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Project Work Plan

Department of Interior USGS GE PES
Fiscal Year 2014 Study Work Plan

Study Title: Across Trophic Level System Simulation Program for the Greater Everglades
Study Start Date: 2004 Study End Date: 9/30/2014
Web Site: atlss.org, sofia.usgs.gov
Location (Subregions, Counties, Park or Refuge): Total System
Funding Source: USGS GEPES
Funding History: FY04, FY05, FY06, FY07, FY08, FY09, FY11, FY12, FY13, FY14
Project Chief: Donald L. DeAngelis
Mail address: Department of Biology, University of Miami, P. O. Box 249118, Coral Gables, Florida 33124
Phone: 305-284-1690 E-mail: don_deangelis@usgs.gov
Study Personnel:
Other Investigator(s): Dr. Craig Conzelman
Email address: conzelmanc@usgs.gov
Phone: 337-266-8842 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: Susan.Walls@usgs.gov
352-264-3507 Fax: 352-264-3508
Mail address:
US Geological Survey, 7920 N. W. 71st Street, Gainesville, Florida 32653-3071

Associated Studies/Complementary Funding Sources:

Climate and Land Use Research and Development Program: "Past and Future Impacts of Climate Change on Coastal Habitats and Species in the Everglades -- An Integrated Modeling Approach" Start date 03/01/2009, End date 09/30/2013.

USGS - Natural Resources Protection Program project "Predicting Effects of Sea Level Rise and Storm Surge Overwash on Vegetation Interactions on Low-Lying Everglades National Park Coastlines". This project has been funded and will apply the MANTRA model for mangrove-hardwood hammock interaction to sites in the Everglades, End data 09/30/2013.



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.

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.

ATLSS uses South Florida Water Management Model provides hydrology for ATLSS models at a 2 x 2 mile spatial resolution, as well as Everglades Depth Estimate Network (EDEN) data.

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 FY2010, 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 apple snail, 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 collaboration with field ecologists who have years of experience and data from working with the major animal species of South Florida. The model EVERKITE 5.0 has been improved since FY2008, and currently, under FY13 funding, has been greatly updated and the user interface is being expanded to allow much greater flexibility by the user in inputting rules for habitat suitability and snail kite behavior. The output can now be displayed using EverView. Current work will also attempt to combine EVERKITE 5.0 with the dynamic model of the apple snail. The apple snail model has been completed and is now being described in a manuscript in preparation.

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. Ideas from ATLSS are now being applied to the mangrove vegetative community 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 (DeAngelis) involves the modeling of competition between invasive Melaleuca and native vegetation in southern Florida. The third task (Walls) involves developing restoration success indicators for the amphibian community. The fourth task (Conzelman) involves testing and documenting the revised snail kite model, EverKite.

Highlights and Key Findings of Study:

Snail kite modeling. EVERKITE is a spatially explicit, individual-based simulation model designed as a management scenario evaluation tool for the endangered Everglade snail kite (Rostrhamous sociabilis plumbeus) population . This model is part of the overall Across Trophic Level System Simulation (ATLSS) Program of U.S. Geological Survey. The model aims at projecting the effects of changes in hydrology of the major wetlands of southern and central Florida on the movement, reproductive success and mortality of the snail kite. Several journal papers were based on earlier versions of this model. On April 16, 2012, a meeting was held in collaboration with the U. S. Fish and Wildlife Service and University of Florida to plan revisions of the model to take into account recent empirical information on the snail kite. A revision of the model has been completed in collaboration with Dr. Craig Conzelmann of the USGS's National Wetlands Research Center (NWRC) in Lafayette. Spatial model output can be viewed on the EverView Data Viewer, a product of NWRC. The model is now in a testing and application phase.

