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Project Work Plan

U.S. Geological Survey, Greater Everglades Priority Ecosystems Science (GE PES)

Fiscal Year 2005 Study Work Plan

Project Title: Use of Amphibian Communities as Indicators of Restoration Success
Project Start Date: 2004 Project End Date: 2006 (per discussion with Ronnie Best)
Web Site: sofia.usgs.gov
Location (Subregions, Counties, Park or Refuge): Total System
Funding Source: USGS Greater Everglades Priority Ecosystems Science (GE PES) (this task is funded under Don DeAngelis ATLSS' program)
Other Complementary Funding Source(s): CESI: Effects of Public Land Use on Threatened, Endangered, and Indicator Species funded the initial work on this study through 2003.
Principal Investigator(s): Kenneth G. Rice, Frank J. Mazzotti
Project Personnel: Amanda Rice
Supporting Organizations: University of Florida
Associated/Linked Projects: CESI: Effects of Public Land Use on Threatened, Endangered, and Indicator Species

Overview & Objective(s): Declines in amphibian populations have been documented by scientists worldwide from many regions and habitat types. No single cause for declines has been demonstrated, but stressors like acid precipitation, environmental contaminants, the introduction of exotic predators, disease agents, parasites, and the effects of ultraviolet radiation have all been suggested. Because of their susceptibility to these and other stressors, amphibians are important as indicators of ecosystem health. Amphibians are present in all habitats and under all hydrologic regimes in the Everglades. The species present and the occupancy rate of a given species differ greatly across those gradients. These differences are due to hydropattern, vegetation, and other environmental factors. The combination of species composition and proportion of each habitat occupied at a given time form unique communities defined by those environmental factors. Therefore, if these communities can be reliably defined and measured, Everglades restoration success can be evaluated, restoration targets can be established, and restoration alternatives can be compared. This study will develop methodologies for defining and measuring the membership and area occupancy of amphibian communities. Further, we will investigate the relationship of occupancy of amphibians with hydroperiod and other environmental factors. Finally, we will provide a method for measuring restoration success based on these communities. Our objectives include:

  • Define amphibian communities appropriate for evaluating restoration success.
  • Develop methods for measuring the area occupancy of amphibian communities across habitats and environmental gradients.
  • Investigate the relationship of occupancy with hydroperiod and other environmental factors.
  • Develop restoration targets for the amphibian community of the Greater Everglades.
  • Develop a restoration tool for amphibian communities that measures restoration success and also compares restoration alternatives.
  • Develop an index of biological integrity for amphibians that provides a framework for scientifically defensible decisions by restoration managers.

Specific Relevance to Major Unanswered Questions and Information Needs Identified: (Page numbers below refer to DOI Science 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:
    • Monitoring of ecological responses of amphibians to hydrologic change was specifically listed as a science need in the Southern Golden Gate Estates Hydrologic Restoration Project as well as the need for amphibian larval sampling.
    • 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 need for monitoring and modeling of ecological communities and indicator species is specifically mentioned in the Florida Bay and Florida Keys Feasibility Study (p. 78), Ten Mile Creek Reservoir Assisted Stormwater Treatment Area Project (p. 34), Henderson Creek/ Belle Meade Restoration Project (p. 56), Southwest Florida Feasibility Study (p. 52), Florida Bay and Florida Keys Feasibility Study (p. 76), Landscape-Scale Modeling (p. 81), and Everglades National Park Fire Ecology Science Action Plan (p. 125).
  • This project 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 directly address 4 of the 5 science objectives:
    • We examine the effects of hydropattern and develop information required for restoration targets (2B-SG1).
    • We began a monitoring program to establish baselines and examine the current state of Everglades amphibian communities (2B-SG3).
    • We have developed a monitoring program for amphibian communities throughout the Everglades for use in evaluation of restoration success (2B-SG4).
    • We are developing models as tools for predicting the effects of restoration alternatives and determining restoration success (2B-SG5).

