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Project Work Plan

Department of Interior USGS GE PES

Fiscal Year 2008 Study Work Plan

Study Title: Use of Amphibians as Indicators of Restoration Success in Southwest Florida
Study Start Date: 2007   Study End Date: 2009
Web Sites:,
Location (Subregions, Counties, Park or Refuge): Big Cypress National Preserve and Southwest Florida
Funding Source: GE PES and CESI
Other Complementary Funding Source(s): co-funded by CESI to University of Florida
Funding History: Proposed FY08
Principal Investigator(s): Kenneth G. Rice, Frank J. Mazzotti
Project Personnel: Jeff Beauchamp, replacement for Hardin Waddle
Supporting Organizations: University of Florida, National Park Service

Associated / Linked Projects: CESI study of same name.

Overview & Objective(s): The DOI Science Plan for CERP and the research areas outlined by the BAA request for proposals describe a need for scientific research that will develop models that can be used as tools to evaluate restoration alternatives and assess restoration outcomes. The amphibian community of the Everglades ecosystem is a suite of species that are well suited for this task. Amphibians are sensitive to changes in the environment, especially those having to do with water quantity and quality. They are also abundant and readily sampled with established methods. When several species of amphibians are evaluated together, the species composition is a good indicator of habitat quality. Since hydrology is a major driving factor in Everglades habitats, we propose to create a model of amphibian occupancy in relation to hydrology and habitat as a restoration evaluation tool.

Some of the data on amphibian distributions by habitat and hydrology have already been collected in previous studies in Everglades National Park and Big Cypress National Preserve. The work called for in this project would expand the existing research areas into adjacent DOI lands that are of interest, specifically Ten Thousand Island and Florida Panther National Wildlife Refuges. We would also devote more time to developing monitoring methods for cryptic species that were underrepresented in the previous studies. Standard sampling techniques will be employed that have already been tested in south Florida.

The data on amphibian distribution across habitats will be analyzed along with hydrological data to produce an ecological model of occupancy of amphibian communities. This community level occupancy rate will serve as an index. It can serve as a target for restoration assessment and it may also be used in a spatial framework as a tool for evaluation of alternatives.

We will use existing data and data from ongoing and proposed field studies of amphibian occurrence by habitat and hydropattern along with newly developed statistical techniques to create a community index model of amphibians throughout southwest Florida. Estimates of the proportion of sites occupied by amphibian species in various southwest Florida habitats under different hydrologic conditions will elucidate patterns and lead to the creation of an amphibian community index. This index can then be used to predict the effects of various water management scenarios on the amphibian community. Our specific objectives include (Note: objectives expand the spatial footprint of the amphibian models underway through the PES funded ATLSS study):

Specific Relevance to Major Unanswered Questions and Information Needs Identified:

This project addresses 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:

This project applies to the following research areas designated by the BAA RFP:

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

Status: To date this project has accomplished portions of most of the overall objectives of the task. Amphibian data have been collected extensively from Big Cypress National Preserve. Some question remained about the geographic range of two species, barking treefrogs (Hyla gratiosa) and pinewoods treefrogs (Hyla femoralis) within the park. To better understand that issue, additional sampling has been conducted in the northern extent of Big Cypress to test hypotheses concerning the occupancy of these species. These hypotheses include habitat differences and pH of water.

Meetings have been held with US Fish and Wildlife Service staff at the headquarters for Panther and Ten Thousand Islands NWRs in Naples, FL to discuss sampling in those refuges. The proposals for special use permits have been submitted, and the special use permit was obtained for Ten Thousand Islands. Panther NWR is still pending. Sampling these areas will begin prior to the beginning of FY 2008. These data will be combined with data from Big Cypress NP and additional data collected by partners in the Conservancy of SW Florida (not-for-profit NGO) and used to refine the occupancy models.

Hydrology data was requested from the USGS and the PES-funded EDEN project. These data have been received and we are currently working on querying the database to obtain hydroperiod means for each sampling location. Once these data are organized, USGS biometrician colleagues will assist in creating a better model based on Bayes' theorem.

