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Project Work Plan

Department of the Interior USGS GE PES

Fiscal Year 2010 Study Work Plan

TITLE: Use of Amphibian Communities as Indicators of Restoration Success in the Greater Everglades

Investigator(s): Susan C. Walls, Frank J.Mazzotti, Kristen M. Hart

Susan C. Walls, U.S. Geological Survey, Southeast Ecological Science Center, 7920 NW 71st Street, Gainesville, FL 32653. Office: (352) 264-3507; FAX: (352) 395-6608; E-mail: swalls@usgs.gov.

Statement of Problem: Hydrology is a major driving factor in Everglades habitats and strongly influences the occurrence of amphibians across the landscape. Previously, a model of amphibian occupancy in relation to hydrology and habitat (funded through the USGS GE PES) was created for use as a restoration evaluation tool. This model uses estimates of occupancy for assemblages of amphibians. In turn, this community estimate serves as an index, a target for restoration assessment and, in a spatial framework, as a tool for evaluating alternatives. This index is designed to be used to predict the effects of various water management scenarios on the amphibian community. The long-term goal in the current phase of this on-going work is to validate this newly-developed model with respect to predicted responses of an amphibian community to hydrologic and habitat restoration in the Picayune Strand Restoration Project watershed. This model also serves as a promising tool for assessing the potential impact of climate change on amphibians occupying a hydrologically modified/restored landscape.


  1. Estimate amphibian site occupancy within focal area of the Picayune Strand Hydrological Restoration Project, versus occupancy on adjacent conservation lands with relatively intact hydrology.
  2. Use generated occupancy estimates to test the Stressor Response Model (previously funded as restoration science through USGS GE PES).
  3. Forecast potential responses of the amphibian community to the planned hydrological restoration of Picayune Strand.
  4. Provide insight into management options with respect to the effects of various water management scenarios on the amphibian community in the Picayune Strand.
  5. Refine the Stressor Response Model to address how climatic variation may impact the hydrology of sites and, thus, their occupancy by amphibians.
  6. Generate products on estimating site occurrence of amphibians, along with predicting responses of amphibians to hydrological restoration and future climate change across this landscape.
  7. Generate additional products that will include reports, data, presentations, summary fact sheet for SFNRC/CESI website, and peer-reviewed publications.

METHODOLOGY: We will conduct surveys for anuran amphibians within the area targeted in the Picayune Strand Restoration Project (former Southern Golden Gates Estates), as well as the adjacent Belle Meade Conservation and Recreation Lands (CARL) area; together, these two units comprise Picayune Strand State Forest (PSSF). We will also conduct surveys in the adjacent Fakahatchee Strand Preserve State Park (FSPSP). Both Belle Meade and FSPSP are reservoirs of natural habitat that may serve as vital refugia of native flora and fauna for recolonizing Picayune Strand following its restoration. With prior funding from the USGS GE PES Initiative, we expanded our amphibian monitoring in Southwest Florida to include the Picayune Strand and adjacent land management units. In 2008, a total of 27 sites were selected for monitoring in PSSF and FSPSP, and both manual vocalization and visual encounter surveys were conducted to assess amphibian occupancy. In FY 2009, we modified our protocol to use automated recorders (ARU; Song Meter SM1, Wildlife Acoustics) instead of manual surveys. We deployed an ARU at each site and programmed them to record for 5 min at the beginning of every hour, from 1800-0600 h each day. Loggers were installed on trees approximately 2 m above the ground at each site. With FY 2010 funding, we will continue our monitoring at these same sites. Song Scope Bioacoustics Monitoring Software (from Wildlife Acoustics) will be used to build species-specific "call recognizers and to otherwise aid in identifying frog calls at each site. Recordings will be viewed manually as well in the Spectrogram view of Song Scope to locate unique visual signatures of each species. All identified potential calls will be verified by listening to each. A decibel level > 40 dB will be considered to be "at the site" and not a distant call.

Data will be used to generate unbiased estimates of site occupancy for all amphibian species detected. These components, in turn, influence site occupancy and the overall community composition at a site. We will use a dynamic occupancy model (MacKenzie et al. 2003; Royle and Kéry 2007) to derive estimates of species-specific probabilities of occurrence (ψ), extinction (ε), and colonization (γ), summarized by land management unit (e.g., Belle Meade, PSSF, and FSPSP. This model has recently been extended for the joint analysis of communities of species (Walls et al., in review). In these models replicated observations of apparent detection/non-detection data are used to estimate the ecologically relevant model parameters (ψ, ε, and γ) while accounting for errors in detection of each species. These parameters can be formulated as a function of changes in hydrology (based on both restoration activities and yearly cumulative rainfall) and any restoration-related habitat shifts; thus, they will change from one year to the next. However, the expectation is that sites will become persistently wetter over time as hydrology is restored in these areas. In relatively dry years (i.e., before hydrology is restored and/or in drought years), wetlands with currently long hydroperiods may shift to short or intermediate in hydroperiod, increasing local extinctions of species adapted to permanent or semi-permanent wetlands. Also, in dry years local colonizations may occur as individuals disperse from drying wetlands to inundated ones. In relatively wet years (i.e., as hydrology becomes progressively restored and/or in years with above average rainfall), currently short-hydroperiod wetlands may disappear as all sites become persistently inundated, thus increasing local extinctions of amphibians adapted to ephemeral habitats. The dynamic occupancy model will enable us to predict how large-scale shifts in hydroperiod may affect estimates of species' occurrence and attribute whether altered estimates of occupancy in assemblages of amphibians are associated with changes in extinction, colonization, or both.


