USGS - science for a changing world

South Florida Information Access (SOFIA)


projects > effects of hydrological restoration on manatees: integrating data and models for the ten thousand islands and everglades > work plan

Project Work Plan

Department of Interior USGS GE PES and ENP CESI

Fiscal Year 2008 Study Work Plan

Study Title: Effects of hydrological restoration on manatees: Integrating data and models for the Ten Thousand Islands and Everglades
Study Start Date: 1 December 2005   Study End Date: 30 September 2008
Web Sites http://sofia.usgs.gov/projects/integrating_manatee/
http://cars.er.usgs.gov/Manatees/manatees.html
-
Location (Subregions, Counties, Park or Refuge): Total System - Ten Thousand Islands NWR, Collier County; Everglades National Park, Monroe County.
Funding Sources: USGS Greater Everglades Priority Ecosystems Science (GE PES) and ENP Critical Ecosystems Studies Initiative (CESI)
Other Complementary Funding Source(s): We have potential complementary funding pending from FWS.
Funding History: Funding began FY06
Principal Investigators: Catherine Langtimm, Eric Swain, Brad Stith, James Reid, Daniel Slone
Study Personnel: Melinda Wolfert, Robert Renken, Susan Butler (USGS contract), Skip Snow (ENP), Terry Doyle (USFWS-TTINWR), Robert Dorazio (USGS), Eduardo Patino (USGS)
Supporting Organizations: U.S. Fish and Wildlife Service - Ten Thousand Islands National Wildlife Refuge; National Park Service - Everglades National Park, Big Cypress National Preserve; Florida Fish and Wildlife Conservation Commission - Fish and Wildlife Research Institute
Associated / Linked Studies: This study is an extension of the PES study "Predicting effects of hydrologic restoration on manatees along the southwest coast of Florida", which focused on the TTI region. This extends the research to a larger region. (Sofia website: http://sofia.usgs.gov/projects/manatees/ ). Additional linkages to other studies/databases include TIME model, ATLSS model, and associated PES/CESI studies including "Southwest Florida Coastal and Wetland Systems Monitoring Project" (E. Patino) ( http://sofia.usgs.gov/projects/sys_monitor/ ).

Overview & Objectives: A significant population of the endangered West Indian manatee occurs in southwest Florida, throughout extensive estuarine and coastal areas within the Ten Thousand Islands (TTI; managed primarily by FWS) and Everglades National Park (ENP; managed by NPS). Planned restoration activities for the Everglades and Picayune Strand (an Acceler-8 project which discharges into TTI) may impact manatees by changing availability of freshwater for drinking, the quality and availability of seagrass forage, and the quality and availability of passive thermal basins used for refuge from lethal winter cold fronts. We expect changes in freshwater availability and forage to result in a shift in manatee distribution, which could necessitate new management actions to reduce human-manatee interactions. Restoration also could negatively impact important passive thermal refugia by increasing cold sheet flow during winter or disrupting haloclines that maintain warm bottom layers of salty water. Recent telemetry and aerial survey studies of manatees in TTI have revealed much about their use of this area: this project will extend the study into ENP, where manatees have not been intensively studied. To ascertain how restoration may affect the distribution and abundance of manatees in the region, an individual-based model has been under development, but completion of that model requires a hydrologic model for the rivers and estuaries affected by the accelerated Picayune Strand restoration. This study will provide integrated regional hydrologic models covering nearly the entire southwest coast below Naples, including portions of Picayune Strand and Big Cypress, providing much needed hydrologic modeling capabilities for evaluating restoration effects on coastal, estuarine, and freshwater ecosystems. This effort will enable us to model manatee response to restoration, and more adequately address science and management needs. Three Tasks (described in detail below) will be undertaken to develop the necessary components for this regional model: (TASK 1) Link the TIME hydrology model and the ATLSS manatee model to assess restoration effects in the Everglades and Picayune Strand, (TASK 2) Model changes to manatee thermal refugia due to hydrological restoration, (TASK 3) Design and implement a regional manatee monitoring program using aerial surveys and use robust statistical analysis techniques to estimate manatee distribution and abundance before restoration.

