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Project Work Plan

Greater Everglades Science Program: Place-Based Studies

Project Work Plan FY 2003


Project Title:American Alligator Ecology and Monitoring for CERP
Project start date:10/1/2002 Project end date: 12/31/2006
Principal Investigator: Kenneth G. Rice
Email address:
Phone: 954-577-6305 Fax: 954-577-4091
Mail address: USGS, University of Florida Field Station, 3205 College Ave., Fort Lauderdale, FL 33314

Other Investigator(s): Frank J. Mazzotti
Email address:
Phone: 954-577-6304 Fax: 954-475-4125
Mail address: University of Florida, Fort Lauderdale Research and Education Center, 3205 College Ave, Fort Lauderdale, FL 33314

Project Summary: Many important questions concerning the effects of Everglades restoration on alligator populations remain unanswered such as the impacts of decompartmentalization, the role of alligator holes as aquatic refugia, and the effects of hydrology on population growth and condition. Further, the methods for monitoring and evaluating restoration success are not clear or have not been adapted for use during CERP. Also, we need to continue to update and validate restoration tools such as population models for use in alternative selection, performance measure development, and prediction. This project will directly address the questions outlined above, develop monitoring methods, and validate restoration tools for use in CERP. All project tasks have been requested by management agencies in South Florida (NPS, USFWS), listed as critical CERP priority research needs (see USGS Ecological Modeling Workshop), and/or highlighted as science objectives for CESI (see Science Objectives for CESI FY02).

Project Objectives and Strategy: This project will accomplish several tasks with a combination of field data collection, GIS mapping, and computer simulation. Our main objectives are designed to answer questions critical to restoration success and to provide the tools necessary for evaluation:

  • Develop monitoring methods necessary for evaluation of restoration success in alligator populations.
  • Understand the effects of decompartmentalization and other CERP projects on restoration of alligator populations.
  • Identify and quantify the extent of aquatic refugia maintained by alligators throughout the system and develop relationships necessary to predict restoration of refugia.
  • Validate and update ecological models for use in prediction of the effects of restoration.

Potential Impacts and Major Products:

  • Tools and scientific data necessary for evaluation of restoration success.
  • Methods and data necessary for RECOVER's adaptive assessment process and monitoring program.
  • Models, Maps, and other GIS products needs for evaluation and prediction of the effects of restoration.
  • Model interpretation and simulation for management and public needs.
  • Peer-reviewed publications, web-based model output, and PC simulation models.

Collaborators: Leonard Pearlstine, University of Florida; Laura Brandt, USFWS
Clients: National Park Service, United States Fish and Wildlife Service


Title of Task 1: Relative distribution, abundance, and demographic structure of the American alligator in relation to habitat, water levels, and salinities.

This is a continuing CESI project funded by NPS during FY02.

Task Leaders: Frank J. Mazzotti, Kenneth G. Rice, Laura A. Brandt
Phone: 954-577-6305
Fax: 954-577-6347
Task Status (proposed or active): Active
Task priority: High
Task Personnel: Geoff Cook, University of Florida

Task Summary and Objectives: The purpose of this project is to evaluate the relative distribution, abundance, and demographic structure of alligators in various habitats in relation to water levels and salinities. The relative distribution and abundance of alligators is a key indicator component of the conceptual ecosystem models for Big Cypress, marl prairie/rocky glades, ridge and slough, and mangrove transition zone ecosystems and has been identified as a performance measure in the CERP monitoring and assessment plan. Demographic data are needed for development of models to assess the potential impacts from operation of CERP projects (CERP science objective 3004-3).

Currently, the only surveys for alligators in Everglades National Park are SRF surveys for nests. The Florida Fish and Wildlife Conservation Commission conducts limited surveys for alligators in and adjacent to Water Conservation Areas 2 and 3 as part of their public hunt program. Yet, as restoration occurs in ecosystems such as the rocky glades and the mangrove transition zone it will take more than 10 years for dispersing juveniles to become nesting animals. Evaluating the relative distribution, abundance, and demography of alligators allows for a more rapid assessment of the impacts of CERP projects on target systems.