MacKenzie, D.I., J.D. Nichols, J.E. Hines, M.G. Knutson, and A.B. Franklin. 2003. Estimating site occupancy, colonization, and local extinction when a species is detected imperfectly. Ecology 84:2200-2207.

Royle, J.A. and M. Kéry. 2007. A Bayesian state-space formulation of dynamic occupancy models. Ecology 88:1813-1823.

Walls, S.C., J.H. Waddle, and R.M. Dorazio (in review). Estimating occupancy dynamics in an anuran assemblage. The Journal of Wildlife Management.


  2009/QTR 2010/QTR 2011/QTR 2012/QTR
Activity 1 2 3 4 1 2 3 4 1 2 3 4 1 2
Purchase ARU's     x                      
Deploy ARU's in the field       x                    
ARU maintenance: retrieval of recordings/replacement of batteries, etc. (every 100 days)

        x x x x x x x x    
On-going data Summarization         x x x x x x x x    
Final data synthesis, modeling                         x x
Annual Progress Summaries to GE PES, PSSF, FSPSP         x       x       x  
Preparation of Publications                 x       x x
Preparation of Fact Sheet for GEER           x x              
Presentations at Meetings             x       x      

**NOTE: Due to logistical difficulties, funded field work was not initiated in FY 09 until the 4th quarter of the fiscal year. Thus, this work plan reflects an extension of our field schedule into FY 2011, at no additional cost, to compensate for this delay.

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

Product Milestone Date
Journal Article:
Waddle, J.H., R.M. Dorazio, S.C.Walls, K.G. Rice, J. Beauchamp, M.J. Schuman, and F.J. Mazzotti. A new parameterization for estimating co-occurrence of interacting species. Ecological Applications, in press.
FY 2010
Fact Sheet for GEER Conference 07/2010
Reports/progress summaries for Picayune Strand State Forest, Fakahatchee Strand Preserve State Park, and coordinator of the Greater Everglades Priority Ecosystems Science program 12/2010, 2011
Oral and poster presentations at professional meetings 07/2010, 2011
Additional journal articles as data become available (e.g., "Use of amphibians to establish a baseline for measuring restoration success at a hydrologically degraded site in Southwest Florida, USA". Goal for submission: the journal Restoration Ecology). FY 2011


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

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

COMMUNICATION PLAN, TECHNOLOGY and INFORMATION TRANSFER: The results of our work will aid in understanding how amphibians respond to wetland restoration, modification, and creation efforts, as well as hydrological variation over time and space. This information will be useful if restoration plans for the Picayune Strand are refined with respect to the hydrological and habitat needs of amphibians. This information will also be useful for natural resource managers and conservation biologists affiliated with federal (U.S. Fish & Wildlife Service, U.S. Forest Service, National Park Service, and the USGS ARMI program), state (Fakahatchee Strand Preserve State Park, Picayune Strand State Forest, Florida Fish and Wildlife Conservation Commission) and 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.



Role: In-kind, technical support. Oversight of participating support staff.

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

Our focal study site, the Picayune Strand State Forest (PSSF), is targeted for hydrological restoration through the Picayune Strand Restoration Project (PSRP), one of 60+ planned projects to be implemented under CERP. The goal of the PSRP is to counteract the overdrainage that resulted from a failed real estate development project (the Southern Golden Gates Estates) of the 1960's. The development of this area (by the Gulf American Corporation) involved dredging 48 miles of canals and building 290 miles of shell-rock roads. Restoration plans for this area include the installation of a combination of spreader channels, canal plugs, road removal and pump stations in the Western Basin and Big Cypress of Collier County. Thusfar, by 2006 the northern 7 miles of the Prairie Canal (the eastern-most of four large canals originally constructed to provide drainage and flood protection for the planned residential development) were plugged. Most roads adjacent to the canal have also been removed and exotic plant species were removed from the canal banks. The effort completed thusfar is expected to be especially beneficial in terms of reducing drainage of the adjacent Fakahatchee Strand State Preserve.

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

ANIMAL WELFARE: Our study does not require handling of any animals as it is based on recording calling anurans. A current University of Florida Institutional Animal Care and Use Committee approval (# 001-09FTL) has been obtained should an unforeseen need for animal capture arise.

LEGAL AND POLICY-SENSITIVE ASPECTS: The PI already possesses a Scientific Collecting Permit from the Florida Fish and Wildlife Conservation Commission that authorizes any necessary handling of amphibians in PSSF and FSPSP (permit # WX08477; expiration date 12/31/2011). Frank Mazzotti (partner) possesses current permits from Picayune Strand State Forest (09-010, expires 3/20/2010) and Fakahatchee Strand Preserve State (4-09-37, expires 12.31.2009) that grants access to these properties.