Specific Relevance to Major Unanswered Questions and Information Needs Identified:

This study will provide integrated regional hydrologic models covering nearly the entire southwest coast below Naples, including portions of Picayune Strand and Big Cypress, providing much needed hydrologic modeling capabilities for evaluating restoration effects on coastal, estuarine, and freshwater ecosystems. As the hydrology/manatee model focuses on temperature and salinity change, it will be a powerful tool to assess potential impacts to the Greater Everglades coastline with predicted climate change. This study also will address two of the three overarching restoration questions in the DOI Science Plan. First, what actions will recover South Florida threatened and endangered species? The models produced will allow the effects of hydrologic modifications to the system to be evaluated in terms of the factors which affect manatees and other estuarine species sensitive to these factors. Second, what actions will improve the quantity, timing, and distribution of clean fresh water needed to restore the South Florida ecosystem? To determine the quantity, timing, and distribution needed in manatee habitats, a comparison of CERP restoration scenarios is needed. Additionally, the Tasks in this study will address three questions identified as priorities under Science Integration and Synthesis Questions for the FY06 and FY07 funding initiative:

1. Synthesis of regional scale information and model development are needed that integrate and depict key factors of landscape change and their effects on the hydrology, biology, geology, and geography of the landscape, together with the identification of how policy, regulatory, and management strategies of national parks and refuges may influence these effects. Conceptual models and potential management options need to be developed with stakeholders. (TASK 1, TASK 2, TASK 3).

2. Research to understand the impacts of restoration projects on hydrology, habitats, and wildlife within Ten Thousand Islands NWR and Everglades National Park. (TASK 1, TASK 2, TASK 3).

3. Collection and synthesis of data for the verification and calibration of hydrologic and ecological models used for ecosystem assessment and restoration planning including those developed through the ATLSS program. (TASK 3).

Potential impacts: The endangered Florida manatee is a high priority species for management and recovery by USFWS and Florida's Fish and Wildlife Conservation Commission. In addition to concerns about the impact of restoration on manatees, the TTI/ENP region is the last major manatee habitat with minimal information on manatee population status. The results of this work will provide invaluable information to managers. The hydrology model provides data for the individual-based and landscape-based manatee models; defining the flow, salinity, and temperature information needed to model manatee movement and distribution. Comparisons of CERP restoration alternatives and associated alterations to the flow system in the hydrology model will show how habitat conditions change spatially and temporally. These hydrologic variables in turn will drive the individual-based model, which will project changes in manatee distribution and abundance across the region. Robust aerial surveys and analysis will provide the means to monitor impact as the restoration proceeds and provide independent data for validation of the model.

Status: Funded and initiated in FY06, active through FY2008

Products 2007:

Stith, B. M., E. D. Swain, C. A. Langtimm, and J. P. Reid. Integrating water temperature into hydrology models to assess restoration effects in Southwest Florida: manatees as mobile temperature probes. 2nd National Conference on Ecosystem Restoration. Kansas City, Missouri. April 22-27, 2007

Swain, E. D. and Decker, J. D., 2007, Developing a Heat-Transport Formulation for a Two-Dimensional Hydrodynamic Model of Coastal Wetlands: Second National Conference on Ecosystem Restoration, April 23-27, 2007, Kansas City Missouri p. 340.

Langtimm, C. A., M. D. Krohn, B. M. Stith, J. P. Reid, C. A. Beck, and S. Butler. In press. Research on the Impacts of Past and Future Hurricanes on the Endangered Florida Manatee in Science and the Storms: USGS Response to the Hurricanes of 2005. USGS Circular

Langtimm, C.A. E.D. Swain, B.M. Stith, J.P. Reid, D.H. Slone, J. Decker, S.M. Butler, T. Doyle, and R.W. Snow. In press. Integrated Science: Florida Manatees and Everglades Hydrology. USGS Fact Sheet

2007 Presentations and workshops for information transfer to resource managers and users:

South Florida Water Management District, U.S. Fish and Wildlife Service, and USGS Florida Integrated Science Center. The Picayune Strand Restoration Project and integrated manatee/hydrology research. Meeting in Gainesville, FL. January 31, 2007

Workshop with U.S. Fish and Wildlife Service - Vero Beach and Jacksonville Offices. Meeting at Vero Beach, FL. May 4, 2007. USGS integrated manatee and hydrologic research in the Greater Everglades

  • Catherine Langtimm. USGS-Florida Integrated Science Center: Manatee research objectives in support of Department of Interior management objectives.
  • Eric Swain. Application of hydrologic models for manatee ecology in Everglades and Ten Thousand Islands.
  • Brad Stith. Modeling manatee movements in relation to salinity, temperature, and forage: the individual-based model.
  • Jim Reid. Detailed manatee movement patterns and use areas: implications for Everglades National Park and Ten Thousand Islands National Wildlife Refuge management plans.
  • Catherine Langtimm. Manatee aerial survey methods for TTI and ENP: a new design for multiple objectives.
  • Daniel Slone. Planned research: Picayune Restoration Project - monitoring during and post restoration; seagrass distribution and characterization.