Everglades fish community modeling. Work with Prof. Joel Trexler (Florida International University), Dr. Doug Donalson (Army Corps of Engineers) has resulted in the development of a spatially explicit simulation model of the freshwater marsh fish; GEFISH. A paper on the model is in press in Ecological Modelling. This work is helping in the formulation of restoration performance criteria for fish. The modeling will be used to determine potential impacts of changes in Everglades hydrology on the production of fish biomass and local concentrations of fish biomass that are highly available to wading birds. In particular, the model will be applied to make predictions relevant to the CERP DECOMP project. Dr. Trexler has stated "I predict that there is a hump shaped relationship between fish production and bird foraging opportunity when aggregated at the landscape scale...I believe that we can prove this hypothesis of a modal relationship using the GEFish model."

In work performed in FY2013, GEFish was used to better understand how landscape topography, hydrology, and fish behavior interact to create high densities of stranded fish. A square region of Shark River Slough was selected and the topography digitized. Simulations of population dynamics of small fish were performed within a dynamic food web with different traits for movement strategy and growth rate across an artificial, spatially explicit, heterogeneous, two-dimensional marsh slough landscape using hydrologic variability as the driver for movement. Model output showed that fish with the highest tendency to invade newly flooded marsh areas built up the largest populations over long time periods with stable hydrologic patterns. A higher probability to become stranded had negative effects on long term population size, and offset the contribution of that species to stranded biomass. The details of the topography were highly important in channeling the movements of fish and creating spatiotemporal patterns of fish movement and stranding. This output data showed concentrations of stranded fish or 'hotspots' of fish availability to wading birds in the marsh.

Apple snail modeling. This work has developed a spatially explicit simulation model, EverSnail, to describe the dynamics of apple snail populations across the Everglades landscape as a function of hydrology and temperature. In particular, the numbers and size distribution of the snails is simulated, which allows total numbers in within a given size range to be calculated for any day of the year. The effects of any scenario of sequences of drydowns or high water events can be projected with the model. The apple snail is the primary prey of the endangered snail kites and has been declining in population size. This work is being done with Prof. Phil Darby of Western Florida University and with researchers from USGS, U. S. Fish and Wildlife Service, and Everglades National Park. Simulations have been performed by the National Wetlands Research Center, using hydrological input from Everglades Depth Estimation Network (EDEN). The first version of AppleSnail has been completed. Reviewing of the output and writing a manuscript for publication are in progress.


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 models: Cape Sable seaside sparrow (SIMSPAR). ATLSS models will continue to be used for scenario evaluations for the Comprehensive Everglades Restoration Plan.

Currently, three important components of the Everglades are being modeled using SEIB models; snail kites (EVERKITE), apple snails (EverSnail), and the community of small freshwater fishes (GEFISH). The snail kite is endangered and apple snails are its key prey. The community of freshwater fish provides the food base for higher trophic levels; in particular wading birds and alligators. The model GEFISH focuses on predicting the spatial and temporal dynamics of stranded fish biomass, which is available to wading birds.

Recent Products:

Publications and Presentations (2013-2014):

Papers published in 2013-2014:

Bryant, J. P., K. Joly, F. S. Chapin, III, and D. L. DeAngelis. 2014. Will plant defense mediate browsing impacts on treeline and shrub advance into tundra? A case study of Betula in a warming climate. Ecography 37:204-2011.

Jiang, J., D. L. DeAngelis, G. H. Anderson, and T. J. Smith, III. 2014. Analysis and simulation of propagule dispersal and salinity intrusion from storm surge on the movement of a marsh-mangrove ecotone in South Florida. Estuaries and Coasts 37:24-35. DOI:10.1007/s12237-013-9666-4.

Jiang, J. and DeAngelis, D.L. 2013. Strong species-environment feedback shapes plant community assembly along environmental gradients. Ecology and Evolution. 3(12): 4119-4128.

Teh, S. Y., H. L. Koh, D. L. DeAngelis, and M. Turtora. 2013. Interaction between salinity intrusion and vegetation succession. Theoretical & Applied Mechanics Letters 3:032001. Published On-line in June 2013.

Haines, S. S. et al. 2013. A framework for quantitative assessment of impacts related to energy and mineral resource development. Natural Resources Research. Published on-line. DOI: 10.1007/s11053-013-9208-6.

