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Project Summary Sheet

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

Fiscal Year 2006 Study Summary Report

Study Title: Computer Simulation Modeling of Intermediate Trophic Levels for Across Trophic Level Systems Simulation of the Everglades/Big Cypress Region
Study Start Date: 1997 Study End Date: 12/31/07
Web Sites: ATLSS.ORG
Location: The Greater Everglades ecosystem
Funding Source: ENP Critical Ecosystem Studies Initiative (ENP CESI)
Principal Investigator: Michael S. Gaines, Department of Biology, University of Miami, Coral Gables, FL 33124 Phone: 305-284-3974 e-mail:
Study Personnel: Donald L. DeAngelis, Phone: 305-284-1690 e-mail:
Other Supporting Organizations: USGS/BRD, NPS, ACE, EPA
Associated Projects: Component of ATLSS Program

Overview & Objectives: This project has had the goal of developing models for key components of the Everglades landscape as part of the overall Across Trophic Level System Simulation. Past research has developed the basic model for freshwater fish biomass and a model of energy flow in the reptile and amphibian community. Current work has involved modeling and empirical studies on the snail kite, small mammals, and the oak toad. The objectives have been to understand the effects of hydrologic conditions on each of these taxa.

Status: No new PES money has been added to this project and existing funding has been extended through a no-cost extension to the December 31, 2006. However, the University of Miami has received funding from the U. S. Fish and Wildlife Service to continue funding of the EVERKITE model. Small mammal research by Dr. Gaines will continue under other funding.

Recent Products:

Snail kite modeling:
The snail kite population model, EVERKITE, has recently been applied to examining the effects of the exact nature of the water level variation within a year, which has been ignored in previous simulations, is just as important as the variation in mean values between years.

To test this we artificially introduced various levels of within-year seasonal variation in water depths in each of the breeding sites, keeping the mean annual depth constant. The idea was to see if this within-year variability made any difference in the projected population dynamics (value of lambda). For example, if the within-year water depth variability was made to be higher than the historical seasonal variation, the possibility of a dry-down of a breeding site was more likely during that year.

We looked at effects of three aspects of variations in water levels that were likely to affect kites: (1) drought frequency; (2) drought duration; and (3) drought timing within the year. We modeled a 31-year historical scenario using four different scenarios in which the average water level was maintained constant, but the amplitude of water level fluctuations was modified.

Recent papers and presentations:

Mooij, W. M., J. Martin, W. M. Kitchens, and D. L. DeAngelis. Exploring the temporal effects of seasonal water availability on the snail kite of Florida. Pulsed Resources and Wildlife Population Response: The Importance of Time. Editors: John Bissonette and Ilse Storch. Springer-Verlag Publisher. (In press.)

Mooij, W. M., J. Martin, W M. Kitchens, and D. L. DeAngelis. 2006. Modeling snail kites in a variable environment. GEER Meeting, Lake Buena Vista, FL

Related papers:

Grimm, V, E.. Revilla, U. Berger, F. Jeltsch, W. M. Mooij, S. F. Railsback, H.-H. Thulke, J. Weiner, T. Wiegand, and D. L. DeAngelis. 2005. Pattern-oriented modeling of agent-based complex systems: Lessons from ecology. Science 310:987-991.

DeAngelis, D. L., and W. M. Mooij. 2005. Individual-based modeling of ecological and evolutionary processes. Annual Reviews of Ecology and Evolutionary Systematics 36:147-168.

Small mammal studies:
This project has attempted to determine the effects of patch size and hydrology on population dynamics of small mammals in the Everglades. In particular, the project has focused on cotton rats (Sigmodon hispidus) and rice rats (Oryzomys palustris). The study area is a set of 17 tree islands near Rock Reef Pass in the central Everglades, and the study has lasted 11 years. The methods involve mark-recapture using traps.

The initial hypotheses were as follows:

Hypothesis set 1 (eight hypotheses): Increasing island size would have positive effects on the density, reproduction, and survival of both the rice rat and cotton rat, but would have negative effects on the tendency of each of these species to move. The results so far show that density and reproduction of the cotton rat increased with island size, but density of the rice rat decreased, falsifying that hypothesis. Movement rates of both species were smaller for large islands. Tests of the other hypotheses were not significant.

Hypothesis set 2 (eight hypotheses): Increasing water levels would have negative effects on abundance, reproduction, survivorship of the cotton rat, and positive effects on the abundance, reproduction, and survivorship of the rice rat, and negative effects on movement of both. The results of the study indicate that increasing water levels have negative effects on abundance, reproduction, and movement of the cotton rat, and also negative effect on rice rat abundance. All other hypothesis tests were inconclusive.

In addition to these mark-recapture studies, a manipulation experiment was carried out. In this study, rice rats were removed from two tree islands, cotton rats were removed from two others, and two islands were left as controls. The predictions were that (1) removing cotton rats would result in an increase in rice rat abundance on larger hammock islands, (2) removing rice rats will not have an effect on cotton rat abundance on larger hammock islands. The results confirmed the first prediction - cotton rats have an antagonistic effect on rice rats which suggests competition. However, the second prediction was not confirmed. It appeared that rice rats have a facilitative effect on cotton rats, rather than a neutral effect.

A report on the 11-year study is in preparation. Completion of the report has been delayed, but a talk at the 2006 GEER meeting summarized some of the main findings.

