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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: Development of Selected Model Components of an Across-Trophic-Level System Simulation (ATLSS) for the Wetland Systems of South Florida
Study Start Date: 1997 Study End Date: 12/31/2008
Web Sites: ATLSS.ORG
Location: The Greater Everglades ecosystem
Funding Source: ENP Critical Ecosystems Studies Initiative (CESI) and USGS Greater Everglades Priority Ecosystems Science (GE PES) Initiative
Principal Investigators: Louis J. Gross, The Institute for Environmental Modeling (TIEM), University of Tennessee, Knoxville, TN 37996-1610 Phone: 865-974-4295 e-mail: gross@tiem.utk.edu
Study Personnel: Donald L. DeAngelis, Phone: 305-284-1690 e-mail: ddeangelis@umiami.ir.miami.edu§
Other Supporting Organizations: USGS Greater Everglades PES Funding, NPS, ACE, EPA
Associated Projects: Component of ATLSS Program, SFWMD Hydrology and Environmental Modeling; USGS National Wetlands Research Center

Overview & Objectives: The ongoing goals in this project have been the following: 1) As part of the ATLSS Program combine biological and physical models using multiple approaches, including trophic system components at differing spatial and temporal scales, to estimate landscape-level responses of biotic systems to environmental changes. 2) Produce models capable of using detailed behavioral and physiological data and dynamically linking these with spatially-explicit abiotic information. 3) Produce models capable of generating testable hypotheses about trophic component responses to alternative possible anthropogenic influences. ATLSS provides a mechanism to evaluate the relative impacts of alternative hydrologic scenarios on various trophic components. The methodology to integrate components involves: i) a landscape structure for dynamic communication between models; ii) a high resolution topography to estimate high resolution water depth across the landscape; and, iii) a variety of visualization tools to aid model development, validation, and comparison to field data.

The current objectives shifted somewhat during FY2006 to accommodate the need by DOI agencies to have ATLSS models working in South Florida on PCs. Currently the USGS's Across Trophic Level System Simulation (ATLSS) models are run at the University of Tennessee using 2 x 2 mile hydrology provided by the South Florida Water Management Model (SFWMM). The initial step in this process is converting SFWMM topography and hydrology to the 500 x 500 meter scale of resolution used by the ATLSS models. The 500-m hydrology is used in the ATLSS models, which include Spatially Explicit Species Index (SESI) models for wading birds, snail kites, white-tailed deer, American alligator, Cape Sable seaside sparrow, crayfish, Florida panthers, and apple snails, as well as population demographic models of the American alligator and the forage fish functional group (ALFISH model). In order to transfer these functions to DOI agencies, the University of Tennessee will cooperate in training between two and four persons from these agencies during a series of visits to the University of Tennessee beginning in early 2006. In addition, source code and documentation of the models and procedures will be transferred to the involved agencies. The objectives of the proposed work are the following,

  1. A team of at least two DOI agency scientists from southern Florida should develop an understanding of the process for creating the ATLSS 500-m resolution topography and hydrology.
  2. Together with staff of the Institute for Environmental Modeling, University of Tennessee (TIEM), the DOI team should run every usable ATLSS model against a standard 2x2 hydro scenario, converted to 500-m hydrology. This should include ALFISH, and, for comparison, the PALFISH version.
  3. The team should, along with the TIEM staff, write down a standard operating procedure for updating the 500-m topography for SFWMM hydrology input, as well as for the stand-alone program that Scott Sylvester wrote for Doug Donalson. This is important, because this topography may be used in the future not only for the Cape Sable seaside sparrow model, but may be incorporated into a marl prairie performance measure.
  4. The team, together with TIEM staff, will explore ways that we can modify the ATLSS suite of models to run under the Windows environment on DOI computers. This task shall culminate in the installation of the ATLSS code on DOI machines.
  5. The team, together with TIEM staff, will examine and discuss the present ATLSS input and output files, in order to see if there are ways to better facilitate parameter sensitivity analysis and post-run data analysis.
  6. A written agreement will be developed that sets up a protocol for software configuration management that protects the source code while still allowing for needed updates and modifications to be performed both at UT and DOI agencies.