Giacomini, H., D. L. DeAngelis, J. C. Trexler, and M. Petrere, Jr. 2013. Trait contributions to fish community assembly emerge from trophic interactions in an individual-based model. Ecological Modelling 251:32-43.

Yurek, S., D. L. DeAngelis, J. C. Trexler, F. Jopp, and D. D. Donalson. 2013. Spatially explicit mechanistic model of dynamic hydrology driving small fish biomass dispersal and stranding. Ecological Modelling 250:391-401.

Sibly, R. M., V. Grimm, B. T. Martin, A.S.A. Johnston, K. Kulakowska, C. J. Topping, P. Calow, J. Nabe-Nielsen, P. Thorbek, D. L. DeAngelis. 2013. Representing the acquisition and use of energy by individuals in agent-based models of animal populations. Methods in Ecology and Evolution 4:151-161.

Paper in press:

Liu, R., D. L. DeAngelis, and J. P. Bryant. Dynamics of herbivore and resource on a landscape of resources and refuges interspersed on a landscape. (Accepted, Theoretical Ecology)

Paper in revision:

Bernal, N. A., D. L. DeAngelis, P. J. Schofield, K. S. Sealey.Predicting spatial and temporal distribution of Indo-Pacific lionfish (Pterois volitans) in Biscayne Bay through habitat suitability modeling. (Submitted to Biological Invasions)

Paper in review:

Jiang, J., D. Fuller, S. Y. Teh, H. L. Koh, D. L. DeAngelis, and L. da Silveira Lobo Sternberg. Bistability of mangrove forests and competition with freshwater plants. (Submitted to Agricultural and Forest Meteorology)

DeAngelis, D. L., J. P. Bryant, Rongsong Liu, S. A. Gourley, C. J. Krebs, P. B. Reichardt. A plant toxin mediated mechanism for the lag in snowshoe hare population recovery following cyclic declines. (Submitted to Oikos)

Paper in preparation:

P. Darby, D. L. DeAngelis, S. Romañach, K. Suir, J. Bridevaux. Apple Snail dynamics on the Everglades landscape.

Planned Products: See tasks below

Collaborators: Collaborators during the project have included the following: Florida International University, University of Miami, University of Tennessee, University of West Florida, National Wetland Research Center (USGS), 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
Time Frame for Task 1: 10/01/2004 - 9/31/2014
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 complete writing of a paper on the Apple Snail Dynamics Model, developed by Phil Darby, Don DeAngelis, and Stephanie Romañach, at the JEM Lab. The model is complete and has been tested. Parts of the paper are now written. We have waited to obtain hind-cast information on water depths in WCA-3A going back to 1991. Now these data are available, and the simulation runs have been done over the needed time periods and are now being evaluated.

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. Based on a Snail Kite Workshop in April 2012, EVERKITE will be revised to take into account current information on the snail kite. 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. In particular, it will be applied to the CERP DECOMP project, which involvess decompartmentalization and re-creation of seasonal patterns of sheetflow between areas of the Everglades that are currently disconnected. The objective of this work is to use modeling, based on and complementing monitoring data, to determine the effects of seasonal depths and hydroperiod in the Everglades on the ability of fish to exploit the flooding landscape to build large populations, and also become concentrated continuously across the drying landscape. Critically, simulation modeling allows researchers to visualize and quantify experimentally different spatiotemporal patterns of biomass growth and concentration as they emerge in real-time, and compare them to empirical measurements. In this way, modeling provides an essential testing framework for relationships found in monitoring studies. This work will explicitly take into account the highly complex topography of the Everglades landscape and fish movement behavioral rules to explore how different hydrologic scenarios interact with topography to yield different outcomes of fish biomass. In particular, we will address the question of how decompartmentalization, by increasing habitat connectivity, can affect these fish dynamics. The proposed work will be computer simulation modeling based on patterns found in empirical monitoring studies. The proposed work will use GEFish simulations to study the effects of the seasonal depths and hydroperiod water on the ability of fish to exploit the flooding landscape to build large populations. These simulations will be focused on both areas of intact ridge and slough landscape characterized by highly complex topography, and areas where this ridge and slough topography has 'degenerated' due to restrictions in water flow. In both landscapes a series of water regulation will be performed, in which hydroperiods will be varied.

