (written in ArcView by USGS staff) to allow users from various agencies to carry out their own evaluations of the results of model runs.

Prior work on this subagreement since 2006 has focused primarily on: moving much of the software for ATLSS to be usable on Linux rather than Solaris UNIX platforms; developing the documentation for the ATLSS high-resolution hydrology and HMDT (high-resolution multidataset topography); collaborating with staff members from USGS, NPS/ENP, the Interagency Modeling Center and the University of Florida to transfer knowledge of how to make ATLSS runs to these agencies; developing an ATLSS official release of HMDT compatable with the calibration/verification run for release 5.4 of the South Florida Water Management Model; collaborating with developers of the Everglades Landscape Model to run ATLSS on similar hydrology to that derived from this model and carrying out ATLSS runs on the new scenario releases by the SFWMD.

The principle task proposed to be carried out with the additional funding provided through this modification involves updating ATLSS SESI models in response to the projected completion of the new SFWMM model for hydrology across south Florida, the Regional Simulation Model (RSM). As time and resources permit, ATLSS SESI models will be modified to incorporate recent information while being made compatable with RSM by updating the SESI models to utilize ATLSS Landscape Classes v3. This would allow ATLSS SESI models to utilize the variable spatial mesh output of the RSM.

Work to be undertaken during the proposal year and a description of the methods and procedures.
With prior funding support, several years ago the University of Tennessee ATLSS Team developed a new ATLSS landscape class structure (ATLSS Landscape Classes v3) that provided the infrastructure to allow ATLSS models implementation on hydrology inputs in quite different formats than that obtained through the South Florida Water Management Model. The SFWMM operates on a square grid and the objective of the Landscape Classes v3 is to allow for inputs to ATLSS models from a much larger diversity of hydrology model outputs, including RSM and other hydrologic models that do not use uniform grid elements. The Landscape Classes are the methodology used in ATLSS to provide georeferenced data movement both within particular ATLSS models and between them. They provide the basic code structure that allows ATLSS to function as a multimodel, linking together component models with different scales and structures. Due to funding constraints and requests to proceed on other ATLSS projects, there has not been much further development of the ATLSS capability to utilize RSM model results and the objective of the tasks associated with this modification is to further develop the ATLSS Landscape v3 classes to implement ATLSS models with RSM.

As part of the previous funding, one SESI model (the SESI Deer model) was modified to use the more general hydrology provided through a much earlier version of RSM. Numerous scaling issues will require careful thought in the reconfiguring the remaining ATLSS SESI models to utilize RSM, in addition to making the specific coding changes necessary to make these models compatible with ATLSS Landscape Classes v3.

The objectives of the proposed study are as follows:

The proposed work has several components. The following list provides a summary of activities. These tasks will be carried out collaboratively by the UT staff members for whom support is requested, under the guidance of the Principal Investigator. Note that no funds are requested for the time of the Principal Investigator, whose efforts will be provided as an additional cost-sharing by the University of Tennessee. We propose to continue and extend our previous efforts toward making ATLSS models flexible with regard to the cell size/shape and format of hydrologic inputs in the following tasks:

Task 1. Incorporate the types of changes made in the Deer SESI into at least two other ATLSS SESI models, allowing them to be run with Landscape Classes v3 (while maintaining backward compatability with Landscape Classes v2).

Task 2. Add appropriate functionality required by specific SESI models currently lacking in v3 Landscape Classes, including necessary links to the neighborhood region procedures implemented in Landscape v3.

Task 3. Concurrent with SESI modifications to adapt the models to v3 Landscape Classes in Tasks 1 and 2, update and expand internal model documentation.

Work to be undertaken during future FYs and proposed funding:

Recent Products: See earlier list.

  1. ATLSS Hydrosuite documentation (2008):
  2. LSESI_WATER model, that takes as input the 2-mile x 2-mile SFWMD hydrology file (December 2008).
  3. Final Report on Extensions to Variable Spatial Grid Hydrologic Models (December 2008).

Specific Task Products:
Incorporate the types of changes made in the Deer SESI into at least two other ATLSS SESI models, allowing them to be run with Landscape Classes v3 (while maintaining v2).

Concurrent with SESI modifications to adapt the models to v3 Landscape Classes in Tasks 1 and 2, update and expand internal model documentation.