Status: Current PES funding has been extended to 12/31/2006. This includes additional (FY07) PES funding added in August 2006.

Recent Progress: A series of three visits to the University of Tennessee (UT) by a team from DOI in South Florida has been started, with the first two visits occurring in April and June 2006. A final version of the SOW was developed and the team learned the process of developing ATLSS's high resolution topography (HRT) and hydrology (HRH). The UT staff started the documentation of the process of developed HRT and HRH, and also of converting ATLSS SESI models from UNIX work stations to LINUX boxes.

As part of the preparation for the third meeting, UT staff delivered to Everglades National Park in July, 2006, the following handbooks:

ATLSS High Resolution Topography (HRT) Manual
ATLSS High Resolution Multi-Source Topography (HRMST) Implementation Manual
ATLSS HydroSuite (HS) Implementation Manual

These draft versions of instruction manuals cover the complete ATLSS hydrology creation process from SFWMM Calibration/Verification to generation of ATLSS hydrology from Scenario runs. In the draft version, separate manuals are provided for HRT, HMDT, and HydroSuite.

In addition, a copy of the linux version of the ATLSS SESI_deer code has been delivered.

Because of the current emphasis on bringing ATLSS models to South Florida, currently only slow progress is being made on testing the reliability of ATLSS's Spatially Explicit Species Index (SESI) models by comparing year-to-year trends in SESI outputs with year-to-year trends in empirical data. An example of such comparisons is the Cape Sable sparrow population for a given sub-region, the 'western subpopulation,' of its range. Data are available for 1981 and the period 1992-present. Because the SESI model produces values that are on the interval 0 to 1, in order to compare SESI model trends with population data, the SESI values must first be normalized to the population data. When this is done the SESI index does seem to track population values over most of the period from 1992 to 2002. An ATLSS vegetation succession model, VSMod, encompassing 24 vegetation types, has been developed. VSMod simulates the pattern of spatial and temporal changes in the distribution of vegetation in the Greater Everglades landscape as a function of the hydrologic regime, patterns of fire disturbance and nutrients. A primary goal is to quantify the relative differences between various hydrologic scenarios as reflected in their impacts on vegetation succession. VSMod incorporates a spatially explicit, stochastic cellular automata model to simulate vegetation succession. At any given time, each 500x500-meter plot is in one of a finite number of states. The transition between states occurs with a probability that varies in both space and time, dependent on local hydrologic and fire history as well as on the current vegetation. The model runs on a yearly time step, synchronized with the fire model, and produces annual maps of vegetation over the model area. VSMod rules are based on reports by Wetzel (2001a, 2001b). Three modeled factors influence the succession of one plant association to another: fire, nutrient change, and prolonged change in hydrologic conditions. The model is now available for use, though parameterization of the fire component is still ongoing. The fire distribution data available to us is restricted to Everglades National Park, and this limits the ability to compare model estimates of fire size distribution across the entire ATLSS modeling region. To address this, a series of extensive simulations are underway, using parallel processors, to provide best estimates of model fire parameters of the mean fire size distribution restricted to the region and time period for which data are available. A set of sample VSMod simulations have been posted on the ATLSS web pages to allow input from interested agencies on the process. These simulations have been done using a range of fire scenarios (high, medium and low) to allow comparisons of the effect of different fire regimes.

A new SESI model has been developed for the Florida panther. The Florida Panther Spatially-Explicit Species Index Model (FPSESI) provides annual indicators of potential suitability for panther movement, dispersal, and prey resources across the Everglades and Big Cypress landscapes. FPSESI was developed to assess the relative suitability of alternative hydrologic scenarios by evaluating beneficial and adverse effects on the panther and its primary prey, white-tailed deer. The model considers the panther's typical behaviors and life-history traits that influence responses to a range of spatial and temporal hydrologic conditions. The user will be provided with options for weighting positive and negative factors to produce a combined suitability index. Water depth is modeled as a factor in daily movements of panthers within home ranges and in the dispersal of subadults from the natal range. Metrics of connectivity across Shark River Slough include depth, spatial extent, and periodicity of innundation. Impacts to panthers via prey are evaluated as effects of water depths on the movement behaviors and breeding and foraging habitat of white-tailed deer. Restoring and maintaining 4-to-7 month hydroperiods in the habitats that produce high quality deer forage would have a beneficial effect, while prolonged periods of innundation would have adverse impacts on deer movements and breeding success.