As important as alligators are in the Everglades ecosystem, surprisingly little is known about them outside of Everglades National Park. In this project alligator surveys will be continued in A.R.M. Loxahatchee National Wildlife Refuge, incepted in Water Conservation Areas 2 and 3, through Everglades National Park, and continued in the estuaries of the Gulf of Mexico. The alligator survey network described above is the first system-wide, systematic effort to look at Everglades alligators. Perhaps the most important aspect of the proposed continuation of the alligator survey network is its contribution to evaluating CERP projects.

There are two critical CERP issues that the alligator survey network can provide information required for making policy decisions:

  1. How do canals affect alligator populations, and more importantly, how will the proposed removal of canals affect alligator populations and subsequently the surrounding marsh habitat?
  2. Alligators were formerly abundant in fresh and brackish water tidal areas of Everglades National Park. An identified weakness of CERP is the lack of evidence for significant improvement of freshwater deliveries to estuarine areas, especially those draining into the Gulf of Mexico and Florida Bay. Because the distribution and abundance of alligators in estuaries is limited by the availability of freshwater, restoring alligator populations in areas of former importance would be an excellent indicator of restoration success.

In both cases, baseline data are needed now to provide post restoration feedback to the policy making process. Without the continuation of the alligator survey network next year there will be insufficient baseline data for making before and after comparisons, and no substantial input into the restoration process.

Night light surveys are a well-established, cost effective method for gathering the required information (Bayliss 1987, Woodward and Moore 1990).

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

During FY03, we will concentrate our work on:

    • Continued development of monitoring methods and correction factors for environmental conditions and sighting proportions.
    • Continued monitoring of South Florida's alligator populations through night-light surveys on routes developed during FY02. Also, we will begin development of new survey routes based on the 2x2 mile cells developed for monitoring and evaluation of restoration success by RECOVER.
    • Continued alligator capture for comparison of condition through South Florida and through time.

After examining past survey data in Everglades National Park and evaluating the ability to detect change in an alligator population we believe it most effective to concentrate surveys to peak wet season and peak dry season replicate spotlight surveys along with capture surveys of alligators to assess the relative distribution, abundance, and demographic structure of the American alligator. Established survey routes of estuarine rivers and freshwater canals and marshes extending from the mangrove fringe of Everglades National Park north to Arthur R. Marshall National Wildlife Refuge will continue to be performed at night by skiff, canoe, jon boat, airboat, and truck. Alligator locations will continue to be recorded using GPS and field maps, and sizes of alligators will be estimated whenever possible. Environmental data including habitat type, air and water temperature, salinity, wind and wave action, and spot water levels will be recorded. Regional hydrologic data will be obtained from the SFWMD and the USGS.

To determine demographic structure (size class and sex) structure semi-annual capture surveys will be preformed using the same vehicles and locations described above. Alligators will be captured by hand, noose, dart, or tongs. Total length, snout-vent length, tail girth, and weight will be measured, and sex determined. In addition the relative condition of alligators will be determined by doing a condition factor analysis (Leslie 1997, also see CESI project Compilation of America Alligator Data Sets in South Florida for Restoration Needs to be completed in FY02 for specific condition methods).

Planned Outreach: This project will develop an index of relative abundance and condition of alligators in different habitats in relation to water levels and salinities. The results will be reported in technical reports, fact sheets, scientific and public presentations and peer reviewed publications. The survey routes and data summaries will be available on a web site. The data from this project will be used to update and validate population models (e.g. ATLSS) and can be used for the development and validation of other assessment tools (i.e. HSI models). In addition, the data will be available for use in the RECOVER adaptive assessment process and for inclusion in the annual report card.

Literature Cited:

Bayliss, P. 1987. Survey methods and monitoring within crocodile management programmes. Pages 157-175 In Webb, G. J. W., S. C. Manolis, and P. J. Whitehead (eds). Wildlife Management: Crocodiles and Alligators. Surrey Beatty and Sons, Chipping Norton, NSW.

Leslie, A. J. 1997. The ecology and physiology of the Nile crocodile, Crocodylus niloticus, in Lake St. Lucia, Kwazulu/Natal, South Africa. PhD Dissertation: Drexel University, Philadelphia, PA.

