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Project Work Plan

Department of Interior USGS GE PES

Fiscal Year 2008 Study Work Plan

Project Title: Benthic Habitat Characterization and Habitat Use of Endangered Sea Turtles in Dry Tortugas National Park
Study Start Date: 1 August 2008
Study End Date: 30 September 2013
Web Sites:
Duration: 2 months in FY 2008+ 5 years from FY 2009–2013
Location (Subregions, Counties, Park or Refuge): Southern Florida Keys, Dry Tortugas National Park (Monroe County)
Funding Source: GE PES, Coastal and Marine Geology (CMG)
Other Complementary Funding Sources: USGS State Partnership Program (SPP), Fish and Wildlife Conservation Commission (FWCC), National Park Service
Funding History: This project integrates with the new USGS FISC Coral Reef project, with FWCC funds and joint funds shared by USGS and FWCC.
Principal Investigator: Kristen M. Hart
Study Personnel: TBD
Supporting Organizations: U.S. National Park Service
Associated/Linked Studies: High-resolution mapping of the Dry Tortugas (USGS PI Zawada), Habitat use of sea turtles in the Dry Tortugas (USGS PI Hart, NPS funded)

Overview & Objective(s): Institution of marine protected areas (MPAs) in which human use is highly regulated has become a priority management tool for at risk coral reef habitats. The effectiveness of MPAs may be heavily dependent upon reserve factors such as size, placement or location, and enforcement of protected area boundaries, as well as whether adequate protection for vulnerable life stages of key species is provided in protected habitats. In the Dry Tortugas National Park (DRTO), several MPAs have been established to protect natural and fisheries resources and associated coral reef habitats. This project proposes exploratory research to conduct a coupled habitat and species sampling project within and around the new Research Natural Area (RNA) of Dry Tortugas National Park (DRTO). Specifically, we will assess use of habitat in and around no-take areas of the RNA by several species of federally endangered sea turtles (i.e., greens (Chelonia mydas), hawksbills (Eretmochelys imbricata), and loggerheads (Caretta caretta). Green turtles are almost exclusively herbivorous, consuming seagrasses and algae, hawksbills eat sponges, and thus are found associated with coral reefs and sponge cover, and loggerheads feed on benthic invertebrates such as lobsters and crabs, as well as on fishery discards. Thus, these species are directly linked to key habitats of interest in DRTO and the surrounding waters. All three species are particularly suitable for immediate monitoring because they also nest on sandy upland areas of the Tortugas islands.

Specific objectives of the project are as follows:

Specific Relevance to Major Unanswered Questions and Information Needs Identified:
Data is lacking on the use of protected areas (MPAs) by endangered species. Despite detailed knowledge of general sea turtle nesting trends in Dry Tortugas National Park (DRTO) (i.e., on Loggerhead and East Keys), little information is available about in-water sea turtle use of natural resources. The southern and eastern boundaries of the newly designated RNA in DRTO will be ringed with acoustic listening stations in summer 2008 through USGS SPP funding. By capturing and acoustically tagging endangered sea turtles from within and around the RNA, we will address fine-scale patterns of sea turtle habitat use and movement patterns within and around the RNA. Because we will also attach satellite tags to a subset of the acoustically-equipped turtles, we will determine the proportion of time these endangered turtles are spending in areas adjacent to the RNA (i.e., in other protected areas in DRTO or outside the park). This project addresses the specific resource management information need regarding endangered species use of park resources, and condition and location of those resources (i.e., seagrass, sponge, and hardbottom habitats, as well as nesting beaches). The significance and priority of the issue to the park or the NPS is that such habitat in DRTO may serve as critical habitat for this endangered species. Such critical habitats must be considered in recovery plans for the species aimed at restoring sea turtle population numbers. In addition, with climate change scenarios, critical nesting beaches must be included in recovery plans and population restoration efforts. The condition of the nesting beaches in DRTO has been affected by invasive Australian pines (Casuarina equisetifolia), and a removal program in the mid-1990s failed to remove roots and stumps from Loggerhead Key. Thus, significant restoration of this important nesting beach remains an issue for both adults and hatchlings of these endangered marine turtle species.