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


Title of Task 2: Model community recovery following biological control of Melaleuca quinquenervia. Coordination of the projects and tasks under ATLSS
Task Funding: USGS Priority Ecosystem Science
Task Leaders: Donald L. DeAngelis
Phone: 305-284-1690
Time Frame for Task 2: 08/01/2014 - 05/31/2015
Task Personnel: D. L. DeAngelis, Bo Zhang (graduate student, University of Miami)

Task Summary and Objectives:

Melaleuca quinquenervia (pine-bark tree) is an invasive non-native tree, native of Australia, that has spread over wide areas of the freshwater ecosystems of southern Florida, displacing native vegetation such as slash pine (Pinus elliottii), pond cypress (Taxodium ascendens), and sawgrass (Cladium jamaicense), threatening native biodiversity (Serbesoff-King 2003, Martin et al. 2008, Martin et al. 2011). Suppression of Melaleuca has been accomplished by the introduction of insect species, including the weevil, Melaleuca snout beetle (Oxyops vitiosa), and the psyllid (Boreioglycaspis melaleucae) (Tipping et al. 2008, 2009; Center et al. 2012). Introduction of the Melaleuca snout beetle has been especially effective in decreasing Melaleuca's internal allocation of resources to growth and reproduction (Tipping et al. 2008), such that the Melaleuca has lost its competitive advantage over native southern Florida vegetation. Former pure stands of Melaleuca are being invaded by native species (Tipping et al. 2012).

Because the Melaleuca snout beetle, the biocontrol agent having strongest effect on Melaleuca, was only introduced in 1997, it is too early to see its long-term effects on plant communities infested by Melaleuca. However, a substantial amount of information is available about both the dynamics of Melaleuca (e.g., Greenway 1994, Kaufman and Smouse 2001, Meskimen 1962, Myers 1983, Rayachhetry et al. 1998, 2001, Serbesoff-King 2003, Van et al. 2000, 2002), and the response of the Melaleuca to the biocontrol agent (e.g., Martin et al. 2010, Pratt et al. 2005., Rayamajhi et al. 2007, Tipping et al. 2008, 2009). This information appears to be sufficient to support a well known forest simulation computer, JABOWA (Botkin 1993, Botkin et al. 1972, Ngugi and Botkin 2011) that can be used to project both past and future changes in these plant communities. JABOWA and the many descendents of that model have provided successful simulations of forest succession in hundreds of cases around the world. It is important to both better understand the plant community changes that occurred with the introduction of Melaleuca and the changes that are now occurring in Melaleuca-dominated areas with the introduction of biocontrol, as well as to project future changes that might be expected over the next decades. Given the compatibility of the data needs of JABOWA and the information available on the Melaleuca in southern Florida, JABOWA seems well positioned to help provide such understanding and forecasts.


The proposed work will use the forest simulation model, JABOWA (Botkin et al. 1972, Botkin 1993, Ngugi and Botkin 2011) to develop a model to simulate successional processes, regeneration, growth, and mortality of Melaleuca in competition with native Florida species occurring in areas of the Everglades, both in the absence and presence of the biological control agent (the weevil, Oxyops vitiosa Pascoe). Our objective is to help provide a better understanding of the dynamics of the Melaleuca in native southern Florida plant communities, and the effect that the biocontrol is having on those dynamics. In addition, we will use the model to project likely future changes in the plant communities over the next few decades. In particular, the model will be applied in areas where the native vegetation is sawgrass (Cladium jamaicense), pond cypress (Taxodium ascendens), or slash pine (Pinus elliotti), but which have been taken over by Melaleuca in recent years. Because Melalueca has shown strongest invasion capability in drained pondcypress forest and recently burned transition zone between pine and pondcypress forest, properties of these sites will be given special attention.