Status: We continue to use data previously collected from Everglades National Park to develop methods for defining amphibian communities using the Proportion Area Occupied (PAO) model and multivariate statistical techniques (see Fact Sheet 2004-3106). In Everglades National Park and adjacent Water Conservation Areas 3A and 3B, we have begun a large scale study to determine the PAO by each amphibian species across habitats defined by hydropattern. The PAO method estimates the abundance of sites at which each species occurs based on the capture results of several visits to each site. This method takes into account that some species are more difficult to detect, given that they are present, than others. This sampling is done along a hydrologic gradient from very long hydroperiod sloughs to the extremely short hydroperiod rocky glades of eastern Everglades National Park. We have initiated sampling including call count, visual encounter surveys, PVC refugia captures, and trapping in over 20 sites.

Recent Products: We have completed Fact Sheet 2004-3106 and have presented our initial findings and models to national and international conferences (presentations and posters).

Planned Products: We are presenting the results of this work at the NCER conference in December. We plan to complete peer-reviewed manuscripts on the study upon completion and provide the monitoring program and simulation models to CERP managers.

WORK PLAN

Title of Task 1: Use of Amphibian Communities as Indicators of Restoration Success
Task Funding:
USGS Greater Everglades Priority Ecosystems Science (GE PES)
Task Leaders: Kenneth G. Rice, USGS; Frank J. Mazzotti, University of Florida
Phone: 954-577-6305
FAX: 954-577-6347
Task Status (proposed or active): Active
Task priority: High
Time Frame for Task 1: 2004-2006
Task Personnel: Amanda Rice, University of Florida

Task Summary and Objectives: Declines in amphibian populations have been documented by scientists worldwide from many regions and habitat types. No single cause for declines has been demonstrated, but stressors like acid precipitation, environmental contaminants, the introduction of exotic predators, disease agents, parasites, and the effects of ultraviolet radiation have all been suggested. Because of their susceptibility to these and other stressors, amphibians are important as indicators of ecosystem health. Amphibians are present in all habitats and under all hydrologic regimes in the Everglades. The species present and the occupancy rate of a given species differ greatly across those gradients. These differences are due to hydropattern, vegetation, and other environmental factors. The combination of species composition and proportion of each habitat occupied at a given time form unique communities defined by those environmental factors. Therefore, if these communities can be reliably defined and measured, Everglades restoration success can be evaluated, restoration targets can be established, and restoration alternatives can be compared. This study will develop methodologies for defining and measuring the membership and area occupancy of amphibian communities. Further, we will investigate the relationship of occupancy of amphibians with hydroperiod and other environmental factors. Finally, we will provide a method for measuring restoration success based on these communities. The importance of amphibian communities to 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).

We will use established sampling methodologies such as PVC refugia trapping to investigate amphibian occupancy rates, develop new methods for sampling across hydroperiod gradients (drift fence arrays, PVC arrays), and use newly developed statistical techniques to estimate the proportion of area occupied by and to define amphibian communities. Our objectives include:

  • Define amphibian communities appropriate for evaluating restoration success.
  • Develop methods for measuring the area occupancy of amphibian communities across habitats and environmental gradients.
  • Investigate the relationship of occupancy with hydroperiod and other environmental factors.
  • Develop restoration targets for the amphibian community of the Everglades.
  • Develop a restoration tool for amphibian communities that measures restoration success and compares restoration alternatives.
  • Develop an index of biological integrity for amphibians that provides a framework for scientifically defensible decisions by restoration managers.

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

During FY05, we will concentrate our work on:

  • Developing methods for defining amphibian communities.
  • Developing methods for measuring the occupancy rate of communities across habitats and hydroperiod gradients.
  • Establishing restoration targets for amphibian communities in appropriate habitats.
  • Developing models and methods to measure restoration success across these communities and compare restoration alternatives.
  • Developing an overall index of amphibian community integrity.

Duellman and Schwartz (1958) produced the first scientific survey of the amphibians of south Florida. This work serves as an excellent reference for the historical distribution of many species before the extensive habitat loss in south Florida during the second half of the 20th century. Meshaka et al. (2000) produced a species list of the herpetofauna for ENP, but little information about the habitat associations and population status of the species was contained in that report. Dalrymple (1988) provided a good description of the herpetofauna of the Long Pine Key area in ENP, but no attempt has been made to sample amphibians throughout the Everglades.