Everglades National Park Seminar Series in Homestead, FL. May 31, 2007

  • Catherine Langtimm. Overview of the USGS PES/CESI Integrated Research Study.
  • Brad Stith. Modeling manatee movement in response to hydrologic parameters: an individual perspective.
  • Eric Swain. Application of hydrologic models for manatee ecology in Everglades and Ten Thousand Islands.
  • Catherine Langtimm. Manatee aerial survey methods for TTI and ENP: a new design for multiple objectives.
  • Jim Reid. Manatee movement patterns and high use areas in ENP from recent telemetry data.

Department of the Interior - Southeast Bureau Partnership meeting in New Orleans, LA. August 9, 2007

  • Melinda Wolfert-Lohmann, Eric Swain, Christian Langevin, Jeremy Decker, and John Wang. The Relationship of USGS Hydrologic Modeling Efforts to Ecosystem Restoration.

U.S. Fish and Wildlife Service - Research Partnership meeting. Research in support of manatee recovery in Southwest Florida. Austin Carey Forest, Gainesville, FL September 6, 2007.

  • Catherine Langtimm. USGS Integrated Manatee and Hydrologic Research in the Greater Everglades.
  • Jim Reid. Manatee movement patterns in the Greater Everglades.

Products 2006:

Langtimm, C. A., M. D. Krohn, J. P. Reid, B. M. Stith and C. A. Beck. 2006. Potential effects of hurricanes on manatee survival and movement, 2004 and 2005. Estuaries and Coasts 29 (6A):1026-1032.

Langtimm, C.A., J. P. Reid, D. H. Slone, B. M. Stith, E. D. Swain, T. Doyle, R. Snow. 2006. Effects of hydrological restoration on manatees: A research program to integrate data, models and long-term monitoring across the Ten Thousand Islands and Everglades. Greater Everglades Ecosystem Restoration Conference, 5-9 June 2006, Orlando Florida. [Poster]

Langtimm, C. A., and E. D. Swain. 2006. PES-CESI 2006 work plan. Effects of hydrological restoration on manatees: Integrating data and models for the Ten Thousand Islands and Everglades http://sofia.usgs.gov/projects/workplans06/integrating_manatee.html

Langtimm, C., E. Swain, B. Stith, J. Reid, D. Slone. 2006. Fiscal Year 2006 Project Summary Report, USGS, Greater Everglades Priority Ecosystems Science (GE PES) and ENP's CESI. Effects of hydrological restoration on manatees: Integrating data and models for the Ten Thousand Islands and Everglades

Stith, B.M., C.A. Langtimm, E. Swain, J. Reid. 2006. Linking a manatee individual-based model with the TIME hydrology model to assess restoration effects in the Everglades and Ten Thousand Islands. Greater Everglades Ecosystem Restoration Conference, 5-9 June 2006, Orlando Florida. [Presentation]

Swain, E., and B.M. Stith. 2006. Numerical modeling of heat and salinity transport for West Indian manatee habitats in southwest Florida. Greater Everglades Ecosystem Restoration Conference, 5-9 June 2006, Orlando Florida. [Presentation]

Metadata Record. Effects of hydrological restoration on manatees: Integrating data and models for the Ten Thousand Islands and Everglades.

SOFIA Project Page. Effects of hydrological restoration on manatees: Integrating data and models for the Ten Thousand Islands and Everglades. http://sofia.usgs.gov/projects/integrating_manatee/

CESI 2006 annual progress report to Everglades National Park. 30 December 2006. Effects of hydrological restoration on manatees: Integrating data and models for the Ten Thousand Islands and Everglades

Planned Products:

Stith, B., E. Swain, J. Reid, and C. Langtimm. Integrating a manatee and hydrology model to assess restoration effects in the Everglades and Ten Thousand Island, Florida, USA. 17th Biennial Conference on the Biology of Marine Mammals. Dec. 2, 2007.

Swain, E., J. Decker, et al. Incorporation of heat transport in a linked surface-groundwater model. Publication in professional journal.

Stith, B. M. C. A. Langtimm. Estimation of manatee movement probabilities among habitat types for implementation into a spatially-explicit, individual-based model. Publication in professional journal.

Stith, B. M. Individual-based, spatially-explicit manatee model: application to the Everglades restoration. Publication in professional journal.

Final reports for each task to be completed by 30 Sep 2008.

Modeling results comparing the differences in manatee distribution for different restoration scenarios.

Datasets provided for use in the ATLSS viewer.

Planned direction in FY09 after this study ends: The results of the three Tasks of this study will be synthesized into a larger regional model. Task 2 may be extended to model thermal refugia across a broader region, providing more extensive capabilities for modeling winter temperatures for manatees and other cold-intolerant species (especially invasive species). In addition to information transfer to FWS and NPS, the PIs will coordinate with the FWS Florida Manatee Recovery and Implementation Team and its working groups to identify and develop research, policy, regulatory, and management strategies related to the results of this work.