Title of Task 3: Use of Amphibian Communities as Indicators of Restoration Success in the Greater Everglades
Task Funding: USGS Priority Ecosystems Science
Task Leaders: Kristen Hart, USGS; Frank J. Mazzotti University of Florida
Phone: 954-577-6335
FAX: 954-475-4125
Task Status (proposed or active): Active
Task priority: High
Time Frame: 2004–2010
Task Personnel: TBD
Task Summary and Objectives: : Declines in amphibian populations have been documented by scientists worldwide from many regions and habitat types. No single cause for declines has been demonstrated, but stressors like acid precipitation, environmental contaminants, the introduction of exotic predators, disease agents, parasites, and the effects of ultraviolet radiation have all been suggested. Because of their susceptibility to these and other stressors, amphibians are important as indicators of ecosystem health.

Amphibians are present in all habitats and under all hydrologic regimes in the greater Everglades. The species present and the occupancy of a given species differ greatly across those gradients due to differences in hydroperiod, vegetation, and other environmental factors. The combination of species composition and proportion of each habitat occupied at a given time form unique communities defined by those environmental factors. Therefore, if these communities can be reliably defined and measured, Everglades restoration success can be evaluated, restoration targets can be established, and restoration alternatives can be compared. This study will develop methodologies for defining and measuring the membership and area occupancy of amphibian communities. Further, we will investigate the relationship of occupancy of amphibians with hydroperiod and other environmental factors. Finally, we will provide a method for measuring restoration success based on these communities. The importance of amphibian communities to greater Everglades restoration has been recognized and listed as critical priority research needs (see USGS Ecological Modeling Workshop and the DOI science plan in support of Greater Everglades Ecosystem Restoration).

We will use established sampling methodologies such as PVC refugia trapping to investigate amphibian occupancy rates, develop new methods for sampling across hydroperiod gradients (drift fence arrays, PVC arrays), and use newly developed statistical techniques to estimate the proportion of area occupied by and to define amphibian communities. We will also explore using frog-loggers and camera traps as new technologies that may contribute to our understanding of occupancy. Our objectives include:

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

During FY10, we will concentrate our work on:

Duellman and Schwartz (1958) produced the first scientific survey of the amphibians of south Florida. This work serves as an excellent reference for the historical distribution of many species before the extensive habitat loss in south Florida during the second half of the 20th-century. Meshaka et al. (2000) produced a species list of the herpetofauna for ENP, but little information about the habitat associations and population status of the species was contained in that report. Dalrymple (1988) provided a good description of the herpetofauna of the Long Pine Key area in ENP, but no attempt had been made to sample amphibians throughout the Everglades.

We used two primary methods to accomplish the objectives of the project:

Proportion area occupied by a species (Field work FY04–FY05, First Analysis FY06, new data added (from southwest Florida study) and models re-analyzed FY07-08).-- One problem with many of the methods used to sample amphibians is the lack of any control of the myriad environmental factors that affect the behavior and activity of the animals. Abiotic factors like temperature, humidity and hydrology as well as biotic factors like the presence of predators or conspecifics can affect the observability of amphibians. The observability of species' population is a function of the population size, the behavior of the individuals, and the ability of the observer to locate the animals in the particular habitat. Many monitoring programs simply count animals and do not control for this observability or capture probability (p). Therefore, comparisons over time or space are not possible or are biased. If the monitoring program can assume the cost of marking individual animals, then p can be determined and population size or density determined (standard mark-recapture methods, see Williams et al., 2002). However, this would be cost prohibitive in a monitoring program for all amphibian species throughout the Everglades. MacKenzie et al. (2002) has developed a novel approach to this problem. Rather than mark the individual, we "mark" the species. Therefore, presence/absence data from several plots within a habitat (or along a hydroperiod gradient in our study) provides an estimate of p and will allow estimation of the proportion of a stratum occupied by a given species at a given time.

Sampling units were chosen randomly within each stratum. Within Everglades National Park these were along the Main Park Road and Context Road. We chose five permanent sites along each road accessed by foot. The sites were located within 300–900 feet of the road. In Water Conservation Area 3A, we selected five permanent sites in each stratum along a north-south transect from I-75 to SR-41. Each stratum was defined by the hydroperiod observed from existing hydrologic data and habitat type as defined by existing GIS vegetation layers. Sites were visited twice biweekly, April through September. Further sites in each stratum were visited twice during the study to provide further information on a broader geographic scale.