Planned Products: Several additional ATLSS SESI models will be delivered by the end of October 2006. These will include the Wading Bird Foraging Index, the Crayfish Index, the Cape Sable Seaside Sparrow Index, and the Alligator Index. Objectives 1, 2, 3, 4, and 5 will be completed by that time.

As time permits, work will continue on other aspects of ATLSS. A new ATLSS landscape class structure is being developed that will allow ATLSS runs to be effectively carried out on any hydrology model output, including hydrologic models that do not use uniform grid elements (e.g., finite element methods). As part of the CESI funding, some effort will be made to upgrade the SESI models to use this more general hydrology. However, there are numerous scaling issues that will require careful thought in all the models. Some FY05 PES funding has been used to adapt the SESI models to the more general hydrologic output. As of this date, the new landscape classes have been developed which allow ATLSS to utilize general mesh hydrology model output, including RSM from SFWMD. The ATLSS SESI Deer model has been modified to allow the use of general mesh grids, with several other SESI models planned to be modified in a similar manner.

There will be continued Testing and Validation of ATLSS Models. At the time the ATLSS SESI models were developed, much of the parameterization and determination of model rules were decided based upon the expertise of those with long field experience in the system. This was done in part due to the very limited and spatially-sparse data available at that time. Since then, a wide variety of data sets for the above mentioned species have been elaborated, and some of these have been done in a spatially-explicit manner (particularly the SRF data sets). We propose to collect these new data in a format amenable to comparison to particular outputs of the SESI models, in order to evaluate and modify the models as needed. This involves placing the data in an appropriate geo-referenced format, and applying needed spatial averaging in order to utilize it in comparisons to model output. In particular, we wish to have the data readable in the ATLSS Dataviewer so that independent assessments of the model performance may be made by various researchers external to UT. These comparisons will be carried out for all SESI models for which data are available.

Recent Products:

Immanuel, A., M. W. Berry, L. J. Gross, M. Palmer, and D. Wang. 2005. A parallel implementation of ALFISH: simulating hydrological compartmentalization effects on fish dynamics in the Florida Everglades. Simulation Modelling Practice and Theory 13:55-76.

Wang, D., E. Carr, M. Palmer, M. W. Berry, and L. J. Gross. 2005. A Grid Service Module for Natural Resource Managers. IEEE Internet Computing 9:35-41.

Wang, D., E. Carr, L. J. Gross, and M. W. Berry. 2005. Toward ecosystem modeling on computing grids. Computing in Science and Engineering 7:44-52.

Wang, D., M. W. Berry, and L. J. Gross. 2005b. A parallel structured ecological model for high-end shared memory computers. First International Workshop on Open MP. Lecure Notes in Computer Science (in press).

Specific Task Products:
Completion of HRT manual and HRMST and HS implementation manuals
Completion of training of DOI staff to use ATLSS models
Delivery of remaining obligated ATLSS SESI models to run on LINUX boxes
Integration of the vegetation succession model into SESI models
New landscape class structure for models
Tests of one or more SESI models
Perform simulation runs for CERP

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's Everglades Science Plan. See Plan on SOFIA's Web site: http://sofia.usgs.gov/publications/reports/doi-science-plan/]:

The ATLSS project links detailed biotic models with spatially-explicit abiotic data at regional extents, in order to provide a scientifically-defensible basis for regional planning that accounts for the complexity of biotic responses from individual-organism levels to that of communities (p. 79). ATLSS models were applied extensively in analyzing Restudy and Mod Water plans. ATLSS products are requested regularly by various agencies in South Florida including the South Florida Water Management District, U.S. Fish and Wildlife Service and Everglades National Park.

Key Findings:

  1. Training started on DOI staff to use ATLSS models in South Florida
  2. Delivery of drafts of manuals on HRT development and HRMST and HS implementation
  3. Delivery of white-tailed deer SESI model

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Last updated: 04 September, 2013 @ 02:08 PM(TJE)