Woodward, A. R., and C. T. Moore. 1990. Statewide alligator surveys. Final Report: Bureau of Wildlife Research, Florida Game and Freshwater Fish Commission, Tallahassee, FL.

Title of Task 2: Mapping and Characterizing Aquatic Refugia in Everglades National Park and Arthur R. Marshall Loxahatchee National Wildlife Refuge

This is a continuing CESI project funded by NPS during FY02.

Task Leaders: Frank Mazzotti, Kenneth Rice, Leonard Pearlstine, Laura Brandt
Phone: 954-577-6305
Fax: 954-577-6347
Task Status (proposed or active): Active
Task priority:
Task Personnel: Karen Minkowski, University of Florida

Task Summary and Objectives: Dry season refugia for aquatic animals, are assumed to be a critical component of the Everglades landscape (Craighead 1968, Mazzotti and Brandt 1994). They are an important attribute in the conceptual models being used to develop the monitoring and assessment plan for the Comprehensive Everglades Restoration Plan. The relationships among dry season refugia, aquatic fauna, birds, and alligators have been identified as a key uncertainty in the CERP monitoring and assessment plan. In addition, the distribution and occupancy of alligator holes has been identified as a performance measure for the marl prairie/rocky glades conceptual model. As important as aquatic refugia are imagined to be, their ecology has remained an almost completely unstudied phenomena. This gap in information concerning aquatic refugia is becoming critical for making ecosystem restoration decisions. The proposed project will integrate GIS/GPS technology with field biology to bridge this gap. The data proposed to be collected here will provide an important step in addressing the role of aquatic refugia in the freshwater Everglades, particularly ridge and slough and marl prairie/rocky glades areas, and will provide critical input for ecosystem model development (contributes to CERP science objective 3004-2 and 3004-3), development of ecological success criteria, evaluation of alternatives for restoration of the Greater Everglades/South Florida Ecosystem and monitoring and assessment of the success of CERP.

This project will address specific uncertainties identified in the monitoring and assessment plan. Data collected during this project will provide critical information needed for modeling of fish and other aquatic fauna distributions in response to changes in hydrology. It also will provide baseline data on aquatic refugia that will be used in the CERP monitoring and assessment process as a performance measure and to help explain patterns of aquatic fauna and wading bird foraging and nesting. It is critical that these data be collected now, prior to major changes, so that the influences of CERP projects can be evaluated.

Because of the interdependence of wading birds, aquatic fauna and aquatic refugia this project is critical to the evaluation of all CERP projects and science objectives that deal with the potential effects of changes in hydropatterns.

Aquatic refugia may be small ponds created by alligators termed alligator holes or may be the result of some other phenomena such as fire or peat-pop-up. As important as aquatic refugia are assumed to be in the Everglades landscape their ecology has remained an almost completely unstudied phenomena. This, despite the fact that one quantitative study of one alligator hole in the Big Cypress Swamp confirmed the general expectations of ecological importance of aquatic refugia (Kushlan 1972,1974). This gap in basic information concerning alligators holes such as, types, location and number, is becoming critical. Modeling efforts such as the Across Trophic Level Simulation System (ATLSS) for fish and wading birds require the information from this study. ATLSS in particular is dependent on information on aquatic refugia. Information on aquatic refugia would also be useful to field and modeling studies on fish, wading birds, and water quality currently underway. In fact, a study of aquatic refugia could be considered a linchpin holding together an number of studies analyzing South Florida ecosystems. Aquatic refugia are critically important in marl prairie/rocky glades habitats and their distribution and abundance is a specific performance measure for that system.


  • Map, classify, and analyze spatial patterns of aquatic refugia. Three tasks have been designed to answer these questions. These tasks will produce a map and associated GIS database for aquatic refugia in Everglades National Park or A.R.M. Loxahatchee National Wildlife Refuge, a classification system for aquatic refugia, and an analysis of their spatial pattern (contributes to CERP science objective 3070-6).
  • To locate and map aquatic refugia in Everglades National Park and Loxahatchee National Wildlife Refuge depending on the availability of aerial photography.
  • To describe aquatic refugia in terms of their geography (location in the landscape), structure (size, shape, substrate, and vegetation association), and function (wildlife habitat, hydrology, and water quality). To classify aquatic refugia using geography, structure, and function.
  • To calculate landscape metrics (dispersion, orientation, proximity, interspersion, size frequency distribution, and others) of aquatic refugia.