JABOWA will first be applied to help confirm the hypothesis that Melaleuca originally displaced the native vegetation due to its massive rate of seed production, which overwhelmed native vegetation. The effects of herbivory by the control agents on Melaleuca will then be simulated. The consequent slower growth and reproduction of Melaleuca will be simulated, along with seed input, or vegetative spread, from native species. Separate simulations in sawgrass marsh, pondcypress forest, drained pondcypress forest, pine flatwood habitats, and transition zone between pine and pondcypress, will be carried out over time scales of 100 years. Various conditions, such as burning, different hydroperiods, and different initial vegetation states, will be considered in model scenarios. JABOWA will next be applied to test various hypotheses for main effects of the Melaleuca snout beetle on the Melaleuca. One hypothesis is that overcompensation of the Melaleuca for foliage loss due to the snout beetle has reduced available energy for reproduction. JABOWA can be used to simulate a sequence of hypothetical levels of effect of the snout beetle on the energetics, and study the resultant effects on dynamics of the Melalueca and native vegetation. The effects of biocontrol combined with other methods of control will also be studied.


The method used will be simulation modeling using the forest gap simulation model, JABOWA (Botkin et al. 1972, Botkin 1993). JABOWA simulates plant succession in a 0.1 hectare plot, given the characteristic of a number of plants and a set of environmental conditions. Each tree is simulated individually from the sapling stage. The model is not spatially explicit. Instead, each tree is assumed able to affect every other tree in the plot, through shading, depending on the relative heights of the trees. Therefore, interactions are averaged over the plot. Non-woody plants (sawgrass in this case) can also be included as a variable, with their growth in height determining their shading effect. JABOWA simulates the processes of seedling survival to sapling stage, growth of sapling and older individuals, both intraspecific and interspecific competition, reproduction, and mortality.

Habitat conditions (soil moisture, temperature, radiation) can be prescribed in the plots on a monthly basis, Separate models will be developed for at least five habitats, sawgrass marsh, pond cypress forest, slash pine forest, drained pondcypress forest and recently burned transition zone between pine and pondcypress forest.

The physiological characteristics of Melaleuca and the key competing species associated with each of the five habitats will be found through data bases and other literature searches. Most of the relevant data for Melaleuca have already been estimated. Three competitive interactions will be simulated; Melaleuca vs. sawgrass, Melaleuca vs. pond cypress, and Melaleuca vs. slash pine.

The procedure used in modeling will be to first simulate the invasion in the five habitats noted above in the absence of biological control. Because experiments on invasions of Melaleuca seeds and seedlings into such habitats have been performed (e.g., Myers 1983, Tipping et al. 2012) data exist to help calibrate and test the model. Next, various levels of biocontrol herbivory effects, induced by the Melaleuca snout beetle in particular, will be simulated, and the dynamics of stands with various starting point mixtures of Melaleuca and native vegetation, will be simulated. Combinations of biological control with other methods of Melaleuca suppression will also be examined.

The modelers will work closely with personnel of the Invasive Plant Research Laboratory in Davie, Florida, at each step in this process.

An outline of the processes simulated in JABOWA are given in the appendix.

Expected Products

Fully implemented models of Melaleuca and key native tree species (or sawgrass) will be produced, along with documentation.

Sets of scenarios will be produced for all cases.

One or more open literature publications will be produced. Any publications coming out of this work will be only with the full approval of and coauthorship by personnel of the Invasive Plant Research Laboratory.


Botkin, D. B. 1993. Forest Dynamics: An Ecological Model. Oxford University Press. Oxford and New York. 309 pp.

Botkin, D. B., J. F. Janak, and J. R. Wallis. 1972. Some ecological consequences of a computer model of growth. Journal of Ecology 60:849-872.

Center, T. D., M. F. Purcell, P. D. Pratt, M. B. Rayamajhi, P. W. Tipping, S. A. Wright, and F. A. Dray, Jr. 2012. Biological control of Melaleuca quinquenervia: an Everglades invader. BioControl. 2012. 57:151-165.