Of the three overarching restoration questions laid out in the U.S. Department of the Interior Science Plan in Support of Ecosystem Restoration, Preservation, and Protection in South Florida, this project directly address two of these:

Additionally, since we have the opportunity to tag nesting female sea turtles using DRTO beaches, the U.S. Fish and Wildlife Service and the National Marine Fisheries Service will benefit from the information derived from the proposed tasks; essentially, the former has jurisdiction and responsibility for endangered sea turtles while they are on land, and the latter has jurisdiction and responsibility for them when they are in the water. Thus, this project not only benefits other DOI agency missions of the USGS, the NPS, and the USFWS, but also that of the Department of Commerce (DOC).

Using new technologies, this project is currently using state of the art underwater acoustic and satellite technology to track movements of endangered sea turtles within and outside of the boundaries of DRTO. Activities proposed here relate to and complement one component of the joint USGS/State-FWC SPP fish proposal (funding to USGS McIvor in 2007, receiver deployment in May 2008) to deploy and utilize an acoustic array in the RNA. The goal of this already-funded joint SPP project is to examine the fine-scale movement patterns and core utilization areas of exploited fish species to determine the spatial adequacy of existing reserve boundaries. The SPP project and the project proposed here would make use of the same array of receivers. This project will add additional receivers to be deployed in specific habitats of interest in DRTO (i.e., in seagrass beds, adjacent to areas of dense sponge cover). Essentially, the tracking components of the two complementary projects differ in that they will be tagging different types of species. However, because the State-FWC will conduct range-testing of the receivers, house the digital database of tag locations, and perform data downloading, we can collaborate with their ongoing efforts. Moreover, this project adds a significantly different dimension than the fish tracking project that is funded through a different source. Whereas the fish project seeks to concentrate acoustic fish tracking efforts solely within the RNA, this turtle tracking project will contain an "outside the RNA" component by utilizing satellite data acquired from satellite tags deployed alongside acoustic tags on sea turtles. Data derived from these satellite tags is already informing managers of turtle habitat use outside the RNA. Such information will reveal whether the boundaries of the RNA should be adjusted in order to more adequately protect endangered turtles using specific benthic habitats for forage and upland habitats for nesting; this question has become a central theme in the USGS Florida Integrated Science Center (FISC) Integrated Cora Reef Project of PIs Hart and Zawada. The integrated project will rely on USGS Coastal and Marine Geology funding to conduct endangered sea turtle tracking with high-resolution mapping and fine-scale benthic habitat characterization using the Along-Track-Reef-Imaging-System (ATRIS).

We have already obtained funding from NPS for a project in 2008 to purchase three acoustic tags specifically for deployment on sea turtles in DRTO, as well as three satellite tags and satellite time for tracking these individuals.This "pilot" type of project has allowed us to obtain permits (federal, state, and DRTO) for the proposed work. In mid-May, we tagged three nesting loggerheads with acoustic and satellite tags, and we have been tracking their daily movements using We also sampled the three nesting turtles for genetic determination of their region of origin which will reveal population-level connections of the loggerhead sea turtles using DRTO to other populations residing in or using habitats outside the park boundaries (i.e., Everglades National Park, Florida Keys National Marine Sanctuary, Key West National Wildlife Refuge, the Marquesas), and elsewhere.

We (USGS-Hart and technicians) currently have an active project on juvenile green sea turtles in the Everglades (funded by the USFWS) that utilizes satellite tracking in association with genetic sampling and conventional internal and external tagging methods. The in-water sampling methods for the Everglades project will be similar to the in-water sampling in the Tortugas (i.e., capture by entanglement net and dip nets). We also have all the training necessary to perform the proposed biological sampling (i.e., oral lavage, satellite tag and acoustic tag attachment, blood sampling, tissue sampling, etc.). USGS also has trained divers to assist with fieldwork and deployment of additional receivers.

