Project Work Plan
Department of Interior USGS GE PES
Fiscal Year 2010 Study Work Plan
Benthic habitat characterization and habitat use of endangered sea turtles in Marine Protected Areas of the Greater Everglades
1 September 2009
30 September 2013
5 years from FY 2009–2013
Southern Florida Keys, Dry Tortugas National Park (Monroe County)
GE PES, Coastal and Marine Geology (CMG)
USGS State Partnership Program (SPP), Fish and Wildlife Conservation Commission (FWCC), National Park Service (FY 2008), GE PES and matching USGS Coastal and Marine Geology (CMG) in FY 2009.
This project integrates with the new USGS FISC Coral Reef project, as well as with FWCC funds and joint funds shared by USGS and FWCC.
Kristen M. Hart
Michael Cherkiss, Keith Ludwig, Ikuko Fujisaki
U.S. National Park Service
High-resolution mapping of the Dry Tortugas (USGS PI Zawada)
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 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.
- The exciting opportunity to examine movement of this key species across acoustically-monitored RNA boundaries (receiver deployment funded by a 2007 USGS/Fish and Wildlife Conservation Commission (FWCC) State Partnership Program (SPP) award, with receiver deployment in May 2008). We will quantitatively determine patterns of endangered sea turtle habitat use inside and outside the RNA by instrumenting turtles with both acoustic and satellite tags. With acoustically-logged data, we are assessing the proportion of time each turtle spends inside the RNA, and with satellite-derived data, we are assessing the proportion of time each turtle spends outside the RNA or in areas not adjacent to acoustic receivers. Such information will be important for park managers to assess appropriateness of current RNA boundaries for these high-profile endangered species.
- Second, we will integrate with USGS FISC Coral Reef Project Scientist Dave Zawada's high-resolution benthic mapping project to characterize benthic cover in areas where turtles are concentrating or repeatedly visiting. This coverage is a novel use of the Along-Track-Reef-Imaging-System ATRIS, and a component of sea turtle habitat use studies that has been lacking to date.
- Further, by also including a molecular genetic component in our project, we will develop an understanding of the linkages and connections among endangered sea turtles using DRTO and potentially other protected areas in the U.S. (i.e., Everglades National Park (ENP), Florida Keys National Marine Sanctuary (FKNMS)) and other countries. Such information is necessary for overall sea turtle population restoration and recovery efforts.
Data is lacking on the use of protected areas (MPAs) by endangered species. Despite detailed knowledge of general sea turtle nesting trends in 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 RNA in DRTO were ringed with acoustic listening stations in summer 2008 through USGS SPP funding. We also deployed seven of our own receivers in 2009 in habitats frequented by sea turtles. By capturing and acoustically tagging endangered sea turtles from within and around the RNA, we are determining fine-scale patterns of sea turtle habitat use and movement patterns within and around the RNA. Because we are also attaching satellite tags to a subset of the acoustically-equipped turtles, we are determining 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:
- What actions will restore, protect, and maintain natural resources on DOI lands in south Florida?
- What actions will recover south Florida's threatened and endangered species?
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 form 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), not just along the boundary lines. The State-FWC will house the digital database of tag locations, and perform most data-downloading, we will collaborate with their ongoing field and data processing efforts. Unlike the fish project, 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 (i.e., in the Bahamas, off Sanibel, and off Naples). 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 Coral Reef Project of PIs Hart and Zawada. The integrated Hart-Zawada project will rely on both USGS GE PES and USGS Coastal and Marine Geology funding to conduct endangered sea turtle tracking in concert with high-resolution mapping and fine-scale benthic habitat characterization using the Along-Track-Reef-Imaging-System (ATRIS).