Greenway, M. 1994. Litter accession and accumulation in a Melaleuca quinquenervia (Cav.) S. T. Blake wetland in Southeastern Queensland. Australian Journal of Marine and Freshwater Research 45:1509-1519.

Kaufman, S. R., and P. E. Smouse. 2001. Comparing indigenous and introduced populations of Melaleuca quinquenervia (Cav.) Blake: response of seedlings to water and pH levels. Oecologia 127:487-494.

Martin, M. R., P. W. Tipping, K. R. Reddy, P. T. Madiera, and D. Fitzgerald. 2011. An evaluation of the impact of Melaleuca quinquenervia invasion and management on plant community structure after fire. Aquatic Botany 95:287-291.

Martin, M. R., P. W. Tipping, K. R. Reddy, S. H. Daroub, and K. M. Roberts. 2010. Interactions of biological and herbicidal management of Melaleuca quinquenervia with fire: Consequences for ecosystem services. Biological Control xxx-xxx. Doi:10.1016/j.biocontrol.2010.06.002.

Martin, M. R., P. W. Tipping, and J. O. Sickman. 2008. Invasion by an exotic tree alters above and belowground ecosystem components. Biological Invasions. doi:10.1007/s10530-008-9366-3.

Meskimen, G. F. 1962. A Silvicultural Study of the Melaleuca Tree in South Florida. Master's thesis, University of Florida, Gainesville, FL.

Myers, R. L. 1983. Site susceptibility to invasion by the exotic tree Melaleuca quinquenervia in southern Florida. Journal of Applied Ecology 20:645-658.

Ngugi, M. R. and D. B. Botkin, 2011, "Validation of a multispecies forest dynamics model using 50-year growth from Eucalyptus forests in eastern Australia," Ecological Modelling. 222: 3261- 3270.

Pratt, P. D., M. B. Rayamajhi, T. K. Van, and T. D. Center. Herbivory alters resource allocation in the invasive tree Melaleuca quinquenervia. Ecological Entomology 30:316-326.

Rayachhetry, M. B., T. K. Van, and T. D. Center. 1998. Regeneration potential of the canopy-held seeds of Melaleuca quinquenervia in South Florida. International Journal of Plant Science 159:648-654.

Rayachhetry, M. B., T. K. Van, T. D. Center, and F. Laroche. 2001. Dry weight estimation of the aboveground components of Melaleuca quinquenervia trees in southern Florida. Forest Ecology and Management 142:281-290.

Rayamajhi, M. B., T. K. Van, P. D. Pratt, T. D. Center, and P. W. Tipping. 2007. Melaleuca quinquenervia dominated forests in Florida: analyses of natural-enemy impacts on stand dynamics. Plant Ecology 192:119-132.

Serbesoff-King, K. 2003. Melaleuca in Florida: A literature review on the taxonomy, distribution, biology, ecology, economic importance, and control measures. Journal of Aquatic Plant Management 41:98-112.

Tipping, P. W., M. R. Martin, P. D. Pratt, T. D. Center, and M. B. Rayamajhi. 2008. Suppression of growth and reproduction of an exotic invasive tree by two introduced insects. Biological Control 44:235-241.

Tipping, P. W., M. R. Martin, R. Pierce, T. D. Center, P. R. Pratt, and M. B. Rayamajhi. 2012. Post-biological control invasion trajectory for Melaleuca quinquenervia in a seasonally inundated wetland. Biological Control 60:163-168.

Tipping, P. W., M. R. Martin, P. D. Pratt, M. B. Rayamajhi, and T. D. Center. 2013. An abundant biological control agent does not provide a significant predator subsidy. Biological Control 67:212-219.