We will use 2 primary methods to accomplish the objectives of the project:

  • Proportion area occupied (PAO) by a species.
    • Vocalization survey
    • Time-constrained searches
  • Proportion area occupied by a community.

    Proportion area occupied by a species.-- One problem with many of the methods used to sample amphibians is the lack of any control of the myriad environmental factors that affect the behavior and activity of the animals. Abiotic factors like temperature, humidity and hydrology as well as biotic factors like the presence of predators or conspecifics can affect the observability of amphibians. The observability of species' population is a function of the population size, the behavior of the individuals, and the ability of the observer to locate the animals in the particular habitat. Many monitoring programs simply count animals and do not control for this observability or capture probability (p). Therefore, comparisons over time or space are not possible or are biased. If the monitoring program can assume the cost 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) has developed a novel approach to this problem. Rather than mark the individual, we "mark" the species. Therefore, presence/absence data from several plots within a habitat (or along a hydroperiod gradient in our study) provides an estimate of p and allows estimation of the proportion of a stratum occupied by a given species at a given time.

    Sampling units will be chosen randomly within each stratum. Within Everglades National Park these are along the Main Park Road and Context Road. We will choose 15 sites along each road accessed by foot. The sites will be located within 300 to 900 feet of the road. In Water Conservation Area 3A, we will select 15 sites in each stratum along a North-South transect from I75 to SR41. Each stratum will be defined by the hydroperiod observed from existing hydrologic data and habitat type as defined by existing GIS vegetation layers. For hydropattern, a stratum will be defined for each 50 day difference (0-50, 51-100, 101-150, 151-201, 251-300, 301-365 days). Sites will be visited twice biweekly, April through September.

    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 2-3 person crews 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 ancillary variables at each plot (air temperature, relative humidity, presence of water, water temperature, wind speed, cloud cover). If any animals are captured show signs of disease or are new exotic species, we will collect them for health assessment by the USGS National Wildlife Health Center and/or identification and preservation by the Park.

    In addition, a maximum of 20-1m tall, 5 cm diameter PVC removable pipes will be installed in each site for refugia of treefrog species. During each visit, animals will be removed from the pipe for identification and measurement as outlined above. All animals will be released into the original PVC refugia. All PVC will be removed at the end of the study.

    At 10 sites in ENP (5 along Context Road and 5 along Main Park Road) we will install a 20m drift fence for capture of aquatic salamanders. The drift fence will consist of 20m of removable erosion control fence with a funnel trap incorporated at each end and in the center. Traps will be placed along the fence for 5 consecutive days once per month during May through October. The traps will be checked each day in the morning to minimize heat stress on captured animals. Animals will be measured as outlined above and released at the capture site. All traps and drift fences will be removed during non-capture periods. All drift fences and traps will be removed at the end of the study. Both drift fences and PVC refugia will be placed behind vegetation to minimize views from the road if possible.

    Individual species capture histories (matrix of presence/absence of each species at a sampling period and plot) and corresponding covariates (habitat, hydroperiod, temperature, humidity) will be assembled. We will then estimate the proportion of each stratum occupied by a species and the capture probability (using MLE and the logistic regression for covariates; MacKenzie et al. 2002). 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 area occupied by a community.-- Given that species occupancy rates differ across hydroperiod gradients and that hydrology is the controlling factor of this difference (see above), we can begin to construct "communities." In Figure 1 below (letters represent species, the size of the circle represents PAO, numbers represent hydroperiod), 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.

    conceptual view of proportion of area occupied by communities of amphibians across a gradient of hydroperiod in the Everglades
    Figure 1. Conceptual view of proportion of area occupied by communities of amphibians across a gradient of hydroperiod in the Everglades. [larger image]

    We have seen this pattern begins to emerge in preliminary data from the Everglades (Table 1).