WORK PLAN

Title of Task 1: Linking an individual-based manatee model with TIME and a new TTI hydrology model to assess CERP restoration effects on the Everglades and Ten Thousand Islands estuaries
Task Funding: USGS Greater Everglades Priority Ecosystems Science (GE PES) and ENP Critical Ecosystems Studies Initiative (CESI)
Task Leaders: Eric Swain and Brad Stith
Phone: (BMS) 352-264-3554, (EDS) 954-377-5925
FAX: (BMS) 352-374-8080, (EDS) 954-377-5901
Task Status: Active
Task priority: High
Time Frame for Task 1:
Task Personnel: E. Swain, B. Stith, J. Decker, J. Reid, M. Wolfert, S. Butler, D. Slone, C. Langtimm, E. Patino,

Task Summary and Objectives:

The major objectives of this task are to develop heat-transport capabilities for the FTLOADDS hydrology model (Swain et al., 2004) using a pre-existing application to the TIME area (Wang et al, 2007), develop an application to the TTI area, and integrate an individual-based manatee model with the hydrology model of the TTI estuaries to evaluate how proposed restoration changes will affect the endangered manatee. In conjunction with the existing TIME model of the Everglades region, the new model will generate key hydrologic parameters that manatees respond to, including salinity and water temperature. The modified FTLOADDS model generates key hydrologic parameters that manatees respond to, including salinity, water level, and water temperature. To improve the value of the TIME model for evaluating manatees in this region, the model is applied in the TTI region south of I-75 to include the Acceler-8 Picayune Strand restoration area important to manatees and identified as priorities in the DOI Science Plan. A base simulation for the time period 1998-2005 is created and the same period is simulated with hydrologic alterations planned for the Picayune Strand Restoration Plan (U.S. Army Corps of Engineers, 2001). The two scenarios provide information for comparison of water level, salinity, and temperature at the points of interest to manatee habitats.

The TTI hydrology model, using the FTLOADDS code, has been largely completed in FY2007 and is producing model results suitable to parameterize the manatee model. Synoptic surveys of water salinity in the TTI region show that the Faka Union Canal has much lower salinities for longer periods during the dry season than any other freshwater source in the region, making it the primary source of freshwater in the area. Winter water temperatures measured across the region show that the inland bays, rivers, and canals are significantly warmer than the preferred offshore feeding areas. Winter temperatures show complex vertical stratification, which could be affected by restoration, as described in Task 2. For this task, winter water temperatures will be modeled in 2 dimensions only. Hydrologic results from both a base (existing conditions) simulation and a representation of the Picayune Strand Restoration changes are generated by the TTI model. To help parameterize the modeled response of manatees to restoration, telemetry data is being collected and analyzed for manatees captured in ENP in addition to existing data from TTI telemetry studies. Relationships between hydrologic conditions and variables such as manatee movement and habitat use will be incorporated into the manatee model. Coupling hydrological and individual-based manatee models will provide a useful tool for comparing the response of manatees to different hydrologic restoration scenarios.

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

In FY08 we will focus on:

1) utilizing the output of the TTI hydrology model to develop representative input parameters for the individual-based manatee model;

2) using the manatee model's response to further refine the hydrology model's parameterization; and

3) demonstrating the ability of the manatee model to use results from the hydrology model restoration scenario to predict the effect of restoration on manatees.

The linkage between the hydrology model and the manatee model takes output parameters from the TTI application of the FTLOADDS model, including salinity and temperature distributions, to develop individual-based manatee model input. The manatee movements are defined along pathways (identified by manatee telemetry data) that will be correlated with the TTI-model output grid and time series. Model-generated time series will be obtained for a small subset of grid cells identified as being critical nodes in the landscape network used by manatees. A comparison of the field-calibrated manatee model with the model base-case will help evaluate the utility of the linkage. The capabilities needed to transfer time series datasets from the hydrology model to the manatee model have been developed, but will be further refined to increase model efficiency.