Tipping, P. W., M. R. Martin, K. R. Nimmo, R. M. Pierce, M. D. Smart, E. White, P. T. Madeira, and T. D. Center. Invasion of a West Everglades wetland by Melaleuca quinquenervia countered by classical biological control. Biological Control 48:73-78

Van, T. K., M. B. Rayachhetry, and T. D. Center. 2000. Estimating above-ground biomass of Melaleuca quinquenervia in Florida, USA. Journal of Aquatic Plant Management 38:62-67.

Van, T. K., M. B. Rayachhetry, T. D. Center, and P. D. Pratt. 2002. Litter dynamics and phenology of Melaleuca quinquenervia in South Florida. Journal of Aquatic Plant Management 40:22-27.

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 (Lead PI) and Stephanie Romañach, USGS-SESC; J. Hardin Waddle, USGS-NWRC
Phone: 352-264-3507
FAX: 352-395-6608
Task Status (proposed or active): Active
Task priority: High
Time Frame: 2014-2015
Task Personnel: S. Walls and S. Romañach (SESC); H. Waddle (NWRC)

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. 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).

With previous GEPES funding we have accomplished the following:

  1. With funding that began in 2007 (to K. Rice and continued by S. Walls), we developed a habitat suitability model, called the Amphibian Community Species Richness Model, that predicts the responses of an amphibian community to hydrologic and habitat restoration in the Greater Everglades Ecosystem. In 2011, this model was selected by the Central Everglades Planning Process to be used as one of seven Ecological Planning Tools to help in selecting restoration plans. The National Park Service subsequently requested a modification for how model output is displayed and the model remains in use. This product remains unpublished in the primary peer-reviewed literature, however. Continued funding in FY14 would allow us to generate a peer-reviewed journal manuscript on this model.

  2. During 2007-2008, we estimated patterns of co-occurrence between nonindigenous Cuban treefrogs and native treefrog species by sampling 107 sites across Picayune State Forest, Fakahatchee Strand Preserve State Park, Florida Panther National Wildlife Refuge, and Big Cypress National Preserve in Collier County, southwest Florida. This phase of our work led to the development of a new model for estimating patterns of co-occurrence of interacting species. An analysis of our data revealed that sites occupied by Cuban treefrogs (a predatory species) were 9.0 times less likely to contain Green Treefrogs and 15.7 times less likely to contain Squirrel Treefrogs compared to sites without Cuban treefrogs. This work was published as: Waddle, J.H., R.M. Dorazio, S.C. Walls, K.G. Rice, J. Beauchamp, M.J. Schuman, and F.J. Mazzotti. 2010. A new parameterization for estimating co-occurrence of interacting species. Ecological Applications 20:1467-1475.

  3. With funding from 2009-2011, we placed automated recording units (ARU's) at 27 locations in the Picayune State Forest and Fakahatchee Strand Preserve State Park, which were part of the previous 2007-2008 study described above. We recorded calling male anurans (frogs and toads) and generated 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 units, the Belle Meade CARL area to the west and the Fakahatchee Strand Preserve State Park to the east. The Picayune Strand is an area undergoing active hydrological restoration under the Comprehensive Everglades Restoration Plan (CERP).

    We compared occurrence of anurans at sites in the Picayune restoration area, to nearby locations in the relatively undisturbed habitat of Bell Meade and Fakahatchee Strand (reference sites). We assessed the utility of the latter as restoration targets, using a hierarchical model of community species occupancy to estimate the probability of occurrence of anurans in restoration and reference locations. We detected 14 species, 13 of which were significantly more likely to occur in reference areas. All 14 species were estimated by our model to occur at these sites but, across both years, only 8-13 species were estimated to occur at restoration sites. The composition and structure of these habitats within and adjacent to the Picayune Strand State Forest indicate that they are suitable targets for habitat restoration, as measured by amphibian occurrence and species richness. This work is accepted for publication in Wetlands Ecology and Management as Walls, S.C., J.H. Waddle, W.J. Barichivich, I.A. Bartoszek, M.E. Brown, J.M. Hefner, and M.J. Schuman. Anuran site occupancy and species richness as tools for evaluating restoration of a hydrologically-modified landscape.
    map showing xx
    Fig. 1. Location of 60 Automated Recording Units (ARU's) deployed from October 2011 to December 2012 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. post restoration) based on an integrated surface water-groundwater model developed by Copp et al. (2007).

