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projects > effects of hydrological restoration on manatees: integrating data and models for the ten thousand islands and everglades > work plan
Project Work PlanDepartment of Interior USGS GE PES and ENP CESIFiscal Year 2006 Study Work PlanStudy Title: Effects of hydrological restoration on manatees: Integrating data and models for the Ten Thousand Islands and Everglades 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 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. (TASKS 1, 2, 3). 2. Research to understand the impacts of restoration projects on hydrology, habitats, and wildlife within Ten Thousand Islands NWR and Everglades National Park. (TASKS 1, 2, 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: Newly funded and initiated in FY06 Recent Products: Planned Products: Planned direction in FY09: 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 (CERP Interagency Manatee Task Force, Manatee Population Status Working Group, Habitat Working Group, and Warm Water Task Force) 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 Work to be undertaken
during the proposal year and a description of the methods and procedures: In FY06, USGS manatee researchers will process newly acquired telemetry data and complete various analyses needed to parameterize the individual-based manatee model. This includes data from manatees recently tagged in Whitewater Bay, as well as from 32 manatees tagged in TTI between June 2000 and June 2005, and miscellaneous tagged manatees that used the area (e.g. rescued animals). We will analyze the telemetry data using several approaches reflecting the hierarchical structure of the individual-based model. To capture the variability of individual manatee behavior, we will analyze manatee movement in a 3-level hierarchy. At the broadest scale, we will analyze migratory behavior of manatees in the study area in response to major cold fronts. Our approach will follow 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. At the intermediate scale, we will develop 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 will provide measures of variability among individuals in home range characteristics, such as seasonal home range size and distance from critical resources. Accounting for this variability will be important, since substantial heterogeneity in home ranges has been observed in tagged manatees on the east coast of Florida (Deutsch et al., 2003). The observed distribution of individual home ranges will be used to parameterize the home range allocation module of the individual-based model. At the finest scale, we will analyze movements between different habitat zones during the three primary seasons (dry, wet, cold) using multi-state modeling. This new statistical approach implemented in programs MARK and SURGE (Williams et al. 2002) will generate 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). The resulting distribution of Markovian probabilities will be used to parameterize the individual-based model, providing 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. In FY07, we expect to have simulated hydrologic data from the TIME and TTI applications for different hydrologic restoration scenarios. These scenarios are designed to represent proposed system changes to support ecosystem objectives. At this time we will run the final set of restoration simulations with different hydrologic restoration scenarios and will compare the resulting manatee distribution for the dry, wet, and cold seasons. Comparison of the outcomes of these different restoration scenarios, with different quantities, timing, and distribution of freshwater flow into areas used by manatees will allow the effects of hydrologic modifications on manatees to be evaluated. 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 (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 Work to be undertaken
during the proposal year and a description of the methods and procedures: Also in FY06, we plan to further characterize the manatee use of these passive thermal refuges and correlate with hydrologic findings at each site. Manatees have been tracked in the TTI as part of a study on manatee use patterns and freshwater flows within the region, which primarily focused on movements outside the winter season. 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 provides data on numbers of manatees present before, during, and after major cold fronts. 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. Development of a 3-D hydrological model will be initiated in FY07. Briefly, the hydrologic numerical modeling effort will use key manatee aggregation sites in the TTI as representative sites for the region as a whole. These specific winter-use areas have been observed to be deeper portions of inland canals, which 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. This can be done with a three-dimensional flow and transport code that allows for salinity and temperature transport with associated density variations. The 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. 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: (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. (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 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: 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: (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, 77p. 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. (In review). Hierarchical models of animal abundance and occurrence. Journal of Agricultural, Environmental, and Biological Statistics. 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. Royle, J. A. 2004. N-mixture models for estimating population size from spatially replicated counts. Biometrics 60:108-115. Royle, J. A., and J. D. Nichols. 2003. Estimating abundance from repeated presence-absence data or point counts. Ecology 84:777-790. Williams, B. K., J.D. Nichols, and M.J. Conroy. 2002. Analysis and Management of Animal Populations. Academic Press. N.Y. 835 pp. |
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