Telemetry data from TTI and ENP will be used to parameterize the individual-based manatee model. To capture the variability of individual manatee behavior, we analyzed manatee movement in a 3-level hierarchy. At the broadest scale, we analyzed migratory behavior of manatees in the study area in response to major cold fronts. Our approach followed Deutsch et al. (2003), who identified several discrete categories of migratory behavior of manatees tagged on the east coast of Florida, ranging from long distance migrants to year-round residents. Similar variability in migration behavior was observed in manatees tagged in TTI. At the intermediate scale, we developed seasonal home ranges for each tagged animal for the dry, wet, and cold seasons using fixed kernel analysis with least-square cross validation. Resulting home ranges provide measures of variability among individuals in home range characteristics, such as seasonal home range size and distance from critical resources. The observed distribution of individual home ranges is used to parameterize the home range allocation module of the individual-based model. Home range size changed substantially with season, showing large, offshore home ranges during the wet season, and smaller, inshore home ranges during the winter. Dry season home ranges were intermediate. At the finest scale, we analyzed movements between different habitat zones, focusing initially on the dry season, using multi-state modeling. This new statistical approach implemented in programs MARK and SURGE (Williams et al. 2002) generates transition probabilities for movement between several broad habitat zones (e.g. offshore, bay, river) for each individual at a 6-hour time interval (reflecting the sampling interval of the Argos telemetry tags). Among various multistate models analyzed for dry versus wet season, the best model included differences among individuals, but not season, suggesting that movement of individuals is similar in both seasons, but that individuals behave differently from each other. The model generates probabilities of transitioning among different habitat zones. These probabilities are used to parameterize the individual-based model, and provide a useful technique for quantifying individual heterogeneity in movement behavior observed in tagged manatees as they make regular movements between offshore foraging zones and inshore zones with freshwater or thermal refugia (See Stith et al. 2004 and Reid et al. 2003 for further details on the observed movement patterns).

The manatee model was written in C++, allowing for the development of a flexible interface to read hydrologic output from the FTLOADDS model. The binary output from FTLOADDS will be processed to extract the data for the specific nodes representing destination sites for feeding, drinking, and sheltering from cold, with connections representing travel corridors. This network data structure will allow directed movements to be simulated in an efficient manner using well-known graph theory algorithms. The manatee model will increment through the seasonally changing hydrologic data, and manatees will respond to the availability of freshwater or warm water as they move across the network, using the parameters developed from the telemetry data. Large-scale migratory movements to winter home ranges are triggered by offshore water temperatures falling below 20 degrees Celsius on the network. Within a seasonal home range, transition probabilities obtained from the multi-state analysis are used to simulate the movement of manatees among ecological zones as a Markov chain process. To calibrate the model, simulations are run where each manatee is initially assigned a randomly located home range. As they move around the network seeking different resources, manatees are exposed to the simulated hydrologic conditions and experience positive or negative reinforcement (e.g. while transitioning up a river to find freshwater). Initially, manatees have no preferences for different parts of the network within their home range, but as they explore the network these preferences change based on a simple reinforcement model (see Sutton and Barto, 1998). During this learning phase, individuals shift their home ranges in response to positive and negative reinforcement. Once all individuals converge on stable home ranges, snapshots of the aggregate distribution of individuals will be generated and compared to aerial survey data collected for the same time period under similar hydrologic conditions. The aerial survey data will be subdivided, with one subset used to calibrate the model, and a holdout set to validate the model. Model calibration will primarily involve modifying the 2 or 3 parameters of the reinforcement model, which control the tradeoff between exploring less rewarding sites and maintaining site fidelity.

The results from the completion of this task will contribute to answering two of the overarching restoration questions in the DOI Science Plan: what actions will recover South Florida's threatened and endangered species; and what actions will improve the quantity, timing, and distribution of clean fresh water needed to restore habitats and species in the South Florida ecosystem? Additionally, the results will address two issues identified as priorities under Science Integration and Synthesis Questions for the FY06 and FY07 funding initiative: 1) the synthesis of regional scale information and model development to integrate and depict key factors of landscape change and their effects on the hydrology, biology, geology, and geography of the landscape; 2) understanding the impacts of restoration projects on hydrology, habitats, and wildlife on Ten Thousand Islands NWR.

Specific Task Products

(1) Annual report to be completed by 30 Sep 2008. Report will contain: a) an analysis of the actual movement of tagged manatees, showing their movement patterns, travel corridors, home ranges, use of freshwater sites, foraging areas, winter refugia, and observed movements; b) results of the hydrologic model showing pre-restoration hydrological parameters relevant to manatee behavior; c) results of model calibration and validation using manatee aerial survey analyses; d) maps, graphs, and tables.

(2) Journal articles to be submitted for peer review in scientific journals will be completed as the various components of this task are completed. Manuscript preparation and publication may extend into or beyond FY08.

(3) Updates and reports on important findings will be conveyed to NPS, USFWS and the Manatee Recovery and Implementation Team as they become available. This will facilitate the identification and development of research, policy, regulatory, and management strategies relevant to manatees and restoration, and pave the way for the development of conceptual models and potential management options with stakeholders. This is one of the key issues identified by DOI for the FY06 and FY07 funding initiative.

