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Project Work Plan

Department of Interior USGS GE PES
Fiscal Year 2012 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: GE PES
Other Complementary Funding Source(s): CESI, NSF
Funding History: FY04, FY05, FY06, FY07, FY08, FY09, FY11, FY12
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 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): Susan C. Walls, USGS
Email address:
Phone: 352-264-3507
Fax: 352-264-3508
Mail address: U.S. Geological Survey
7920 N.W. 71st Street
Gainesville, Florida 32653-3071

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 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.

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 modeling has been considerably improved during FY 2010, to produce a new model, called GEFISH, which contains three species of small fishes, crayfish, and a piscivore, as well as a simplified lower trophic food web.

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 model EVERKITE.2 has been greatly improved since FY 2008, and the output are now displayed using EverView. A current project is to combine EVERKITE.2 with a dynamic model of the apple snail.

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. Ideas from ATLSS are now being applied to the mangrove vegetative community and estuarine fish through the USGS Project "Future Impacts of Sea-Level Rise on Coastal Habitats and Species (FISCHS) in the Greater Everglades."

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). ATLSS models will continue to be used for scenario evaluations for the Comprehensive Everglades Restoration Plan.

Recent Products:
Publications (2011):
Papers dealing with the fish community of the Everglades:
There has been continuing work on fish modeling. This includes adapting ATLSS fish modeling for specific issues regarding water regulation. The specific objective here is to estimate the amount and spatial distribution of fish biomass available for consumption by wading birds over the course of their breeding season.

Obaza, A., DeAngelis, D.L., and Trexler, J.C., 2011. Using data from an encounter sampler to model fish dispersal. Journal of Fish Biology, 78:495–513.

Trexler, J.C., DeAngelis, D.L., and Jiang, J., 2011. Community assembly and mode of reproduction: Predicting the distribution of livebearing fishes, Chapter 9, in Evans, J., Schlupp, I., and Pilastro, A. eds., Ecology and Evolution of Poeciliid Fish. Chicago: University of Chicago Press.

Paper in preparation on fish biomass produced on Everglades landscape:
"Analyzing Fish Dynamics in a Spatiotemporally Varying Marshland" S. Yurek (graduate student at University of Miami), D. DeAngelis, J.C. Trexler, D.D. Donalson, and F. Jopp. (In preparation. Expected completion, January 2012.)

Paper submitted on effects of salinity on fish in Florida Bay:
Kelble, C.R., DeAngelis, D.L., Ortner, P.B., and Hitchcock, G.L., Modeling bay anchovy, Anchoa mitchilli, and mosozooplankton communities in subtropical embayments: A transient trophic cascade: (In journal review.)

Papers related to Everglades tree islands:
DeAngelis, D.L., Ju, S., Liu, R., Bryant, J.P., and Gourley, S.A., 2012. Plant allocation of carbon to defense as a function of herbivory, light, and nutrient availability. Theoretical Ecology, 5(3) pp. 445–456.

Other papers:
DeAngelis, D.L., Wolkowicz, G.S.K., Lou, Y., Jiang, Y., Novak, M., Svanback, R., Araujo, M.S., Jo, Y., and Cleary, E.A., 2011. The effect of travel loss on evolutionary stable distributions of populations in space. The American Naturalist, 178:15-29.

DeAngelis, D.L., 2011, Compartmental models, in: Hastings, A. and Gross, L.J., eds., Sourcebook in Theoretical Ecology. Berkeley, California:University of California Press.

Ph.D. dissertations:
Fernandes, M.V., 2011. Effects of changes in the Everglades on two indicator species: Sigmodon hispidus and Oryzomys palustris. Coral Gables, University of Miami, Ph.D. dissertation, 125 p., 35 figs.

Invited talk.
Giacomini,H.; DeAngelis, D.L., and Trexler, J.C., 2011. Comparative analysis of marine ecosystems using individual-based modeling of communities with multiple life-history traits. American Fisheries Society Annual Meeting, (Seattle, Washington) September 2011.

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. Develop certain components within the ATLSS model 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.

A primary goal will be to write a paper on the Apple Snail Dynamics Model, developed by Phil Darby, Don DeAngelis, Stephanie Romañach, and Rena Borkhataria at the JEM lab. The model is complete and has been tested. Parts of the paper are now written. We have waited to obtain hindcast information on water depths in WCA-3A going back to 1991. Now these data are available, so the simulation runs can be done over the needed time periods.