Significance of Results - The results of this project will be used to increase certainty identified in specific areas identified in the monitoring and assessment plan. Data collected during this project will be used for modeling the distribution and abundance of fish and other aquatic fauna in response to changes in hydrology. It also will provide baseline data on aquatic refugia that will be used in the CERP monitoring and assessment process as a performance measure for the marl prairie rocky glades system and to help explain patterns of aquatic fauna and wading bird foraging and nesting. The results of the mapping effort in WCA 2 and 3 have been used in ATLSS models by the SFWMD in analyzing SRF flight data for wading birds.

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

The project began in FY02 in Loxahatchee NWR. We anticipate finishing the work in Loxahatchee in early FY03 and moving our work to Everglades National Park for completion during FY03.

The following subtasks have been designed to achieve the project objectives.

Subtask 2.1. Mapping.

Description: Aquatic refugia will be located and mapped using a combination of aerial photography (supplied by Everglades National Park and/or Loxahatchee National Wildlife Refuge) and global position system (GPS) technology. Photographic imagery will be analyzed using a geographic information system (GIS). All GPS data will be managed using GIS.

Subtask 2.2. Ecological characterization.

Description: The geography of aquatic refugia will be described using the map and GIS database completed in Task 1. Location of refugia can be categorized by position in central slough or peripheral wetland and by proximity to landscape features such as canals. Structure and function of aquatic refugia will be determined from field studies of selected holes.

Subtask 2.3. Analysis of spatial patterns.

Description: With the emergence of GIS the ability to analyze spatial patterns of ecological resources has advanced significantly. State-of-the-art spatial statistics will be used to analyze the data obtained from Task 1.

The methods described below is a proven cost effective method for mapping aquatic refugia at high resolution over a large area and has been used to map alligator holes in Water Conservation Areas 2 and 3 (Campbell and Mazzotti 2001). It is important that these data be collected now, prior to major changes, so that the influences of CERP projects can be evaluated.

Alligator holes will be mapped using color infra-red (CIR) aerial photography. CIR photography will be obtained from Everglades National Park or Loxahatchee National Wildlife Refuge. Selected photographs will be professionally scanned at one meter resolution and the digital images stored on CD-ROM. Photographic prints (contact prints) of the original film also will be made.

Potential alligator holes will be located on the contact prints using a light table and magnifying lens. The alligator holes found on each image will be plotted on a 9x9 inch clear acetate overlay with a permanent marker. For each image the location of the two to four ground control points also will be plotted on the overlay. Ground control for the photos will be plotted on a clear overlay, and included with the original data set.

All image overlays will be assembled and potential alligator holes mapped. Then a second, continuous transparent overlay will be placed over the mosaiced overlays, and all alligator holes and control points retraced onto a final single sheet. The large overly will be photographically reduced and scanned into the computer using a standard flatbed scanner.

The digital image, with potential alligator holes and ground control, will be imported into an image processing software, and the coordinates (Universal Transverse Mercator ) for the ground control entered into the computer. The digital image will then be reprocessed by the software producing a complete spatially referenced image.

The spatially referenced image will then be imported into GIS software after conversion to raster image format. A point layer for the GIS then will be digitized on screen and a database for the individual points with their locations can be developed.

Other layers of information for the GIS will be created in the same manner from the photographic contact prints. These include the study area boundary, canals and levees, major airboat trails, minor airboat and buggy trails, and islands. The GIS system also will include information obtained from other sources. These data layers include the Florida Landcover vegetation layer, developed form landsat satellite imagery by the Florida Cooperative Fish and Wildlife research Unit, University of Florida, and vegetation information from other sources.

Field measurements to describe alligator holes will include structure (size, shape, substrate, and vegetation) and function (hydrology, wildlife use, and water quality).