  4. In October, 2011 we expanded our sampling design from 27 ARU's to 60 and, based on the predictions of an integrated surface water-groundwater model (Copp et al. 2007), we hypothesized that the composition of amphibian communities following restoration would vary with predicted differences (pre- versus post-restoration) in water depths across the Picayune landscape. We selected 40 new locations (in addition to 20 previous locations within Belle Meade) at which we deployed an ARU. 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 et al.'s (2007) predicted change in water depth (Fig. 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 mid-range 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 (some adjacent to the western-most canal) and 20 sites around each of the remaining three canals.

    The data collection component of this project ended in December 2012. Since then, contract employees at both SESC and NWRC have been transcribing data from the recordings. We anticipate that this process will be complete by September, 2014, but manuscript preparation can begin immediately.

With current funding, our objectives are to:

  1. Generate a peer-reviewed journal article on the Amphibian Community Species Richness model.

  2. Generate an additional peer-reviewed journal article that tests the utility of Copp's (2007) integrated surface water-groundwater model in evaluating whether the composition of amphibian communities following restoration varies with predicted differences (pre- versus post-restoration) in water depths across the Picayune landscape.

    Additional long-term goals are to:

  3. Provide insight into management options with respect to the effects of various water management scenarios on the amphibian community in the Picayune Strand.

  4. Refine the Amphibian Community Species Richness model to address how climatic variation may impact the hydrology of sites and, thus, their occupancy by amphibians.

PROPOSED ANALYSIS FOR OBJECTIVE #2: We will use a hierarchical formulation of a multi-species 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 & Royle 2008; Royle & Dorazio 2008). In this community-level occupancy model each species has its own detection probability, occurrence, and treatment response. Binomial detection and non-detection 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 et al. 2006), non-detection 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)

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:

zik ~ Bern(Ψik).       (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 & 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 et al. 2003).


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

Copp, R., C. Rowney, and A. Nath. 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. World Environmental and Water Resources Congress 2007: Restoring Our Natural Habitat.

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

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

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

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: Mrc Biostatistics Unit, www.mrc-bsu.cam.ac.uk/bugs/


  2014/QTR 2015/QTR










Preparation of Publications

    xx xx        

Presentations at Meetings

          xx xx  

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.

Task Product(s):

Specific Products / Milestone Date


This wrap-up of our previously funded work 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. 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 non-governmental 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.



FACILITIES, EQUIPMENT, and STUDY AREA(S): All of our remaining work will be conducted at the SESC and NWRC office facilities.

Title of Task 4: ATLSS Support for Greater Everglades Landscape Ecological Modeling
Task Funding: USGS
Task Leader: Craig Conzelman
Phone: 337-266-8842
Fax: 337-266-8616
e-mail: conzelmanc@usgs.gov
Time Frame for Task: Fiscal Year 2014
Task Personnel: Craig Conzelmann, Sumani Chimmula, Jimi Darcey

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 and the Joint Ecosystem Modeling (JEM) 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 recently developed the EverVIEW suite of visualization, data manipulation, and modeling software. This scope will address the needs for programming resources focused on several upper trophic models, investigating the dynamic integration of said models, along with initiating the port of ATLSS Data Viewer System (ADVS) functionality into an EverVIEW plugin.

FY2014 will be largely committed to working with DOI on testing, making minor modifications, and documenting the snail kite model (EverKite).


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 / EverVIEW and modify them for specific purposes relevant to resource manager's needs.

  1. Continue to support natural resource managers and the IMS related to use of ADVS.
  2. Provide training on the usage of the modified ATLSS DVS.
  3. Provide run support for ATLSS models.
  4. Provide the programming resources to help with the testing and documentation of EverKite.


  • Tasks 1, 2, 3, and 4 are on-going tasks which will be complete by August 31, 2014

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