As a second goal, the Apple Snail Dynamics Model will be combined with the grid-based version of the EVERKITE model of Snail Kites in central and southern Florida for use in scenario evaluation for the Comprehensive Everglades Restoration Plan (CERP), which was developed by Irene van der Stap, Wolf M. Mooij, Donald L. DeAngelis and Michael S. Gaines. The output of the combined model will be capable of being viewed using EverView.

A new Everglades landscape model for fish, GEFISH, has been completed. It is an improvement over the original fish model ALFISH, and it is being developed in close collaboration with Dr. Joel Trexler of FIU, who has Army Corps of Engineers support. GEFISH can be used to predict fish biomasses on subregions of the Everglades, including canals. Papers on this model have been published over the past year. Now the emphasis with be on adapting the model to real Everglades landscapes and a new paper is in preparation.

Regional Simulation Model. Continued work will be done at the University of Tennessee to adapt the ATLSS SESI models to the new Regional Simulation Model (RSM). This is a difficult technical challenge that must be faced by all habitat suitability type models. Some progress has been made for a simple SESI model (white-tailed deer), but this needs to be generalized.

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 extend models of 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 (Ju and DeAngelis, 2009 and 2011).


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 FY12
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: 2004–2013
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:

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 principal tasks have included developing the models, parameterizing the models, linking the models to various inputs, including hydrology and spatially explicit habitat information, applying the models to evaluate numerous hydrologic scenarios.

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.
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. 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 provides the infrastructure to allow implementation of ATLSS models on hydrology inputs that differ fundamentally from the square grid format of outputs produced by the South Florida Water Management Model. 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 the south Florida Regional Simulation Model (RSM) and other hydrologic models that do not use uniform grid elements.

Due to postponement of the initial release timetable for RSM and uncertainty about the final format and structure of RSM releases, there has been little further development of the ATLSS capability to utilize RSM model results. The current anticipated release date for hydrologic scenarios generated by RSM is January 2012 for selected components of the Everglades landscape. A restoration planning document, Regional Simulation Model Overview (, describes the proposed application to the southern Everglades of a full mesh and canal network implementation of the RSM under development for the CERP DECOMP project, which will provide detailed (cell-based) stage and flow information consistent with anticipated Everglades-based performance measures.

It is our understanding that these scenarios are slated for fast-track evaluation associated with the Central Everglades Planning Process (CEPP), a planning effort that responded to the 2008 and 2010 recommendations from the National Academy of Sciences about the need to address unnatural water levels in the water conservation areas and Everglades National Park as a major challenge facing restoration managers.

The objective of tasks associated with this modification is to provide support for the evaluation of scenarios generated by RSM and related variable spatial grid hydrologic models. This objective will require further development of the ATLSS Landscape v3 classes and associated tools in conjunction with modifications to the SESI models to enable ATLSS models to run with RSM.

The following tasks will be carried out collaboratively by the University of Tennessee 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:

Task 1. Examine and evaluate 2012 RSM releases with respect to format, structure, modeling assumptions, and spatial and temporal extents. Compare RSM 2012 with the earlier 2005 RSM release that was used as input for the the development and testing of ATLSS Landscape Classes v3 and basic processing tools.

Task 2. Make any necessary modifications to the ATLSS Landscape Classes and tools for input conversion, formatting, and data storage to allow processing of RSM 2012 hydrologic outputs.

Task 3. Modify selected ATLSS SESI models to enable them to be used to evaluate RSM 2012 scenarios, with priority given to long- and short-legged wading bird and Snail Kite models. Other SESI models that are in preliminary stages of development, including crayfish and apple snail models, may still be useful in evaluating RSM hydrologic inputs.

Task 4. Evaluate RSM 2012 scenarios as they become available. Compare and contrast water depth patterns and biotic impacts of alternative scenarios. Explore the relative effects of alternative water depth formats for processing by biotic models, e.g. compare the use of native RSM variable mesh formats for regridding to 500-m x 500-m cell raster grids.

Task 5. Explore ways in which ATLSS Landscape Classes and processing tools can be useful to make RSM 2012 model outputs accessible to managers and researchers.

Task 6. Update the ATLSS website ( to reflect the current status of ATLSS projects and personnel and to incorporate current web programming techniques and practices.