Planned Products: Products that will result from this project include at least two major publications (one to share tracking data and one to present genetic analysis results, likely to Endangered Species Research, Marine Ecology Progress Series), as well as presentations at regional, national and international scientific conferences (i.e., Annual Sea Turtle Symposium). Also, annual and project end reports will be filed in compliance with USGS and NPS, State of Florida, and NMFS permit requirements. A USGS Fact Sheet will be prepared to disseminate information about sampled resources to managers, policy makers, and scientists to direct the flow of information outside of the scientific community. The public will be informed through and through the annual USGS open house in St. Petersburg. Funding agencies and other interested parties may log in to the website daily to observe turtle locations and habitat use trends. As well, we will generate GIS layers of benthic habitat maps each year after Tortugas cruises. Maps will be made available to the USGS and the NPS after processing, generally several months after a cruise. Hart will ensure transfer of key results on sea turtle habitat use patterns and genetic composition to the NMFS for inclusion in recovery plans for green sea turtles.

Title of Task 1: Sea turtle use of benthic habitats within DRTO and surrounding areas
Task Funding: GE PES, NPS
Task Leaders: Kristen M. Hart
Phone: 954-650-0336
Task Status (proposed or active): Active
Task priority: High
Time Frame for Task 1: August 2008 fieldwork then 2009–2013
Task Personnel: TBD, Keith Ludwig, Adam Brame

Task Summary and Objectives: The purpose of this task is to capture and tag sea turtles in the Dry Tortugas National Park with standard PIT and flipper tags, as well as state-of-the-art acoustic and satellite tags. Capture sites will be on nesting beaches (i.e., Loggerhead Key, East Key) and in the water near Bush Key and Long Key as well as near Pulaski Light; capture sites will be both inside and outside the RNA. We will work-up each individual sea turtle to obtain diet and genetic samples, and morphometric information. Tracking efforts will involve downloading data from acoustic receivers several times a year as well as daily uploads of locations derived from satellites.

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

Specific Task Products: We will present the initial results of sea turtle tracks at the October 2008 meeting of the Florida Integrated Science Center in Orlando and at the annual Sea Turtle Symposium in February 2009 (an international meeting). We plan to submit one manuscript on the results of the acoustic and satellite tracking. Maps of turtle movement patterns will be available on

Title of Task 2: Benthic Characterization of Habitats Used by Sea Turtles in the Dry Tortugas
Task Funding: GE PES, CMG
Task Leaders: Kristen M. Hart, Dave Zawada
Phone: 954-650-0336
Task Status (proposed or active): Active
Task priority: High
Time Frame for Task 1: 2009–2013
Task Personnel: Kristen M. Hart, Dave Zawada, Adam Brame

Task Summary and Objectives: The purpose of this task is to characterize the habitats used by sea turtles in the Dry Tortugas. Information on habitats occupied will come from sightings and observations of sea turtle presence as well as data obtained from satellite tags and acoustic tags deployed on sea turtles. Bottom type will be identified and categorized using ATRIS as well as underwater digital photography and quadrat sampling.

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

Specific Task Products: Maps of benthic cover and turtle locations, and a peer-reviewed manuscript.

Title of Task 3: Genetic Diversity of Sea Turtles in the Dry Tortugas
Task Funding: GE PES, CMG
Task Leaders: Kristen M. Hart, Eugenia Naro-Maciel (AMNH)
Phone: 954-650-0336
Task Status (proposed or active): Active
Task priority: High
Time Frame for Task 1: 2009–2013
Task Personnel: Kristen M. Hart, Eugenia Naro-Maciel

Task Summary and Objectives: The purpose of this task is to identify the genetic diversity of sea turtles found in the Dry Tortugas and compare it to other previously sampled sea turtles from other areas in south Florida and beyond.

Work to be undertaken during the project and a description of the methods and procedures: Each sea turtle will be sampled for genetics during the work-up procedure. Samples will be sent for analysis to Dr. Eugenia Naro-Maciel at the American Museum of Natural History (AMNH) in New York City, New York. By using previously developed molecular markers and analyzing mitochondrial DNA from each turtle to obtain genotypes, we can assess the likelihood that these turtles are all from the same or several different nesting beaches. This analysis will reveal genetic linkages to other sea turtle populations sampled elsewhere. We will analyze mitochondrial DNA control region sequences and nuclear microsatellite genotypes and compare data from DRTO turtles to sequences posted on GENBANK. The program ARLEQUIN version 3.01 (Excoffier et al., 2005) will be used to characterize genetic diversity, and to assess genetic structure through exact tests of population differentiation (Raymond and Rousset, 1995). Bayesian clustering analyses implemented by STRUCTURE version 2.1 will be used to estimate connectivity revealed by microsatellite markers without assuming prior population definitions (Pritchard et al., 2000). In addition, the Mixed Stock Analysis (Pella and Milner, 2001) method will be used to trace natal origins of these sea turtles.

