Project Work Plan
Department of Interior USGS GE PES
Fiscal Year 2008 Study Work Plan
Benthic Habitat Characterization and Habitat Use of Endangered Sea Turtles in Dry Tortugas National Park
1 August 2008
30 September 2013
2 months in FY 2008+ 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
This project integrates with the new USGS FISC Coral Reef project, with FWCC funds and joint funds shared by USGS and FWCC.
Kristen M. Hart
U.S. National Park Service
High-resolution mapping of the Dry Tortugas (USGS PI Zawada), Habitat use of sea turtles in the Dry Tortugas (USGS PI Hart, NPS funded)
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.
- 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 will assess the proportion of time each turtle spends inside the RNA, and with satellite-derived data, we will assess 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 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.
- 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 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 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:
- 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 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 www.seaturtle.org. 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.
www.seaturtle.org/tracking 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 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
Sea turtle use of benthic habitats within DRTO and surrounding areas
GE PES, NPS
Kristen M. Hart
August 2008 fieldwork then 2009–2013
TBD, Keith Ludwig, Adam Brame
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.
- Deploy 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 green sea turtles from both nesting beaches and in-water feeding grounds. Each of three green turtles will be outfitted with both an acoustic tag and a satellite 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 green 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.
- Analysis of location information will allow us to determine the spatial adequacy of existing reserve boundaries for these endangered 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
- Assessment of beach conditions will involve inventories of native and exotic species along transects at East and Loggerhead Keys, the main nesting beaches. On Loggerhead Key in particular, we are interested in whether the stumps and roots of Australian pines that remain after eradication efforts in the mid-1990s are indeed impacting the adult and hatchling turtles. Stumps can prevent turtles from nesting and trap hatchlings, as well as affect the temperature of the sand which for reptiles affects the gender of the developing hatchlings. Such impacts may prevent successful reproduction efforts for these endangered species, rendering the nesting beach useless.
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:
- Work with USGS PI Zawada to examine benthic cover data collected 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).
- Measure general effects of turtle grazing on seagrass beds and sponges using transects and ½ m2 quadrats and sampling both before and after receiver deployment. During each sampling trip, 25 quadrats will be assessed at each of five sites (the same site chosen for acoustic receiver deployment). Measures will include seagrass and sponge species identification and percent cover (Braun-Blanquet method), blade length, blade density, percent of quadrat grazed, type of grazing evidence, epifaunal load, and presence of turtles.
Maps of benthic cover and turtle locations, and a peer-reviewed manuscript.
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.
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.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
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.
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.
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.
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.
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.