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).

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: Susan C. Walls, USGSSESC; J. Hardin Waddle, USGSNWRC
Phone: 352-264-3507
FAX: 352-395-6608
Task Status (proposed or active): Active
Task priority: High
Time Frame: 2011–2012
Task Personnel: TBD
Task Summary and Objectives: Amphibians are known to be experiencing worldwide population declines, primarily because of loss and/or modification of suitable habitat (Collins and Storfer, 2003). Alteration of hydrologic cycles can reduce larval survival, and the fragmentation of natural habitats from timber harvesting, agriculture, roads, drainage canals or urban development inhibits dispersal of amphibians between adjacent wetlands (Semlitsch, 2000). The overall decline or disappearance of amphibians from some habitats, together with their sensitivity to key characteristics of their terrestrial environment, underscore the need to restore habitats that have historically served as breeding sites and to document the responses of amphibians to various successional stages of restoration efforts.

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 measure the membership and site occupancy of amphibian communities in an area undergoing active hydrological restoration, the Picayune Strand Restoration Project (PSRP) in Collier County, Florida. Further, we will investigate the relationship of occupancy of amphibians with hydroperiod, habitat and other environmental factors. Finally, based on these communities we will provide a methodology for evaluation and assessment of restoration success of Comprehensive Everglades Restoration Plan (CERP) projects such as the PSRP. 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).

The first step of our planned research is to generate annual estimates of site occurrence for an assemblage of anuran amphibians associated with a diverse array of habitats and hydroperiods in the degraded Picayune Strand and its more intact neighboring land unit, the Belle Meade CARL area. The results of preliminary surveys (conducted in 2008) revealed that Belle Meade had significantly higher amphibian species richness than did Picayune Strand. Moreover, 80 percent of the sites at which Pinewoods Treefrogs (Hyla femoralis, a specialist of fishless, ephemeral wetlands in pinewoods habitat) were detected, were within the boundaries of the Bell Meade area. Based on our 2008 results, we anticipate that community-level estimates of site occupancy in future surveys will be much lower in Picayune, compared to the Belle Meade area. In particular, based on an integrated surface water–groundwater model (Copp and others, 2007) we hypothesize that the composition of amphibian communities following restoration will vary with predicted differences (pre versus postrestoration) in water depths across the Picayune landscape. The second phase of our research will be to use these occupancy estimates to test a newly developed Stressor Response Model for amphibians in southwest Florida and to forecast potential responses of the amphibian community to the planned hydrological restoration of Picayune Strand. We anticipate that the results of this model validation will then likely lead to predictions concerning the responses of amphibians (in terms of site occupancy) under an array of various restoration alternatives. These predictions can then be considered in making management decisions with respect to targeting a particular overall habitat suitability for amphibians of southwest Florida.

Our objectives are to:

  1. Estimate amphibian site occupancy on lands included in the Picayune Strand Hydrological Restoration Project versus occupancy on adjacent conservation lands with relatively intact hydrology. These parameter estimates may be used to test predictions of the newly-developed expansion of the Stressor Response Model.
  2. Generate products on estimating site occurrence of amphibians, along with predicting responses of amphibians to hydrological restoration and future climate change across this landscape.
  3. Generate additional products that will include reports, data, presentations, summary fact sheet for SFNRC/CESI website, and peer-reviewed publications. Forecast potential responses of the amphibian community to the planned hydrological restoration of Picayune Strand.
  4. Long-term goals:

  5. Provide insight into management options with respect to the effects of various water management scenarios on the amphibian community in the Picayune Strand.
  6. Refine the Stressor Response Model to address how climatic variation may impact the hydrology of sites and, thus, their occupancy by amphibians.

