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Project Work Plan

Department of Interior USGS GE PES

Fiscal Year 2008 Study Work Plan

Study Title: Alligator Ecology, Modeling, and Monitoring to Complement MAP
Study Start Date: 2003   Study End Date: in 2008 became companion study to CERP MAP "Alligators"
Web Sites:,
Location (Subregions, Counties, Park or Refuge): Total System
Funding Source: GE PES
Other Complementary Funding Source(s): American Alligator Distribution, Size, and Hole Occupancy and American Crocodile Juvenile Growth & Survival USCOE MAP
Funding History: FY03; FY04; FY05; FY06; FY07; Proposed FY08
Principal Investigator(s): Kenneth G. Rice, Frank J. Mazzotti, H. Franklin Percival
Project Personnel: Chris Bugbee, Brian Jeffery, Wellington Guzman, Mike Rochford
Supporting Organizations: University of Florida

Associated / Linked Projects: CERP MAP study: American Alligator Distribution, Size, and Hole Occupancy and American Crocodile Juvenile Growth & Survival, CESI study: Relative Distribution, Abundance, and Demographic Structure of the American Alligator in Relation to Habitat, Water Level, and Salinity.

Overview & Objective(s): 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.

  • 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.

Specific Relevance to Major Unanswered Questions and Information Needs Identified:

  • This study is part of a larger study funded and guided by science questions identified by the NPS (Critical Ecosystem Studies Initiative) and USCOE (CERP Monitoring and Assessment Plan).
  • This study addresses questions identified in DOI's Science Plan in Support of Ecosystem Restoration, Preservation, and Protection in South Florida (DOI's Everglades Science Plan) including:
    • The role of alligator holes in providing dry season refugia was identified specifically as a science need for the Ten Mile Creek Reservoir - Assisted Stormwater Treatment Area Project (p. 35), the Water Preserve Area Projects (p. 45), and the Water Conservation Area 3 Decompartmentalization and Sheetflow Enhancement Project (p. 65, 69).
    • The study supports the L-31N Seepage Management Pilot and Everglades National Park Seepage Management Projects (p. 48) and Water Conservation Area 3 Decompartmentalization and Sheetflow Enhancement Project (p. 65, 69) by providing ecological monitoring and assessment of restoration impacts on the alligator.
    • Both models developed in this study (habitat suitability model and spatially explicit demographic model) are identified as Landscape-scale Science Needed to Support Multiple CERP Projects (p. 83).
    • The study supports the Arthur R. Marshall Loxahatchee NWR Internal Canal Structures project as it (1) provides monitoring and assessment of responses of aquatic communities and habitats (p. 37) and (2) helps understand the ecological effects of hydrology and water quality on refuge resources (p. 40).
    • The study support the Southwest Florida Feasibility Study Project by providing modeling to predict species-level responses to habitat change (p. 50) and monitoring of key indicators (p. 51).
    • The study provides improvement of ecological model to make them more suitable for application and analysis as identified in the Combined Structural and Operational Plan Project (p. 64).
  • This study addresses several science objectives in the USGS Science Plan in Support of Everglades Restoration. Primarily, this work is concentrated under Goal 2B "Restore, Preserve, and Protect Natural Habitats and Species - Ecological Indicators." The tasks address all 5 science objectives:
    • We examine the effects of hydropattern and develop information required for restoration targets (2B-SG1).
    • We have used historical data sets and simulations to predict the historical status of alligator populations throughout the Everglades (2B-SG2).
    • We began a monitoring program to establish baselines and examine the current state of Everglades alligator populations (2B-SG3).
    • We have developed a monitoring program for alligators throughout the Everglades for use in evaluation of restoration success (2B-SG4).
    • We have developed simulation models as tools for predicting the effects of restoration (2B-SG5).

Status: We are continuing to provide parameter information to the ATLSS alligator population model. We are adding to our information concerning the impacts of canals on alligator populations with investigations into alligator production. We have established monitoring of alligator population growth, condition, and size distribution throughout the Greater Everglades. We have also implemented monitoring of juvenile growth and hatchling survival of American crocodiles as part of the MAP crocodilian modules. We are investigating quantitative and field methods to improve the precision and accuracy of our monitoring through the use of double-observer surveys, artificial surrogates, radio telemetry, and mark recapture. We have completed mapping alligator holes and aquatic refugia within Everglades National Park and are preparing a final manuscript. The ATLSS Alligator Production Index is now available for use in the restoration process but is also undergoing further calibration, validation, and updating with new data. The ATLSS Alligator Population Model has been completed and has undergone expert review, calibration, and some validation. Both models are fully functional and available for use in comparison of restoration alternatives.

Recent Products: In FY07, 2 peer-reviewed journal articles and 1 major technical report were published. We also gave several presentations at Local, National and International Conferences and 1 additional manuscript were submitted to peer-reviewed journals.

Planned Products: We plan on submitting further manuscripts on the Alligator Population Model and our body condition and population trend analyses to peer-reviewed journals. We will present results of our study at national and international meetings during FY08. We will also provide results of model simulations on the web.


Title of Task 1: Relative distribution, abundance, and demographic structure of the American alligator in relation to habitat, water levels, and salinities.
Task Funding: GE PES
Task Leaders: Kenneth G. Rice, Frank J. Mazzotti, Laura A. Brandt
Phone: 352-264-3544
FAX: 352-378-4956
Task Status (proposed or active): Active
Task priority: High
Budget and Time Frame for Task 1: in 2007 will be companion study to CERP MAP "Alligators"
Task Personnel: Brian Jeffery, Chris Bugbee, University of Florida

Task Summary and Objectives: The purpose of this task 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).