USGS-Hart obtained funding from the 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 2008, we tagged three nesting loggerheads with acoustic and satellite tags, and we have been tracking their daily movements using www.seaturtle.org. Later, in August 2008, we initiated our in-water capture efforts and captured 23 juvenile green turtles and three juvnenile hawsbills; we outfitted the three hawksbills with satellite and acoustic tags and have been tracking their daily movements using www.seaturtle.org. We sampled all turtles for genetic determination of their region of origin, which will reveal population-level connections of the 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 + technicians) currently have another project on juvenile green sea turtles in the Everglades (funded by the USFWS until FY08) 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.
In 2008 we successfully obtained all three necessary project permits (State of Florida Marine Turtle Permit #176, National Marine Fisheries Service Endangered Species Permit #13307, and DRTO-2008-SCI-0008) and worked out sampling protocols. We began intercepting reproductive females on the nesting beach in May 2008 and catching turtles in the water using dip-nets and hand capture in August. During all sampling in 2008, we tagged six turtles (three loggerheads on East Key, three hawksbills from Bird/Long Key flat) with satellite and acoustic tags; three of these tags are still transmitting daily location data as of November 11, 2009. We also captured, tagged, and sampled 23 juvenile green turtles on the Bird/Long Key flat. Fieldwork during 2008 was successful largely due to use of the NPS M/V Fort Jefferson for research. In 2008 we also secured additional support for the project from two USGS Programs (CMG and the Priority Ecosystem Studies (PES) Program). In May 2009 we delineated the 50% core use areas for loggerheads and hawksbills tagged in 2008 and worked with USGS PI Dave Zawada to create transects through these areas to be photographed in June 2009 using the USGS underwater Along Track Reef Imaging System (ATRIS). In June 2009, we satellite tagged four more reproductive female loggerheads on East Key to assess interannual differences in core areas used by loggerheads. We also initiated in-water rodeo captures and satellite-tagged six subadult and adult green turtles near the North Key Harbor area. In August we focused on nesting work on East Key and affixed acoustic tags to a subset of nesting greens. We also captured new and recaptured juvenile greens in the water using dip-nets. To date we have satellite tagged 16 sea turtles (seven loggerheads, six greens, three hawksbills) and acoustic tagged 25 turtles (10 loggerheads, 13 greens, two hawksbills); 14 of these turtles are double-tagged with both satellite and acoustic tags (seven loggerheads, five greens, two hawksbills). Thus far we have worked primarily on East Key to intercept nesting female loggerheads and greens and have been successful with in-water captures near North Key Harbor and in shallow water near the Fort, inside the Natural/Cultural Zone "bubble" of the RNA.
The size distribution for all 63 sea turtles captured in the park includes juvenile, subadult, and adult greens of both sexes; subadult and adult loggerheads of both sexes; and juvenile, subadult, and adult hawksbills (unknown sex). Green turtles were the most common species captured (N=49), followed by loggerheads (N=10) and hawksbills (N=4) . From October 2007–August 2009, we collected 300+ georeferenced sightings of sea turtles in various areas of the park. Satellite-tracking results indicated that loggerhead females tagged on East Key utilize core areas outside the RNA more frequently than areas within the RNA, and hawksbills captured near the Bird/Long key flat used a core area that overlaps with the Natural/Cultural zone "bubble". Subadult and adult green turtles of both sexes were park residents, utilizing an area of lush seagrass near North Key Harbor outside the RNA. In contrast, adult female loggerheads were resident in the park only from ~May through July/early August. Juvenile/subadult hawksbills appeared to be full-time residents of the park, as two tagged individuals were each still resident after ~460 tracking days. Migratory pathways and destination points of satellite-tagged loggerhead females indicated that three of seven tagged turtles migrated to, and took up residence in, the Bahamas, whereas four migrated to the southwest coast of Florida. One hawksbill departed DRTO after 265 days of residence and travelled to the north coast of Cuba, where it was harvested by fishermen. As of November 11, 2009, we have logged 3,262 turtle tracking days (1,446 days for loggerheads, 618 days for greens, and 1,198 days for hawksbills). In 2009 we also deployed seven acoustic receivers and downloaded and exchanged acoustic data with State FWC biologists and Mote's Wes Pratt; acoustic data processing is ongoing. In 2009 we recaptured 13/29 or 44.8 percent of juvenile greens (21-50 cm straight carapace length (SCL) size class) that were originally captured and tagged in August 2008. For these 13 juveniles, mean SCL at initial capture was 34.8 cm (5.01 SD; range 26.8-42.6 cm) and mean annual growth rate was 3.7 cm SCL (2.56 SD; range 0.9-10.2 cm). Diet of juvenile greens was primarily Thalassia.