METHODOLOGY: We will conduct surveys for anuran amphibians within the area targeted in the Picayune Strand Restoration Project (former Southern Golden Gates Estates), as well as the adjacent Belle Meade Conservation and Recreation Lands (CARL) area; together, these two units comprise Picayune Strand State Forest (PSSF). Belle Meade is a reservoir of natural habitat that may serve as a vital refugium of native flora and fauna for recolonizing Picayune Strand following its restoration. With prior funding from the USGS GEPES Initiative, we expanded our amphibian monitoring in southwest Florida to include the Picayune Strand and adjacent land management units. In 2008, a total of 27 sites were selected for monitoring, and both manual vocalization and visual encounter surveys were conducted to assess amphibian occupancy. In FY09–10, we modified our protocol to use automated recorders (ARUs); Song Meter SM1, Wildlife Acoustics) instead of manual surveys. We deployed an ARU at each site and programmed them to record for five minutes at the beginning of every hour, from 1800 to 0600 hours each day. Loggers were installed on trees approximately 2 m above the ground at each site. Song Scope Bioacoustics Monitoring Software (from Wildlife Acoustics) will be used to build species-specific "call recognizers" and to otherwise aid in identifying frog calls at each site. Recordings will be viewed manually, and in the Spectrogram view of Song Scope to locate unique visual signatures of each species. All identified potential calls will be verified by listening to each. A decibel level > 40 dB will be considered to be "at the site" and not a distant call.

With the start of current funding, in October, 2011, we modified and expanded our sampling design. Using the integrated surface water–groundwater model developed by Copp and others (2007) for the Picayune Strand Restoration Project, we selected 40 new locations (in addition to 20 previous locations within Belle Meade; see below) at which we deployed an ARU, set to record as described above. New sites were selected from within a 0.5-mile buffer on either side of each of the canals that comprise the Faka Union Canal System (a 0.25-mile wide zone between adjacent canals was not included in these buffers to eliminate overlap between adjacent canals). We then compiled all the pixels within each buffer and sorted them (from maximum to minimum) based on Copp and others (2007) predicted change in water depth (Figure 1). Within each buffer, we selected pixels representing the four highest and four lowest predicted depth changes to be included among our new sampling sites. We then randomly selected the remaining sites from among the midrange pixels, with the caveat that no two sites could be adjacent to one another. Twenty sites sampled from 2008 to 2010 in the western Belle Meade area were retained as "reference" sites for the current study. This design resulted in a distribution of 20 sites in Belle Meade and adjacent to the western-most canal, and 20 sites around each of the remaining three canals.

PROPOSED ANALYSIS: We will use a hierarchical formulation of a multispecies occupancy model to estimate the probability of detection and occurrence of each anuran species and to derive an estimate of species richness at each site (Kéry and Royle, 2008; Royle and Dorazio, 2008). In this community-level occupancy model each species has its own detection probability, occurrence, and treatment response. Binomial detection and nondetection data (1=present, 0=not detected) of i=1,2,...; N species during j=1, 2,...; J samples of k=1,2,...; K sites are input in the form of an array yijk. Note that species are known to occur at the site with certainty if detected, but as in standard occupancy models (MacKenzie and others, 2006), nondetection of a species does not necessarily mean the species does not occur at the site.

The occurrence of a species at a site is denoted zik where zik=1 if species i is present at site k and is zero if otherwise. The yijk are assumed to be Bernoulli random variables if the species is present, but take the value yijk=0 with probability 1 if the species does not occur at the site (i.e. zik=0). Thus whether a species is observed at a sample of a site is conditional on the occurrence state variable z,
yijk~Bern(pijk zik) (1)

Figure 1. Location of 60 Automated Recording Units (ARU's).
Figure 1. Location of 60 Automated Recording Units (ARUs) deployed in October 2011 to sample vocalizations of anuran amphibians in the Picayune Strand State Forest. Blue lines indicate the Faka Union Canal System. The gradient (yellow to brown) represents predicted water depth differences (pre vs. postrestoration) based on an integrated surface water–groundwater model developed by Copp and others (2007). Where pijk is the probability that a species is detected during a sample of a site. Likewise z is a latent variable that is assumed to be distributed Bernoulli on the probability of occurrence of the species at the site, ψik. [larger image]

zik~Bern(ψik zik) (2)

This model assumes that heterogeneity in p and ψ among species takes a normal distribution such that each species may have a unique value (i.e. species represents a "random effect"). In addition, covariates to both detection and occurrence will be incorporated into the model using a logit transformation. We will consider the environmental measurements made during each sampling period to be important detection covariates.

We will estimate the model parameters and derive summaries from our hierarchical model using Bayesian analysis methods (Royle and Dorazio, 2008). We will use vague priors distributed uniform from 0 to 1 for community-level detection and occurrence, and distributed normal with mean zero and variance=100 for habitat and detection effects. This model will be fit using Markov chain Monte Carlo (MCMC) methods in Program WinBUGS (Spiegelhalter and others, 2003).