Our standardized sampling unit was a circular plot of 20-m radius. Plots were sampled after dark to increase the probability of observing nocturnal amphibians. At each plot 2–3 person crews began by listening for anuran vocalizations for 10 minutes.The abundance of each species was categorized as: no frogs calling, one frog calling, 2-5 calling, 6-10 calling, >10 calling, or large chorus. The intensity of the vocalizations were categorized as: no frogs calling, occasional, frequent, or continuous. After the vocalization survey, we performed a 30-minute visual encounter survey (VES) in each plot. During this time, all individual amphibians observed were identified to species and captured if possible. We recorded the species, categorized the age (egg, larvae, juvenile, subadult, or adult), measured and recorded the snout-to-vent length and recorded the sex when possible. The animal was released at the original capture site. We also recorded the sustrate and perch height of the animal. A University of Florida Institutional Animal Care and Use Committee approval was obtained for animal capture. In addition to VES, we used funnel traps to attempt to capture aquatic amphibians. We also recorded several ancillary variables at each plot (air temperature, relative humidity, presence of water, water temperature, wind speed, cloud cover).

In addition, 20–1-m tall, 5-cm diameter PVC removable pipes were installed in each site for refugia of treefrog species. During each visit, animals were removed from the pipe for identification and measurement as outlined above. All animals were released into the original PVC refugia. All PVC was removed at the end of the study.

At 10 sites in ENP (five along Context Road and five along Main Park Road) we installed 20 m of drift fence for capture of aquatic salamanders. The drift fence consisted of removable erosion control fence with a funnel trap incorporated at each end. The fence was arrayed as four separate 5-m fences in a grid around the center of the site. Traps were placed along the fence for five consecutive days once per month during May through October. The traps were checked each day in the morning to minimize heat stress on captured animals. Animals were measured as outlined above and released at the capture site. All traps and drift fences were removed during noncapture periods and at the end of the study.

Analysis during FY08: Individual species capture histories (matrix of presence/absence of each species at a sampling period and plot) and corresponding covariates (habitat, hydroperiod, temperature, humidity) will be assembled. We then estimated the proportion of each stratum occupied by a species and the capture probability (using MLE and the logistic regression for covariates; MacKenzie et al., 2002). The best model will minimize AIC and adequately estimate the parameters in the model (the candidate model list was developed a priori based on ecological knowledge and did not include all possible combinations). We then used these estimates to construct appropriate communities for each stratum (see proportion of area occupied by a community below).

Proportion area occupied by a community–Finalized in FY08: Given that species occupancy rates differ across hydroperiod gradients and that hydrology is the controlling factor of this difference (see above), we can begin to construct "communities". In Figure 1 below (letters represent species, the size of the circle represents PAO, numbers represent hydroperiod), we can see that in short hydroperiod sites, species A and D dominate. However, as we move to longer hydroperiod sites, other species emerge as the dominate species in the community. This pattern of species composition and PAO forms the set of "communities" along the hydroperiod gradient.

conceptual view of proportion of area occupied by communities of amphibians across a gradient of hydroperiod in the Everglades
Figure 1. Conceptual view of proportion of area occupied by communities of amphibians across a gradient of hydroperiod in the Everglades. [larger image]

We have seen this pattern begin to emerge in preliminary data from the Everglades (Table 1).

Table 1. Proportion area occupied (PAO) values for amphibian species in the Everglades across a gradient of hydroperiod (values are an estimate of the proportion of a stratum occupied by that species):


Cricket Frog

Southern Toad

Squirrel Treefrog


Leopard Frog































At present, the method for defining and then predicting community composition and PAO is not complete. This study will develop this methodology for the Everglades.

Index of Biological Integrity. --Indices of biological integrity (IBI) were originally developed to assess conditions of riverine systems (Karr, 1991, 1993) and also have been developed successfully for use in terrestrial environments (O'Connell et al., 1998). The basic premise of IBI's is that a range of conditions of ecological integrity can be defined based on the structure and composition of a selected biological community (e.g. amphibians, fish, birds, macroinvertebrates). The concept of biological integrity provides an ecologically-based framework in which species-assemblage data can be ranked in a manner that is more informative than traditional measures such as richness and diversity (Karr and Dudley, 1981; Brooks et al., 1998). Therefore, the final step in this project will be to develop an amphibian community index (ACI) for evaluating the success of restoration and management of greater Everglades ecosystems. The amphibian community index (ACI) will be modeled after previously developed IBI's (Cronquist and Brooks, 1991; Karr, 1991, 1993; Brooks et al., 1998; O'Connell et al., 1998). Essentially, we will use the PAO of communities estimated above to index or define the integrity of a given stratum. As restoration proceeds, we can use changes in the index to make informed management decisions and to measure success. Further, we can use the pattern of these communities based on hydopattern to develop restoration targets and to compare alternatives. By providing a reliable and repeatable measure of ecological quality an amphibian community index (ACI) will help managers reach scientifically defensible decisions (Brooks et al., 1998).