In 2010-2011 we plan to conduct both nesting beach work and in-water turtle captures to increase the sample sizes of tagged/sampled individuals for all three species. We will specifically plan capture and tagging efforts to assess: 1) whether reproductively mature female loggerheads nesting on Loggerhead Key utilize the same internesting habitat (50% core use area) outside the RNA as that used by the seven loggerheads previously tagged on East Key in 2008 and 2009; 2) where nesting green turtles from both East Key and Loggerhead Key spend their time in the internesting interval (and whether this area is in the RNA); 3) where additional hawksbills may be found. We also expect to be able to determine through satellite tracking whether reproductive female green turtles nesting at are resident within the park, or instead migrate elsewhere after the nesting season. We will continue to collaborate with the State FWCC biologists and Mote's Wes Pratt on acoustic data download and exchange, and maintain the network of seven acoustic receivers that we deployed in 2009; we currently have three acoustic data-downloading trips planned each year for the next two years. We will continue catching juvenile greens (and hopefully more hawksbills) in the shallow flat around Bird/Long Key and refine growth rate estimates for these young turtles. Additionally, we will process all lavage samples, conduct isotope analysis, and conduct genetic analysis to determine stock structure for each species. We will continue to update information on residence times for turtles residing in and using DRTO. We will also continue to work with USGS PI Zawada to use ATRIS, a benthic habitat mapping and characterization tool, to plan mapping and habitat characterization efforts in turtle internesting habitat and other turtle core use areas in the park. The combined data sets will provide insight into (1) the effectiveness of the RNA for protecting threatened and endangered marine turtles and their requisite habitats, (2) the condition of those habitats (i.e., seagrass beds), and (3) the development of more effective decision-support tools to adaptively manage coral ecosystems.
www.seaturtle.org/tracking, USGS Soundwaves (December 2008 feature article) 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.Products that will result from this project include at least three major publications (two to share tracking data and one to present genetic analysis results, likely in Endangered Species Research, Marine Ecology Progress Series, and Conservation Genetics), 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 in 2010 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
Benthic habitat characterization and habitat use of endangered sea turtles in Marine Protected Areas of the Greater Everglades
Kristen M. Hart
Mike Cherkiss (University of Florida), Dave Zawada (USGS), Eugenia Naro-Maciel (American Museum of Natural History), Ikuko Fujisaki (University of Florida)
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 satellite tags affixed to a proportion of turtles for each species.
- Deploy and maintain acoustic acoustic receivers in areas of interest in DRTO (i.e., in seagrass beds in the northeast area of the park and in shallow water near Long and Bush Keys, where sea turtle observations have been concentrated), both within and outside the RNA.
- Conduct fieldwork to capture and tag sea turtles from both nesting beaches and in-water feeding grounds. Outifit each large turtle with both an acoustic tag and a satellite tag; outfit each smaller turtle with either a satellite tag or an acoustic tag. Each turtle will be sampled for diet and genetics. We will apply internal PIT and external Inconel tags to all turtles captured, and take standard morphometric measurements and weight (if possible). Data will be used to determine: (1) size class and condition (including fibropapillomatosis (FP) disease presence) of green sea turtles using the RNA (because of the remoteness of DRTO, we hypothesize that FP will not be commonly seen on green turtles sampled in the RNA); (2) diet of green sea turtles using the RNA; (3) potential links to other green turtle populations if some turtles are already tagged from other studies.