Collins, J.P. and Storfer, A., 2003. Global amphibian declines: sorting the hypotheses. Diversity and Distributions, 9:89–98.

Copp, R., Rowney, C., and Nath, A., 2007. Development of an integrated surface water-groundwater model for wetland restoration and habitat evaluation in a southwest Florida Basin using MIKE SHE Part III–Application of the regional scale model. Kabbes, K. ed., in: World Environmental and Water Resources Congress 2007. Restoring Our Natural Habitat, 15–19 May 2007, (Tampa, Florida), American Society of Civil Engineers.

Kéry, M. and Royle, J.A., 2008. Hierarchical Bayes estimation of species richness and occupancy in spatially replicated surveys. Journal of Applied Ecology, 45:589–598.

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

Royle, J.A. and Dorazio, R.M., 2008. Hierarchical Modeling and Inference in Ecology: The Analysis of Data from Populations, Metapopulations, and Communities. San Diego, California: Academic Press, 464p.

Semlitsch, R.D., 2000. Principles for management of aquatic-breeding amphibians. Journal of Wildlife Management, 64:615–631.

Spiegelhalter, D.J., Thomas, A,; Best, N.G., and Lunn, D., 2003. WinBUGS User Manual (Version 1.4): Cambridge, United Kingdom: MRC Biostatistics Unit. URL:


2011/Quarter 2012/Quarter
Purchase (ARUs)
Deploy (ARUs) in the field
ARU maintenance: retrieval of recordings/replacement of batteries, etc. (every 100 days)
On-going data Summarization
Final data synthesis, modeling
Annual Progress Summaries to GEPES, Picayune Strand State Forest (PSSF), FSPSP
Preparation of Publications
Preparation of Fact Sheet for GEER
Presentations at Meetings

PRODUCTS: We will publish peer-reviewed journal articles on the refinement of the amphibian stressor response model and other results from previous and on-going funding. We will present results of our study at national and international meetings, and produce data/metadata, summary reports and a summary fact sheet for the SFNRC/CESI website and GEER conference.

Task Product(s):

Specific Products
Milestone Date
Fact Sheet for GEER Conference
Reports/progress summaries for Picayune Strand State Forest, Fakahatchee Strand Preserve State Park, and coordinator of the Greater Everglades Priority Ecosystems Science program.
12/2011, 2012
Oral and poster presentations at professional meetings.
07/2011, 2012
Additional journal articles as data become available (e.g., "Use of amphibians to establish a baseline for measuring restoration success at a hydrologically degraded site in southwest Florida, USA". Goal for submission: the journal Restoration Ecology).
FY 2012 and 2013

RELEVANCE AND BENEFITS: As with our previously funded work, this project continues to address several science objectives in the USGS Science Plan in Support of Everglades Restoration. Primarily, this work is concentrated under the second main goal: Activities to restore, protect, and manage natural resources on DOI lands in south Florida. The tasks directly address four science objectives:

The need for monitoring and modeling amphibian populations during CERP is specifically mentioned in the DOI science plan in Support of Everglades Restoration under several projects such as the Picayune Strand (Southern Golden Gate Estates) Hydrologic Restoration Project. In the DOI science plan, the need for monitoring and simulation projects for indicator species is listed in at least the Ten Mile Creek Reservoir Assisted Stormwater Treatment Area, Henderson Creek/Belle Meade Restoration, Southwest Florida Feasibility Study, Florida Bay and Florida Keys Feasibility Study, Landscape-Scale Modeling, and Everglades National Park Fire Ecology Science Action Plan projects. The need to develop models simulating response of species sensitive to change in hydrology, especially those of threatened and endangered species; and determine response of key indicators to changes in water management is described as a research area/restoration goal of the South Florida Ecosystem Restoration Task Force (SFERTF).