Alligator holes will be located in the field using a GPS receiver and printed field maps of the hole from the digital imagery. At each alligator hole field measurements will proceed in the following order:

    1. Photo of the alligator hole.
    2. Dissolved oxygen, conductivity, pH and temperature (air and water) of the pond will be measured.
    3. Wildlife sightings, including tracks, scats, alligator trails, footprints, and tail drags will be recorded throughout the survey.
    4. Surrounding vegetation will be recorded onto the color infra-red field-maps.
    5. Transects will be established across both the length and width the alligator hole. Transects will extend into the marsh matrix. Depth of water will be recorded with a round fiberglass measuring pole at half meter intervals. Muck depth will be measured by sinking a thin fiberglass baton down to the limestone bedrock and noting the difference on the measuring pole. Vegetation or open water will be recorded at each point.

Based on these field observation alligator holes will be separated into the following descriptive classes: origin, status, size, shape, depth, muck, and island. A description of each of these categories follows:

  1. origin:
    • natural = created by alligators
    • artificial = created by humans
  2. status:
    • active = inhabited by alligators
    • inactive = no alligators present, or signs of alligators
  3. size: area of the alligator pond
    • small = < 20 square meters
    • medium = 20 - 40 square meters
    • large = > 40 square meters
  4. shape: shape of the alligator pond
    • circular = width > half the length
    • oval = width < half the length
    • irregular = any non-elliptical shape
  5. depth:
    • shallow = < 15 cm average water depth
    • medium = 15 - 30 cm average water depth
    • deep = >30 cm average water depth
  6. muck:
    • shallow = < 30 cm average muck depth
    • medium = 30 - 60 cm average muck depth
    • deep = >60 cm average muck depth
  7. island:
    • yes = an island is within 20 meters of the alligator pond
    • no = an island is not within 20 meters of the alligator pond

The spatial patterns of aquatic refugia will be analyzed for all located refugia and for refugia of different type and characteristics as identified in Subtask 2.2. It will be determined if holes are distributed randomly, uniformly, or clumped. In addition, the scale of the pattern will be identified. A combination of indicies of spatial patterning such as: nearest neighbor distances, Pielou's index of dispersion, Clark and Evens' nearest neighbor, and Ripley's K will be used for this task. Pielou's index and the Clark and Evens' index are used to determine if the holes are randomly distributed, uniformly distributed, or clumped. Ripley's K is used to examine the scale of clumping. Density maps that illustrate the concentration of holes will be produced for each area. Distance from canals or other significant features will be calculated for each hole and these data along with available data on vegetation, hydrology, topology, etc. will be used to explore the relationships between hole location and type and physical and ecological landscape features.

Literature Cited:

Campbell, Mark R., Mazzotti, Frank J. 2001. Mapping Everglades Alligator Holes Using Color Infrared Aerial Photography. Florida Scientist.

Craighead, Frank C., Sr. 1968. The role of the alligator in shaping plant communities and maintaining wildlife in the southern everglades. The Florida Naturalist. 41: 3-7, 69-74, 94.

Kushlan, James A. 1972. An ecological study of an alligator pond in the Big Cypress swamp of Southern Florida. Masters Thesis. University of Miami, Coral Gables, Florida.

Kushlan, James A. 1974. Observations on the role of the American Alligator (Alligator mississippiensis) in the southern Florida wetlands. Copiea. (No 4. Dec. 31):993-996.

Mazzotti, Frank J. and Laura A. Brandt. 1994. Ecology of the american alligator in a seasonally fluctuating environment. In Everglades: the ecosystem and its restoration. Steven M. Davis and John C. Ogden. Eds. St. Lucie Press. Delray Beach, FL. pp. 485-505.

Planned Outreach:

  • In addition to a technical report, products from Subtask 2.1 will include a map and supporting GIS data base showing the location of aquatic refugia in Everglades National Park and/or Loxahatchee National Wildlife Refuge. These products will form the basis for the analyses to be performed in Subtasks 2.2 and 2.3.
  • This task will produce a classification system for aquatic refugia. The responses of alligators, fish and wading birds in ATLSS models will be dependent upon the type of aquatic refugia.
  • The spatial analysis of aquatic refugia will form the baseline required to analyze the impacts of CERP on the Everglades landscape.