    Table 1. Proportion Area Occupied values for amphibian species in the Everglades across a gradient of hydroperiod (values are an estimate of the proportion of a stratum occupied by that species):
    Hydroperiod
    Cricket Frog
    Southern Toad
    Squirrel Treefrog
    Pigfrog
    Leopard Frog
    Short
    0.0000
    0.5277
    0.7058
    0.0000
    0.3101
    0.0000
    0.5155
    0.6495
    0.3123
    1.0000
    0.1525
    1.0000
    0.1865
    1.0000
    0.8564
    0.3391
    0.0000
    1.0000
    0.8708
    0.8646
    Long
    0.7080
    0.4333
    0.1718
    0.7068
    0.3558

    At present, the method for defining and then predicting community composition and PAO is not complete. This study will develop this methodology for the Everglades.

    Index of Biological Integrity.-- Indices of biological integrity (IBI) were originally developed to assess conditions of riverine systems (Karr 1991, 1993) and also have been developed successfully for use in terrestrial environments (O'Connell et al. 1998). The basic premise of IBI's is that a range of conditions of ecological integrity can be defined based on the structure and composition of a selected biological community (e.g. amphibians, fish, birds, macroinvertebrates). The concept of biological integrity provides an ecologically-based framework in which species-assemblage data can be ranked in a manner that is more informative than traditional measures such as richness and diversity (Karr and Dudley 1981, Brooks et al. 1998). Therefore, the final step in this project will be to develop an amphibian community index (ACI) for evaluating the success of restoration and management of Greater Everglades Ecosystems. The ACI will be modeled after previously developed IBI's (Cronquist and Brooks 1991, Karr 1991,1993, Books et al. 1998, O'Connell et al. 1998). Essentially, we will use the PAO of communities estimated above to index or define the integrity of a given stratum. As restoration proceeds, we can use changes in the index to make informed management decisions and to measure success. Further, we can use the pattern of these communities based on hydopattern to develop restoration targets and to compare alternatives. By providing a reliable and repeatable measure of ecological quality an ACI will help managers reach scientifically defensible decisions (Brooks et al. 1998).

    Literature Cited:

    Boughton, R. G., J. Staiger, and R. Franz. 2000. Use of PVC pipe refugia as a sampling technique for hylid treefrogs. American Midland Naturalist 144: 168-177.

    Brooks, R.P., O'Connell, T.J., Wardrop, D.H., and Jackson, L.E.: 1998, 'Towards a Regional Index of Biological Integrity: The Example for Forested Riparian Systems,'Environmental Monitoring and Assessment, 51, 131-143.

    Croonquist, M.J. and Brooks, R.P.: 1991, 'Use of avian and mammalian guilds as indicators of cumulative impacts in riparian-wetland areas,' Environmental Management 15, 701-714.

    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.

    Donnelly, M. A., C. Guyer, J. E. Juterbock, and R. A. Alford. 1994. Techniques for marking amphibians. In Heyer, W. R., M. A. Donnelly, R. W. McDiarmid, L. C. Hayek, and M. S. Foster, editors. Measuring and monitoring biological diversity: Standard methods for amphibians. Smithsonian Institution. Washington, D.C.

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

    Enge, K. M. 1997. A standardized protocol for drift-fence surveys. Florida Game and Fresh Water Fish Commission Technical Report No. 14. Tallahassee. 69 pp.

    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.

    Karr, J.R. and Dudley, D.R. : 1981, 'Ecological perspective on water quality goals,' Environmental Management 5, 55-68.

    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. In Press.

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

    O'Connell, T. J., Jackson, L.E., and Brooks, R.P. : 1998, 'A Bird Community Index of Biotic Integrity for the Mid-Atlantic Highlands,' Environmental Monitoring and Assessment, 51, 145-156.

    Williams, B.K., J.D. Nichols, and M.J. Conroy. 2002. Analysis and management of animal populations. Academic Press, London. 817 pp.

    Specific Task Product(s):

    • Tools and scientific data necessary for evaluation of restoration success and comparison of restoration alternatives.
    • Methods and data necessary for RECOVER's adaptive assessment process and monitoring program.
    • Development of a cost-effective monitoring program for amphibians.
    • Development of performance measures for amphibian communities.
    • Peer-reviewed publications and published methodology for evaluation of restoration success.



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