Title of Task 2: Hydrologic modeling and manatee winter use patterns at passive thermal refuges
Task Funding:
USGS Greater Everglades Priority Ecosystems Science (GE PES) and ENP Critical Ecosystems Studies Initiative (CESI)
Task Leader: Eric Swain, James Reid and Daniel Slone
Phone: (EDS) 954-377-5925, (JPR 352-2654-3546) (DHS 352-264-3551)
FAX: (EDS) 954-377-5901, (JPR, DHS) 352-374-8080,
Task Status: Active
Task priority: Medium
Time Frame for Task 2:
Task Personnel: E. Swain, E. Patino, J. Reid, D. Slone, J. Decker

Task Summary and Objectives:

Cold stress is a major source of winter mortality for manatees in TTI and ENP. Previous USGS research in TTI has shown that tagged manatees during cold periods spend more time inshore in canal systems that serve as passive thermal refugia (e.g. Port of the Islands basin in the Faka Union canal, Wooten's basin of the Tamiami canal, and Big Cypress Preserve Oasis Ranger Station canals). During much of the winter season, vertical profiles at these sites indicate a halocline of warmer salt water trapped below a cooler freshwater lens, resulting in a thermal inversion (Reid et al. 2004). The hydrological process producing this halocline and how restoration may disrupt its thermal properties is not well understood. The objectives of this Task are to evaluate the importance of these winter refugia to manatee over-wintering strategies in the region and to collaborate with USGS hydrologists to characterize and model the three-dimensional properties for several key aggregation sites used during winter by manatees in the TTI. This modeling effort will provide important information on the salinity and temperature regimes of canals critical to manatees and other cold-intolerant species, such as invasive, exotic fish species in south Florida. This study has significant implications for understanding passive thermal refuges used by manatees and other species state-wide.

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

Development of the 3-D hydrological model of Port of the Islands (POI) using the Environmental Fluid Dynamics Code (EFDC) will continue in FY08. The POI bathymetry is derived from previous surveys and acoustic-doppler measurements to be fit to the EFDC finite-element mesh. The upstream and downstream boundaries for this will be extracted from the 2-D TTI model for both base and restoration scenarios. This winter-use areas has been observed to typically hold higher temperature water during periods of declining air and ambient water temperatures associated with winter cold fronts. Sufficient field data exists to define the important attributes; salinity, temperature, bathymetry, and flow. It is important to represent vertical variations in salinity and temperature. The EFDC model is the best way to confirm the theory that salinity stratification could maintain a temperature inversion, providing a warm area at the bottom for manatees. A 1 psu change in salinity induces a 0.71 kg/m3 change in water density, and a 1°C change in temperature induces a 0.22 kg/m3 change in water density. This means that for every degree Celsius warmer a lower layer is, a 0.31 psu increase in salinity would be needed to compensate for the buoyancy. A 1 psu stratified salinity layer below freshwater could be 3 degrees warmer than the surface. This would make a significant difference to the manatee; when water temperature drops below 20°C, manatees seek warmer water to avoid hypothermia. The flow regime through manatee aggregation areas may affect the vertical stratification of salinity and temperature, and the value of the refuge. In the Ten Thousand Island region, ecosystem restoration is to be implemented across the Southern Golden Glades Estates/Picayune Strand with effects to flows in manatee-use areas south of US41. This should route water flows away from the current Faka Union canal flowways, but may shift the freshwater-saltwater transition zone seaward, possibly reducing haloclines fed by saltwater intrusion. The Faka Union and Big Cypress canals provide both treatment and control sites for understanding winter aggregations and changes due to restoration. These criteria and the target temperature and salinity will be used in the optimization model to determine the best flow regime based on the available conceptualization.

Developing the boundaries for the 3-D POI model requires that the model parameterization in the TTI model be as well defined as possible. The current base and restoration simulations have been calibrated with existing data, but the atypical heat-transport representation in the TTI coastal wetlands requires a heat storage capacity for the underlying soil. This was estimated and used as a calibration parameter. In order to better define this uncertain term, a lab experiment will be undertaken to look as the temperature change as a function of soil depth beneath wetland water and land cover. This will make use of a box of approximately one meter dimension containing a representative depth of soil, water, and vegetation; insolated on the sides. Temperature probes will be buried at differing depths and the box exposed to normal solar radiation and atmospheric convection. The subsurface temperature fluctuations will lead to a direct calculation of the subsurface heat storage fluctuations on a daily cycle. This data will be used to verify and refine the model parameterization and create more confident results. Description and results will be included in the final report.

We will continue to characterize the manatee use of passive thermal refuges and associated hydrologic findings at additional sites in ENP. Also, a smaller number of manatees initially tagged in the southern Everglades continue to be tracked in the TTI. Additional information collected during ground and aerial surveys at specific aggregation sites provide data on numbers of manatees present before, during, and after major cold fronts. The new aerial survey work will provide additional information to identify and characterize passive thermal refuges. Collectively, tracking and survey data will help identify manatee movement patterns associated with winter cold fronts. These findings, integrated in manatee movement models, will be coupled with hydrologic models on basin temperature and salinity to better understand the dynamics of these sites as passive thermal refuges for manatees and other species.