Title of Task 3: Population-Based Simulation Modeling of American Alligator Populations in Support of CERP

This is a continuation of a CESI project funded by NPS during FY02 to provide model updates, calibration, and validation during the CERP Process.

Task Leaders: Kenneth G. Rice, USGS and Daniel Slone, US Forest Service
Phone: 954-577-6305
Fax: 954-577-6347
Task Status (proposed or active): Active
Task priority: High
Task Personnel: none

Task Summary and Objectives: An alligator population model is currently in the calibration phase for use in evaluating CERP restoration alternatives and developing performance measures (see CESI project "Parameter Estimation and Population-Based Simulation Modeling of American Alligator Populations in Support of ATLSS"). The model will require periodic updates, further calibration, and validation as new data becomes available. This data is being collected during monitoring of the alligator throughout South Florida (see NPS SRF and Task 1 above). During the recent USGS Ecological Modeling Workshop, model validation and calibration were noted as priority research needs by a number of the participants. Further, the National Park Service has requested several model runs and interpretation from USGS during FY03. The specific objectives for this task are:

  • Provide calibration and validation of the ATLSS American Alligator Population Model based on data collected in South Florida through 2002.
  • Provide model runs and interpretation for CSOP (NPS) and others as requested.

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

The core model component is a 3-D matrix that records the density of each stage of alligator in each 500x500m spatial location (500m pixel size based on the mean adult female home range size). This structure is manipulated in its entirety with 3-D matrix operations, and interacts with survival and condition 3-D matrices, each in turn calculated for each time step based on water level, crowding, etc. Alligators either survive and grow to the next stage of development (SD), survive but not grow (SND), or die. The proportion of each stage that falls into the three categories depends on water levels and alligator condition throughout the year, and the density of adult alligators at each spatial location:

Juveniles(x,y)= fSD (Hatchlings, Adults, Water, Condition)(x,y)+gSND (Juveniles, Adults, Water, Condition)(x,y)

Subadults(x,y)=fSD (Juveniles, Adults, Water, Condition)(x,y)+gSND (Subadults, Adults, Water, Condition)(x,y)

Adults(x,y)= fSD (Subadults, Adults, Water , Condition)(x,y)+gSND (Adults, Water , Condition)(x,y)

Adult female alligators produce offspring at each spatial location, depending on water levels during the nesting period, habitat type, and the age and condition of the female over the previous season. The nesting potential of each cell is predicted by the ATLSS American Alligator Production Index which incorporates local habitat data and hydrological dynamics to predict the probability of producing nests and offspring successfully in each cell, if a healthy female is present.

Eggs(x,y)=f (Adults, Water, Habitat , Condition)(x,y)

To disperse alligators, we use a discrete spatial convolution method . This is similar to a "blur filter" used by many image-processing computer programs, and is a process that takes the contents of a cell and redistributes it according to a dispersal kernel (below). The dispersal kernels are sized according to average dispersal distance of each alligator stage. For normal dispersal, the height of the discrete kernel, k[x,y] at each location (x, y) relative to the cell where it is applied is:

equation for dispersal kernals

where s is the standard deviation of the kernel. The subadult stage is most mobile, while adults and hatchlings are more sedentary.

Output of the model is a 3-D alligator density matrix, with space (x and y) along two axes, and the stage classes along the third axis. Also included are a "running average" of the historical health and survival rates of each stage in each cell. This construct is easily summed for total alligator population, or subsampled to check for corroboration with field data. Instantaneous densities, and local rates-of-change can be calculated from this model.

During FY03, we will concentrate our work on:

    • Developing "virtual" night-light and nesting survey routes that correspond with NPS SRF, USFWS, and Task 1 (above) alligator monitoring. This will allow calibration and validation of the current model and checks on future model modifications.
    • Further modification of the model to incorporate new monitoring data.
    • Providing model runs and interpretation for CERP projects.

Planned Outreach: All model results and code will be provided to the ATLSS website(s) and data viewer as needed. Interpretation of results also will be provided. A peer-reviewed publication and presentations at national and CERP meetings will be accomplished.

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