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. 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: Use of Amphibians as Indicators of Restoration Success in Southwest Florida
Task Funding: GE PES
Task Leaders: Kenneth G. Rice, Frank J. Mazzotti
Phone: 352-264-3544
FAX: 352-378-4956
Task Status (proposed or active): Active
Task priority: High
Time Frame for Task 1: 2007-2009
Task Personnel: Jeff Beauchamp, University of Florida, replacement for Hardin Waddle, USGS

Task Summary and Objectives: This is the only task and will accomplish the objectives stated above.

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

Additional field data on amphibian distributions in the Ten Thousand Islands and Florida Panther National Wildlife Refuge will be collected to supplement existing data from Big Cypress National Preserve and Everglades National Park. Further, we will collect further information on cryptic species including aquatic amphibians within Big Cypress National Preserve. In addition we will acquire hydrologic data from different state and federal sources in southwest Florida and USGS-EDEN network to estimate hydrologic parameters of interest (mean annual hydroperiod, days since dry down, etc.) at our sampling locations. Our analyses will combine hydrological and ecological data.

Proportion of area occupied by a species- One problem with many of the methods used to sample amphibians is lack of any control of myriad environmental factors that affect behavior and activity of animals. Abiotic factors like temperature, humidity and hydrology as well as biotic factors like presence of predators or conspecifics can affect observability of amphibians. The observability of a species' population is a function of the population size, the behavior of individuals, and the ability of observers to locate animals in particular habitats. Many monitoring programs simply count animals and do not control for this observability or capture probability (p). Therefore, comparisons over time or space are limited. If the monitoring program can assume costs of marking individual animals, then p can be determined and population size or density determined (standard mark-recapture methods, see Williams, et al. 2002). However, this would be cost prohibitive in a monitoring program for all amphibian species throughout the Everglades. MacKenzie et al. (2002) have developed a novel approach to this problem. Rather than marking individuals, we "mark" species. Therefore, presence/absence data from several plots within a habitat provides an estimate of p and allows estimation of the proportion of a habitat stratum occupied by a given species at a given time (proportion of area occupied or PAO).

Strata will be defined by habitat and hydrology in southwest Florida. Data has already been collected from Big Cypress National Preserve to produce estimates of PAO by habitat (Rice et al. 2005). In this study we will further investigate occupancy of aquatic salamanders within BICY. We propose to conduct additional sampling in the Ten Thousand Islands and Florida Panther National Wildlife Refuges as part of this project. These new areas will fill in data gaps that exist about the amphibian communities in these DOI lands, and expand the contiguous area for which we have data (including Everglades National Park). This will be especially important for indicator species such as the barking treefrog and pine woods treefrog that are very rare within habitats previously surveyed.

Our standardized sampling unit will be a circular plot of 20m radius. Plots will be sampled after dark to increase the probability of observing nocturnal amphibians. At each plot a 2 person crew will begin by listening for anuran vocalizations for 10 minutes. The abundance of each species will be categorized as: no frogs calling, one frog calling, 2-5 calling, 6-10 calling, >10 calling, or large chorus. The intensity of the vocalizations will be categorized as: no frogs calling, occasional, frequent, or continuous. After the vocalization survey, we will perform a 30-minute visual encounter survey (VES) in each plot. During this time, all individual amphibians observed will be identified to species and captured if possible. We will record the species, categorize the age (egg, larvae, juvenile, sub-adult, or adult), measure and record the snout-to-vent length and record the sex if it can be determined. The animal will then be released at the original capture site. We also will record the substrate and perch height of the animal. A University of Florida Institutional Animal Care and Use Committee approval will be obtained for animal capture. In addition to VES, in plots that are completely flooded, we will use dipnets and funnel traps to attempt to capture aquatic amphibians. We also will record several environmental variables at each plot (air temperature, relative humidity, presence of water, water temperature, wind speed, cloud cover).

Individual species capture histories (matrix of detections/non-detections of each species at each sampling occasion of each plot) and corresponding covariates (e.g. habitat, hydrological parameters, temperature, relative humidity, etc.) will be assembled. We will then estimate the proportion of each stratum occupied by a species and the capture probability using maximum likelihood estimation (MLE) with logistic regression for covariates in program PRESENCE (MacKenzie et al. 2002). Information-theoretic methods for model selection based on Akaike's Information Criterion (AIC) will be employed (Burnham and Anderson, 1998). The best model will minimize AIC and adequately estimate the parameters in the model (the candidate model list will be developed a priori based on ecological knowledge and will not include all possible combinations). We can then use these estimates to construct appropriate communities for each stratum (see proportion of area occupied by a community below).