The results from the completion of this task will contribute to answering two of the overarching restoration questions in the DOI Science Plan: what actions will recover South Florida's threatened and endangered species; and what actions will improve the quantity, timing, and distribution of clean fresh water needed to restore habitats and species in the South Florida ecosystem? Additionally, the results will address two issues identified as priorities under Science Integration and Synthesis Questions for the FY06 and FY07 funding initiative: 1) the synthesis of regional scale information and model development to integrate and depict key factors of landscape change and their effects on the hydrology, biology, geology, and geography of the landscape; 2) understanding the impacts of restoration projects on hydrology, habitats, and wildlife on Ten Thousand Islands NWR.

Specific Task Products:

(1) Hydrologic data and manatee observations will be compiled and summarized with available data from previous years. Data sets will be available for modeling efforts in FY08.

(2) Final report to be completed by 30 September 2008. Report will contain: a) discussion of the field measurements and model development process, including calibration and verification; b) results of the hydrologic model indicating predictions of habitat suitability as a function of flow conditions; c) relationships for use in the larger-scale model to represent the basin as an internal boundary. d) results of the soil heat capacity experiment and the effect on model development.

(3) Journal articles to be submitted for peer review in scientific journals will be completed as the various components of this task are completed. Some manuscript preparation and publication may extend beyond FY08.

(4) Updates and reports on important findings will be conveyed to NPS, USFWS and the Manatee Recovery and Implementation Team as they become available. This will facilitate the identification and development of research, policy, regulatory, and management strategies relevant to manatees and restoration, and pave the way for the development of conceptual models and potential management options with stakeholders. This is one of the key issues identified by DOI for the FY06 and FY07 funding initiative.

Title of Task 3: Development of a monitoring design and analysis for manatee aerial surveys, integrating Ten Thousand Islands with Everglades
Task Funding: USGS Greater Everglades Priority Ecosystems Science (GE PES) and ENP Critical Ecosystems Studies Initiative (CESI)
Task Leader: Catherine Langtimm
Phone: 508-335-3029
FAX: 508-867-8346
Task Status: First active in FY07
Task priority: High
Time Frame for Task 3: FY07 and FY08
Task Personnel: C. Langtimm (USGS), B. Stith (USGS), R. Dorazio (USGS), T. Doyle (USFWS-TTINWR), and R. Snow (NPS-ENP)

Task Summary and Objectives:

The three main objectives of this Task are: (1) provide an independent data set for validation of the predictive manatee/hydrology models, (2) develop a statistically robust means to document changes in manatee distributions in association with habitat variables incorporated in the manatee/hydrology models, and (3) develop and implement a regional manatee monitoring design for pre- and post-restoration assessments, integrating TTI with ENP. Development of the manatee individual-based model has focused on time-intensive telemetry studies of a relatively small number of manatees. Aerial surveys, however, offer the best opportunity from a cost-effective and scientifically robust perspective to monitor and document the population across the entire region, as well as to provide independent data for model validation. Site occupancy or abundance of manatees in different "patches" estimated from aerial surveys, may change over time due to restoration activities. Robust statistical analyses of survey data will be important to managers to assess such restoration effects, as well as to assess impact and recovery after natural disturbances, such as hurricanes, which periodically affect this area.

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

A new class of capture-recapture statistical models to estimate habitat site occupancy rates when detection of a species is imperfect has successfully been applied to manatee aerial survey data from TTI. The technique explicitly models detection probability using repeated presence/absence surveys to provide unbiased estimates of the proportion of sites occupied by a species or population (MacKenzie et al. 2002; 2003; Royle and Nichols 2003). In FY06, we modified the current survey designs at TTI National Wildlife Refuge to better meet the requirements for this analytical approach. In FY07 we developed a new application for manatee surveys derived from removal-based, spatially-explicit estimation methods (Dorazio et al. 2005, Royle and Dorazio 2006). This new application is currently being tested for use by manatee researchers with the state of Florida. In FY08 we will 1) use TTI aerial survey data from 2005 to test the efficacy of the hydrology model and manatee individual-based model to describe manatee distribution patterns, 2) co-sponsor an aerial survey workshop with manatee researchers with Florida's Fish and Wildlife Research Institute to peer review methods and designs, 3) define sampling plots along the ENP coast consistent with TTI plots, and 4) conduct pilot surveys in ENP.