Specific Task Products: USGS-Hart will work with Naro-Maciel to synthesize results of genetic analysis for reports, presentations, and publications. We expect that one peer-reviewed manuscript will result from this task.

Title of Task 4: Effects of Australian Pines on SeaTurtle Reproduction on Loggerhead Key.
Task Funding: GE PES, CMG
Task Leaders: Kristen M. Hart, Kate Mansfield (RSMAS)
Phone: 954-650-0336
Task Status (proposed or active): Active
Task priority: High
Time Frame for Task 1: 2009-2013
Task Personnel: Kristen M. Hart, Kate Mansfield (RSMAS), RSMAS graduate student TBD

Task Summary and Objectives: The purpose of this task is to identify whether the stumps and roots of Australian pines on Loggerhead Key are interfering with sea turtle reproductive success. Exotic Australian pines were removed in the mid-1990s from Loggerhead Key, but the stumps and roots were left. This woody debris may deter nesting female sea turtles from using the beach, as well as trap hatchlings and shade the soil, possibly also causing temperature changes in the thermal profiles of the nest chamber.

Work to be undertaken during the project and a description of the methods and procedures: Vegetation transects will be conducted along beach zones as in the 1990s to identify native and exotic vegetation. As well, daily nest monitoring for 2009–2010 will be conducted by a RSMAS student. A comparison of hatch rates for all nests monitored will be conducted, and a comparison of thermal regimes of data loggers deployed in nests and in shaded areas. False crawls of sea turtles will be compared by beach zone and proximity to stumps and exposed roots. We will compare all data collected to all available data from prior to the invasion and removal of exotic Australian pines.

Specific Task Products: We will deliver a prioritized list of problematic stumps and roots that interfere with sea turtle nesting, and a final report that will be turned into a peer-reviewed manuscript.

Literature Cited
Coyne, M.S. and Godley, B.J.. 2005. Satellite Tracking and Analysis Tool (STAT): An integrated system for archiving, analyzing and mapping animal tracking data. Marine Ecology Progress Series, 301:1–7.

Excoffier, L., Laval, G., and Schneider, S., 2005. Arlequin version 3.0: An integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online, 1:47–50.

Fonseca, M.S., Uhrin, A.V., Currin, C.A., Burke, J.S., Field, D.W., Addison, C.A., Wood, L.L., Piniak, G.A., Viehman, T.S., and Bonn, C.S., 2006. Ongoing Monitoring of Tortugas Ecological Reserve: Assessing the Consequences of Reserve Designation. NOAA Technical Memorandum, NOS NCCOS 22.

Franklin, E.C., Ault, J.S., Smith, S.G., Luo, J., Meester, G.A., Diaz, G.A., Chiappone, M., Swanson, D.W., Miller, S.L., and Bohnsack, J.A., 2003. Benthic habitat mapping in the Tortugas region, Florida. Marine Geodesy, 26:19-34.

Pella, J. and Masuda, M., 2001. Bayesian methods for analysis of stock mixtures from genetic characters. Fishery Bulletin, 9:151-167.

Polovina, J.J., Kobayashi, D.R., Parker, D.M., Seki, M.P., and Balazs, G.H., 2000. Turtles on the edge: movement of loggerhead turtles (Caretta caretta) along oceanic fronts, spanning longline fishing grounds in the central North Pacific, 1997–1998. Fisheries Oceanography, 9(1): 71-82.

Polovina, J.J., Balazs,G.H., Howell, E.A., Parker, D.M., Seki, M.P., and Dutton, P.H., 2004. Forage and migration habitat of loggerhead (Caretta caretta) and olive ridley (Lepidochelys olivacea) sea turtles in the central North Pacific Ocean. Fisheries Oceanography, 13(1): 36-51.

Pritchard J.K., Stephens, M., and Donnelly, P., 2000. Inference of population structure using multilocus genotype data. Genetics, 155:945-959.

Raymond, M. and Rousset, F., 1995a. An exact test for population differentiation. Evolution, 49:1280-1283.