Proportion of area occupied by a community– Given that species occupancy rates differ among habitat strata and across hydrologic gradients, we can begin to construct mathematical models of "communities" based on hydrological parameters. Figure 1 presents a hypothetical model that illustrates this; we can see that in short hydroperiod sites, species A and D dominate. However, as we move to longer hydroperiod sites, other species emerge as the dominate species in the community. This pattern of species composition and PAO forms the set of "communities" along the hydroperiod gradient. Presently, the method for defining and then predicting community composition and PAO is not complete. This study will continue the development of this methodology for southwest Florida.

diagrammatic representation of expected amphibian community
change during hydrologic restoration in the Everglades
Figure 1. A diagrammatic representation of expected amphibian community change during hydrologic restoration in the Everglades. Letters represent species, the size of the circle represents the PAO of the species, and numbers represent hydroperiod in days. [larger image]

Specific Task Product(s): [List and include expected delivery date(s).] Anticipated Results:

The ultimate goal of this project is to produce a modeling tool that can be used for decision support for managers interested in the effects of hydrologic restoration on amphibians in the Everglades system. To build this model we will estimate occupancy rates of amphibians in several Everglades habitats across multiple DOI administered parks and refuges. We will then investigate relationships between species occupancy and hydrology. Once this relationship is established a model can be developed of expected amphibian occupancy based on hydrology and habitat.

Additional results will include improved geo-referenced data about amphibian distributions in the national wildlife refuges and parks of southwest Florida. We will provide these detailed survey data in the form of a report to the US Fish and Wildlife Service and National Park Service. This will expand our knowledge about this key group of ecosystem indicator species to a broader geographical area, and this will improve our ability to model how changes in hydrology will impact the amphibian fauna of southwest Florida and the greater Everglades ecosystem.

Reporting schedule is described below. Semiannual report is due 6 months after contract initiation, and final report is due 12 months after contract start. Milestones and deliverables are described below.

Year Deliverable Content/Milestones/Products
1 Semiannual Progress report (Sampling progress)
1 Annual Final Report (Model description and output)

Funded projects will adhere to research data reporting and data custody requirements of the South Florida Natural Resources Center, Everglades National Park, and those of the USGS.

Literature Cited:

Burnham, K.P. and D. R. Anderson. 1998. Model selection and multi-model inference: A practical information-theoretic approach. Springer-Verlag, New York.

Dalrymple, G. H. 1988. The herpetofauna of Long Pine Key, Everglades National Park, in relation to vegetation and hydrology. Pp 72-86 In: Szaro, R. C., K. E. Stevenson, and D. R. Patton, eds. The management of amphibians, reptiles and small mammals in North America. U.S. Dept. of Agriculture, U.S. Forest Service Symposium, Gen. Tech. Rept. RM-166, Flagstaff, AZ.

Duellman, W.E. and A. Schwartz. 1958. Amphibians and reptiles of southern Florida. Bull. Florida State Mus., no. 3.

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

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

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. 83:2248-2256.

Meshaka, W.E., W.F. Loftus, and T. Steiner. 2000. The Herpetofauna of Everglades National Park. Florida Scientist 63(2): 84-103.

Rice, K.G., J. H. Waddle, M. E. Crockett, B. M. Jeffrey, and H. F. Percival. 2004. Herpetofaunal Inventories of the National Parks of South Florida and the Caribbean: Volume I: Everglades National Park. U.S. Geological Survey Open-File Report 2004-1065.

Rice, K.G., J. H. Waddle, B. M. Jeffrey, Amanda N. Rice, and H. F. Percival. 2005. Herpetofaunal Inventories of the National Parks of South Florida and the Caribbean: Volume III: Big Cypress National Preserve. U.S. Geological Survey Open-File Report 2005-1300.

Williams, B.K., J.D. Nichols, and M.J. Conroy. 2002. Analysis and management of animal populations. Academic Press, London.

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

This project is scheduled to end with FY08 funding.