Recent papers and presentations:

Gaines, M. S., D. L. DeAngelis, M. Fernandes, J. Warren, and H. Beck. 2006. Effects of Patch Size and Hydrology on Population Dynamics of Small Mammals in the Everglades. GEER Meeting, Lake Buena Vista, FL

Wang Y.Q., D. A. Williams, and DA, amd M. S. Gaines. 2005 Evidence for a recent genetic bottleneck in the endangered Florida Keys silver rice rat (Oryzomys argentatus) revealed by microsatellite DNA analyses. CONSERVATION GENETICS 6 (4): 575-585 JUL 2005

Amphibian Community Modeling in Everglades National Park, Florida

This work is an extension of the study originally focused only on oak toads.

Data Collection: The data collection for this study is complete. Since the last report, much of the data had to be recollected in order to use the Proportion of Area Occupied Model (described below). More than 120 visits to sites in the park (at least 12 amphibian community samples have been made at each of the 10 field sites within ENP) For the purposes of our model, the first and last observation of each species needs to be discarded. Data still needs to be entered and analyzed using program PRESENCE.

Statistical Methods: We are using Proportion of Area Occupied (PAO) as the primary survey and data collecting method for the duration of the oak toad study in Everglades National Park (ENP). This PAO technique was developed by Doctors Nichols, MacKenzie, and Royle and has been adopted by USGS ARMI (Amphibian Research and Monitoring Initiative) as the standard by which many amphibian populations will be measured. Further, a statistical method was developed by MacKenzie (2002) by which the PAO can be estimated with a single season of field data, while allowing for detection probabilities for the amphibian species of interest. We believe that this new methodology will yield far greater results in a shorter period of time for the ten sites we have selected within ENP. For this reason we intend to broaden our study's focus from Bufo quercicus to include all amphibian species. The major shift in methods can be described as rather than attempting to quantify how many of each species is present at each site, we are now looking at how many sites contain each of the amphibian species.

Tentative Results: Although much data have been collected, it is difficult to estimate community profiles without having analyzed the data using program PRESENCE. Based on previous studies using this model (Rice, 2004; Mackenzie, 2002), we will have more than enough sampling data to create accurate amphibian community profiles in each of the study sites within Everglades National Park.

Additional Result: During course of the field research in ENP, unique behavior was observed in one of the amphibian species regularly encountered. Bufo quercicus (the original study organism) has been described in the literature as diurnal, yet my observations in the field did not follow this description. I designed a small time lapse-videography experiment to attempt to ascertain the rhythm of this species. Preliminary data indicate this toad is arrhythmic which may be the first recorded occurrence of a cathemeral (arrhythmic) amphibian. This research has been presented at The Society of Integrative and Comparative Biology (Jan 2006, Orlando, FL) and at The Joint Meeting of Ichthyologists and Herpetologists (July, 2006, New Orleans, LA).


Mandica, M. The Society of Integrative and Comparative Biology (Jan 2006, Orlando, FL) and at The Joint Meeting of Ichthyologists and Herpetologists (July, 2006, New Orleans, LA).

Planned Products: Work is continuing in the following directions:

Snail kite population modeling

  • To improve the resolution of EVERKITE a grid-based version of this model will be developed, probably using the SFWMM 2*2 mile grid with an extension to the north to cover the northern range of the kites.
  • To improve the ability of agencies to use EVERKITE, a simple but effective user-interface to the grid-based version will be developed with the specific aim to allow the agencies to independently produce grid-based output on critical parameters of the kite population for each hydrological scenario that produces grid-based water levels for the SFWMM grid and the northern wetlands/lakes.
  • To improve the accuracy of EVERKITE, new empirical information will be included in the model on the vital rates and movement rules of the kites in response to hydrological and successional changes in their habitat. A strategy will be developed for inclusion of new empirical knowledge in future versions of the model.

Small mammal studies

  • Final report on project and manuscripts for publication are in preparation
  • Habitat suitability index will be developed for the two species O. palustris than S. hispidus

Amphibian Community Modeling in Everglades National Park, Florida

  • The next logical step is to enter the data into program PRESENCE, analyze it and report any trends that may become evident. Ideally, we will be able to compare the 5 upland (pineland) sites with the 5 wetland sites selected in Long Pine Key, ENP. From there, we can follow our current outline to generate a draft of the written results in order to get feedback to finish writing the thesis.
  • Master's thesis by Mark Mandica, U. of Miami, will be completed.

Specific Relevance to Information Needs Identified in DOI's Science Plan in Support of Ecosystem Restoration, Preservation, and Protection in South Florida (DOI's Everglades Science Plan) [Page numbers listed below are from the DOI Everglades Science Plan. See Plan on SOFIA's Web site:]:

Snail kite and fish landscape models were used in C&SF Restudy assessments (p. 96), in ModWaters Project design, and will be used in new CERP evaluations. Snail kite and amphibian models are critical for implementing the Multi-Species Recovery Plan. Snail kite and amphibian models are all Specific Performance Measures (p. 92).

Key Findings:

  1. Extension of EVERKITE to examine the effects of intrannual variation in water depths of snail kite breeding sites.
  2. GEER presentation of major results of 11-year study of small mammals in the Everglades.
  3. Report showing preliminary data indicate this toad is arrhythmic which may be the first recorded occurrence of a cathemeral (arrhythmic) amphibian

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