Work to be undertaken during future FYs and proposed funding:
In addition to monitoring, we plan to conduct field experiments in association with USGS PI Susan Walls in the Picayune Strand study area. Complementary lab work may be conducted in Gainesville in association with USGS PI Pam Schofield. This work links to both modeling and fieldwork funded separately under PES.

Literature Cited:
Boughton, R.G., Staiger, J., and Franz, R., 2000. Use of PVC pipe refugia as a sampling technique for hylid treefrogs. American Midland Naturalist 144, 168–177.

Brooks, R.P., O'Connell, T.J., Wardrop, D.H., and Jackson, L.E., 1998. Towards a regional index of biological integrity: The example for forested riparian systems, Environmental Monitoring and Assessment, 51, 131–143.

Croonquist, M.J. and Brooks, R.P., 1991. Use of avian and mammalian guilds as indicators of cumulative impacts in riparian-wetland areas, Environmental Management, 15, 701–714.

Dalrymple, G.H., 1988. The herpetofauna of Long Pine Key, Everglades National Park, in relation to vegetation and hydrology. In: Szaro, R.C., Stevenson, K.E., and Patton, D.R., eds. The Management of Amphibians, Reptiles and Small Mammals in North America. U.S. Department of Agriculture, U.S. Forest Service Symposium, July 19–21, 1988, Flagstaff, Arizona. Gen. Tech. Rept. RM-166, p. 72–86.

Donnelly, M.A., Guyer, C., Juterbock, J. E., and Alford, R.A., 1994. Techniques for marking amphibians. In Heyer, W.R., Donnelly, M.A., McDiarmid, R.W., Hayek, L.C., and Foster, M.S., editors. Measuring and Monitoring Biological Diversity: Standard Methods for Amphibians. Washington, D.C.: Smithsonian Institution Press, p. 277–284

Duellman, W.E. and Schwartz, A., 1958. Amphibians and reptiles of southern Florida. Bulletin of the Florida State Museum, vol. 3, no. 5, 181-324

Enge, K.M., 1997. A standardized protocol for drift-fence surveys. Florida Game and Fresh Water Fish Commission Technical Report No. 14. Tallahassee, 69 p.

Karr, J.R., 1991. Biological integrity: a long-neglected aspect of water resource management, Ecological Applications, 1, 66–84.

Karr, J.R., 1993. Defining and assessing ecological integrity: beyond water quality, Environmental Toxicology and Chemistry, 12, 1521–1531.

Karr, J.R. and Dudley, D.R., 1981. Ecological perspective on water quality goals, Environmental Management, 5, 55–68.

MacKenzie, D.I., Nichols, J.D., Lachman, G.B., Droege,S., Royle,J.A., and Langtimm, C.A., 2002. Estimating site occupancy rates when detection probabilities are less than one. Ecology, 83, 2248–2255.

Meshaka, W.E., Loftus,W.F., andSteiner, T., 2000. The herpetofauna of Everglades National Park. Florida Scientist, 63(2), 84–103.

O'Connell, T.J., Jackson, L.E., and Brooks, R.P., 1998, A bird community index of biotic integrity for the mid-Atlantic highlands, Environmental Monitoring and Assessment, 51, 145–156.

Williams, B.K., Nichols, J.D., and Conroy, M.J. 2002. Analysis and Management of Animal Populations. London:Academic Press, 817 p.

Specific Task Product(s):

Title of Task 4: ATLSS Support for Greater Everglades Landscape Ecological Modeling
Task Leader: Steve Hartley
Phone: 337-266-8543
Fax: 337-266-8616
Time Frame for Task: Fiscal Year 2010
Task Personnel: Steve Hartley, Scott Wilson, Sumani Chimmula, and Craig Conzelmann

Task Summary:
The USGS has been requested by the South Florida Ecosystem Restoration Program to assist in integrating ecological models (such as: ATLSS SESI models, EVERKITE and Apple Snail Kite models) into the IMC system of models.
The SESI models are part of the Across Trophic Level System Simulation (ATLSS) Program which 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. Tremendous amounts 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 (ADVS). 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.


Specific Task Products:
Work with the Interagency Modeling Center and as an integral part of the Joint Ecosystem Modeling team (UF, USGS, NPS, and FWS) to help utilize the ATLSS DVS and modify it for specific purposes relevant to implementation at IMC.

  1. Convert EVERKITE code into java and output to netCDF format.
  2. Program the Apple Snail model in java and output to netCDF format.
  3. Modify the ATLSS DVS to be able to view the EVERKITE and Apple Snail output.
  4. Provide training on the usage of the modified ATLSS DVS.
  5. Provide run support for ATLSS models.