COMMUNICATION PLAN, TECHNOLOGY and INFORMATION TRANSFER: The results of our work will aid in understanding how amphibians respond to wetland restoration, modification, and creation efforts, as well as hydrological variation over time and space. This information will be useful if restoration plans for the Picayune Strand are refined with respect to the hydrological and habitat needs of amphibians. This information will also be useful for natural resource managers and conservation biologists affiliated with federal (U.S. Fish & Wildlife Service, U.S. Forest Service, National Park Service, and the USGS ARMI program), state (Fakahatchee Strand Preserve State Park, Picayune Strand State Forest, Florida Fish and Wildlife Conservation Commission) and nongovernmental conservation organizations such as The Nature Conservancy and Partners for Amphibian and Reptile Conservation. Academicians at universities will benefit as well from the intensive data collection proposed in our study. Our publications will be made available by posting them on the USGS ARMI website. Publications will also be distributed to the agencies listed above for their consideration in hydrological restoration and wetland management.

This work is being conducted in partnership with USGS's Amphibian Research and Monitoring Initiative (ARMI). Reports and publications will be made available through the USGS ARMI database. ARMI has a single, multifaceted amphibian database that links field data with statistical parameter estimates for species being studied, health and disease clinical analyses, and geospatial information on potential species ranges. Metadata summarize the goals, locations, and target species of all field data. A complement to ARMI's amphibian database components is the collection of environmental geospatial layers that compose ARMI's geospatial database. The ARMI database already meets NBII metadata standards and is linked to existing NBII data searches.


COOPERATORS and PARTNERS: Conservancy of Southwest Florida, Naples, Florida. Role: ARU maintenance: retrieval of recordings/replacement of batteries, etc. (every 100 days).


FACILITIES, EQUIPMENT, and STUDY AREA(S): All of our work will be conducted in the field; thus, no laboratory equipment or facilities are needed.

Our focal study site, the Picayune Strand State Forest (PSSF), is targeted for hydrological restoration through the Picayune Strand Restoration Project (PSRP), one of over 60 planned projects to be implemented under CERP. The goal of the PSRP is to counteract the overdrainage that resulted from a failed real estate development project (the Southern Golden Gates Estates) of the 1960s. The development of this area (by the Gulf American Corporation) involved dredging 48 miles of canals and building 290 miles of shell-rock roads. Restoration plans for this area include the installation of a combination of spreader channels, canal plugs, road removal and pump stations in the Western Basin and Big Cypress of Collier County. Thusfar, by 2006 the northern seven miles of the Prairie Canal (the eastern-most of four large canals originally constructed to provide drainage and flood protection for the planned residential development) were plugged. Most roads adjacent to the canal have also been removed and exotic plant species were removed from the canal banks. The effort completed thusfar is expected to be especially beneficial in terms of reducing drainage of the adjacent Fakahatchee Strand State Preserve.

The area targeted in the Picayune Strand Restoration Project (the former Southern Golden Gates Estates) is bordered to the east by Fakahatchee Strand Preserve State Park (FSPSP) and, to the west, by the Belle Meade Conservation and Recreation Lands (CARL) area. Belle Meade, together with the former Southern Golden Gates Estates, now comprise the Picayune Strand State Forest (PSSF). Both Belle Meade and FSPSP are reservoirs of natural habitat that, in Belle Meade, is largely hydrologically intact. The FSPSP is threatened by unnatural patterns of water flow and unrestricted use in the private ownerships of the area. Belle Meade includes some of the most extensive examples of remaining old-growth wet flatwoods in southwest Florida, along with high quality, undisturbed subtropical dwarf cypress savanna communities. Fakahatchee Strand is the best example of a strand swamp in the United States, and contains the largest concentration and the greatest diversity of native orchids in North America. These two areas are therefore vital refugia of native flora and fauna that can recolonize the Picayune Strand following its restoration. The results of our field surveys in 2008 revealed that both Belle Meade and FSPSP had significantly higher species richness of amphibians than did Picayune Strand. Moreover, 80 percent of the sites at which Pine woods treefrogs (a pine habitat specialist) were detected were within the boundaries of the Bell Meade area. Because of their proximity to Picayune Strand, along with their high species richness of amphibians, Belle Meade and FSPSP will likely play a crucial role in the recovery of anuran amphibians in this ecosystem.

ANIMAL WELFARE: Our study does not require handling of any animals as it is based on recording calling anurans.

LEGAL AND POLICY-SENSITIVE ASPECTS: The PI already possesses a Scientific Collecting Permit from the Florida Fish and Wildlife Conservation Commission that authorizes any necessary handling of amphibians in PSSF and FSPSP (permit # WX08477; expiration date 12/31/2011), and a permit from Picayune Strand State Forest that grants access to this property.