Prior to this study, the only surveys for alligators in Everglades National Park were SRF surveys for nests. The Florida Fish and Wildlife Conservation Commission conducted limited night surveys for alligators in and adjacent to Water Conservation Areas 2 and 3 as part of their public hunt program. Monitoring that only assesses nesting is limited. For example, 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 monitoring will be continued in A.R.M. Loxahatchee National Wildlife Refuge, Water Conservation Areas 2 and 3, Everglades National Park, and 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.

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

This study is the USGS contribution to the alligator portion of the Monitoring and Assessment Plan of CERP funded by the ACOE and SFWMD.

During FY08, we will concentrate our work on:

  • Continued development of monitoring methods and correction factors for environmental conditions and sighting proportions during alligator survey.
  • Continue monitoring of alligator population density, body condition, and size distribution throughout the Greater Everglades and further develop relationships to hydrologic condition including interaction with the Everglades Depth Estimation Network (EDEN) funded by ACOE and USGS-PES.
  • Continue monitoring of American crocodile juvenile growth and hatchling survival throughout south Florida.
  • Complete research on detection probabilities of alligators during night-light survey including double-observer surveys, distance sampling, and radio-telemetry of submergence rates. This has resulted in 1 MS Thesis completed, 1 MS Thesis to be completed in FY08, as well as several publications.
  • Continue development of a monitoring program of alligator hole occupancy throughout the Everglades system.
  • Begin new radio-telemetry project investigating movement patterns and habitat use of subadult animals to provide paramater estimates to models. This objective was not initiated in FY07 as proposed due to problems with securing final transmitters.
  • Provide data essential for validation of the ATLSS alligator population model.
  • Perform trend analyses of night counts and body condition on routes throughout the Everglades on an annual basis for the MAP assessment update.

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

To determine demographic structure (size class and sex) structure semi-annual capture surveys will be performed 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 completed in FY02 for specific body condition methods).

Since we now have 6 years of data for several areas, initial trend analyses of body condition and alligator counts have been performed and reported to MAP. In FY08, we will investigate the exact relationship between hydrologic variables and these trends using the EDEN hydrologic models.

Specific Task Product(s): This study 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 are available via website. The data from this study 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 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: Population-Based Simulation Modeling of American Alligator Populations in Support of CERP
Task Funding: GE PES
Task Leaders: Kenneth G. Rice, USGS and Daniel H. Slone, USGS
Phone: 352-264-3544
FAX: 352-378-4956
Task Status (proposed or active): Active
Task priority: High
Budget and Time Frame for Task 1: in 2007 became companion study to CERP MAP "Alligators"
Task Personnel: none

Task Summary and Objectives: An alligator population model is currently available for use in evaluating CERP restoration alternatives and developing performance measures. 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 first USGS Ecological Modeling Workshop, model validation and calibration were noted as priority research needs by a number of the participants. Further, CERP (see DOI's Science Plan in Support of Ecosystem Restoration, Preservation, and Protection in South Florida) requires model simulations and interpretation from USGS for several projects. 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 2007.
  • Provide model runs and interpretation for CERP as requested.

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

During FY08, we will:

  • Continue validation and updating of models using "virtual" night-light and nesting survey routes that correspond with NPS SRF, USFWS, and Task 1 (above) alligator monitoring.
  • Continue updates to the ATLSS alligator production index with new relationships developed using ENP nesting data.
  • Continue refining the alligator model, to continue with validation as new data are released, and to actively seek out and gather data from any new scenarios that are developed.
  • Simulate these hydrologic scenarios and provide results to CERP project planners and managers.

The ATLSS (Across Trophic Level System Simulation) project is a long-term, large-scale predictive model of the effects of planned restoration activities in the Florida Everglades on animal and plant species living there. For the last 3 years, we have been writing and implementing a module for ATLSS that simulates alligator populations in the Everglades. We have used this model and data from the South Florida Water Management District, the Florida GAP project, and ATLSS to describe the likely population densities that would occur across the Everglades landscape under various scenarios.

At this time, we have performed simulations using all of the available data sets (calibration 1979-95, 1995 and 2050 base 1965-95, and the restoration scenario D13-R 1965-95). We have also devised a validation regimen that will allow us to check the accuracy of the predicted output from the calibration data set by comparing nighttime spotlighting surveys along geo-referenced trails with a virtual survey performed along the same paths through the simulation output. Tests indicate that the model has a close fit to actual survey counts.

The calibration data have only been provided in the format required for our models through 1995, which is approximately the same time that comprehensive spotlight surveys were started, so we have a very limited overlap from which to draw validation data. In the near future, these data should be released through 2002, at which time we will be able to run a more comprehensive set of comparisons. In addition, new project scenarios have been proposed, and when the water management simulation data is released, there will be a need for alligator population responses to those projects.

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 can 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:

  x+0.5   y+0.5 1   (   x2 + y2 )
k[x,y] =   integral symbol   integral symbol
  exp -  
  x-0.5   y-0.5 2pi symbols2     2s2

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.

Specific Task Product(s): All model results and code are provided to the ATLSS website(s) and data viewer as needed. Interpretation of results also will be provided. Additional manuscripts will be submitted to peer-reviewed journals on model structure and performance.

Work to be undertaken during future FY's and proposed funding:

This project became linked as a companion project to CERP MAP "Alligators" in FY07 and will assume level funding to FY06 (less the reduction for FY08). Primary objectives of the MAP project include development and implementation of a monitoring program for alligator and crocodile populations in the Everglades that will assess distribution, population size, growth, survival, and body condition during restoration. The PES project will fund USGS participation in MAP including proportional salaries of Rice and Slone, USGS vehicles, and associated travel and supplies. Further, PES will fund development, updating, and scenario evaluations of the ATLSS alligator models.

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