- Examine movement patterns of tagged turtles to determine residence times and habitat use relationships. In particular, we will quantify fine-scale movement patterns and core utilization areas of endangered sea turtles to determine the spatial habitat use patterns both inside and outside the RNA by using satellite and acoustic tracking technologies. We will characterize the habitat features that are utilized by these turtles by relating tracks derived from acoustic and satellite telemetry data to both static (i.e., bathymetry) and dynamic (i.e., temperature, salinity, food resource location) features of the RNA. We will analyze location data to examine whether locations received were indicative of directed or nondirected (sedentary) movements and behaviors (i.e., by analyzing perceived swim speed, direction of travel, etc.). We will use the Satellite Tracking and Analysis Tool (STAT) (Coyne and Godley, 2005) available on www.seaturtle.org/tracking to manage satellite telemetry data and maximize the potential of these relatively expensive data. An extremely valuable aspect of STAT is its ability to automatically retrieve, parse, and store telemetry data from the Argos Satellite network. A suite of summary maps, tables, and graphs are updated each day, allowing investigators to easily check each of the tagged animals. STAT also provides an array of mapping, filtering, and export functions to facilitate data analysis, as well as access to bathymetry, sea surface temperature, chlorophyll, sea surface height, and ocean surface currents, thus allowing researchers to see turtle movement in the context of the local environment (Polovina et al., 2000; 2004). The centers of turtle activity will be analyzed using the Animal Movement™ extension for ARCVIEW 3.2 to give home ranges using kernel-based frequency distributions of locations. Home ranges will be compared to spatially explicit environmental data (e.g., distribution of continuous and discontinuous seagrass) based on available and created (through NOAA) GIS layers.
- Analyze location information to determine the spatial adequacy of existing reserve boundaries for these threatened and endangered marine turtle species. We will also compare satellite and acoustic data from the same turtle to determine consistency of location data derived from both remote tracking methods.
- Characterize benthic habitats used by sea turtles in the Dry Tortugas. Bottom type will be identified and categorized using the USGS Along-Track-Reef-Imaging-System (ATRIS) in conjunction with USGS PI Dave Zawada (St. Petersburg), as well as other underwater digital photography and quadrat sampling.
- Work with USGS PI Zawada in 2010 to examine benthic cover data collected in 2009 using ATRIS in areas of interest (i.e., RNA boundary lines, turtle "hotspots"). Conduct additional in-water habitat characterization of soft bottom and hard bottom cover in the RNA, particularly in areas frequented by tagged sea turtles. We will use all data to determine whether the RNA serves as refuge for endangered species and how much critical habitat for green sea turtles lies within the boundaries of the RNA (and potentially other TER protected areas).
- Identify genetic diversity of sea turtles in the Dry Tortugas and compare it to other previously sampled sea turtles from other areas in south Florida and beyond. 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.
www.seaturtle.org, and through USGS PIs. USGS-Hart will work with Naro-Maciel to synthesize results of genetic analysis for reports, presentations, and publications. We expect at least one peer-reviewed manuscript will result from the genetic analysis.We will present the results of sea turtle tracking and capture efforts in January 2010 at the National Park Service Workshop on the 3-year evaluation of the RNA in Homestead, Florida, as well as in July 2010 at the Greater Everglades Ecosystem Restoration (GEER) meeting in Naples, Florida. We will also present results of sea turtle tracking at the annual Sea Turtle Symposia (in April 2010 to be held in Goa, India). We plan to submit several manuscripts on the results of the acoustic and satellite tracking, as well as two manuscripts on turtle habitat use and ATRIS benthic habitat characterization. Maps of turtle movement patterns will be available on
Coyne, M.S. and B.J. Godley, 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., J.S. Ault, S.G. Smith, J. Luo, G.A. Meester, G.A. Diaz, M. Chiappone, D.W. Swanson, S.L. Miller, and J.A. Bohnsack, 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.