The results from the completion of this task will contribute to answering two of the overarching restoration questions in the DOI Science Plan: what actions will recover South Florida's threatened and endangered species; and what actions will improve the quantity, timing, and distribution of clean fresh water needed to restore habitats and species in the South Florida ecosystem? Additionally, the results will address three issues identified as priorities under Science Integration and Synthesis Questions for the FY06 and FY07 funding initiative: 1) the synthesis of regional scale information and model development to integrate and depict key factors of landscape change and their effects on the hydrology, biology, geology, and geography of the landscape; 2) understanding the impacts of restoration projects on hydrology, habitats, and wildlife on Ten Thousand Islands NWR; and 3) collection and synthesis of data for the verification and calibration of hydrologic and ecological models used for ecosystem assessment and restoration planning.

Specific Task Products:

(1) Report detailing the regional monitoring design, protocols, and methods for analysis, completed by 30 Sep 2008.

(2) Report describing the regional pre-restoration assessment of manatee distributions, completed by 2 February 2009.

(3) Datasets provided to modelers for validation analysis, as they become available.

(4) Journal articles to be submitted for peer review in scientific journals will be completed as the various components of this task are completed.

(5) Updates and reports on important findings will be conveyed to NPS, USFWS and the Manatee Recovery and Implementation Team as they become available. This will facilitate the identification and development of research, policy, regulatory, and management strategies relevant to manatees and restoration, and pave the way for the development of conceptual models and potential management options with stakeholders. This is one of the key issues identified by DOI for the FY06 and FY07 funding initiative.

LITERATURE CITED

Deutsch, C.J., Reid, J.P., Bonde, R.K., Easton, D.E., Kochman, H.I. and O'Shea, T.J., 2003. Seasonal movements, migratory behavior, and site fidelity of West Indian manatees along the Atlantic Coast of the United States: The Wildlife Society. Wildlife Monographs No. 151, 77 pp.

Dorazio, R. M., H. L. Jelks, and F. Jordan. 2005. Improving removal-based estimates of abundance by sampling a population of spatially distinct subpopulations. Biometrics 61, in press.

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 83:2248-2255.

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.

Reid, J. P., S. M. Butler, D. E. Easton, and B. M. Stith. 2003. Movements and Habitat Requirements of Radio Tagged Manatees in Southwest Florida; Implications for Restoration Assessment. Poster Presentation. Proceedings of the Joint Conference on the Science and Restoration of the Greater Everglades and Florida Bay Ecosystem, April 13-18, 2003, Palm Harbor, Florida. Website: http://sofia.usgs.gov/geer/2003/posters/radiotrack/.

Reid, J. P., B. M. Stith, and S. M. Butler. 2004. Are Manatee Over-Wintering Strategies and Restoration Efforts Compatible in the Northwestern Everglades Region?. First National Conference on Ecosystem Restoration (NCER), Orlando, FL, December 6-10, 2004. Website: http://sofia.usgs.gov/publications/posters/manatee_winter/

Royle, J. A. and R. M. Dorazio. 2006. Hierarchical models of animal abundance and occurrence. Journal of Agricultural, Environmental, and Biological Statistics 11:249-263.

Royle, J. A., and J. D. Nichols. 2003. Estimating abundance from repeated presence-absence data or point counts. Ecology 84:777-790.

Stith, B., J. Reid, and S. Butler. 2003. Modeling manatee response to restoration in the Ten Thousand Islands and Everglades National Park. First National Conference on Ecosystem Restoration (NCER), Orlando, FL, December 6-10, 2004. Website http://sofia.usgs.gov/publications/posters/modelmanatee/

Stith, B., J. Reid, S. Butler, T. Doyle, and C. Langtimm. 2004. Predicting the effects of hydrologic restoration on manatees along the southwest coast of Florida. USGS Fact sheet 2004-3137.

Sutton, R.S. and A.G. Barto. Reinforcement Learning. 1998. MIT Press, Cambridge, Mass. 322 pp.

Swain, E.D., Wolfert, M.A., Bales, J.D., and Goodwin, C.R., 2004, Two-dimensional hydrodynamic simulation of surface-water flow and transport to Florida Bay through the Southern Inland and Coastal Systems (SICS): USGS Water-Resources Investigations Report 03-4287, 56 p. plus 6 plates.

Williams, B. K., J.D. Nichols, and M.J. Conroy. 2002. Analysis and Management of Animal Populations. Academic Press. N.Y. 835 pp.



| Disclaimer | Privacy Statement | Accessibility |

U.S. Department of the Interior, U.S. Geological Survey
This page is: http://sofia.usgs.gov/projects/workplans08/integrating_manatee.html
Comments and suggestions? Contact: Heather Henkel - Webmaster
Last updated: 04 September, 2013 @ 02:09 PM(KP)