Experimental coral-growth data and time-series imagery for Acropora palmata and Pseudodiploria strigosa in St. Croix, U.S. Virgin Islands

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Frequently anticipated questions:

What does this data set describe?

Title:
Experimental coral-growth data and time-series imagery for Acropora palmata and Pseudodiploria strigosa in St. Croix, U.S. Virgin Islands
Abstract:
The U.S. Geological Survey (USGS) Coral Reef Ecosystems Studies (CREST) project (https://coastal.er.usgs.gov/crest/) provides science that helps Department of Interior and other resource managers tasked with the stewardship of coral reef resources. This data release contains data on coral-growth rates and time-series photographs taken of colonies of the elkhorn coral, Acropora palmata, and the symmetrical brain coral, Pseudodiploria strigosa, grown at three sites at Buck Island Reef National Monument in St. Croix, U.S. Virgin Islands from June 2019 to August 2021. The data will be used to inform resource managers of the capacity for restoration and growth of these habitat-forming species of coral within National Park (and Virgin Islands territory) waters.
Supplemental_Information:
Scientific research permits: The data herein were collected with permission from the National Park Service and the Florida Keys National Marine Sanctuary under permit number BUIS-2019-SCI-0004. To ensure that USGS-St. Petersburg data management protocols were followed, all surveys when data were collected were assigned the following USGS field activity numbers (FANs): 2019-321-FA, 2019-368-FA, 2020-308-FA, 2021-309-FA, 2021-324-FA and 2021-331-FA. Additional survey and data details are available from the U.S. Geological Survey Coastal and Marine Geoscience Data System (CMGDS) at, https://cmgds.marine.usgs.gov/.
  1. How might this data set be cited?
    Kuffner, Ilsa B., Stathakopoulos, Anastasios, Ewen, Kristen A., Holloway, Nathaniel Hanna, Lyons, Erin O., Bartlett, Lucy A., Pollock, Clayton G., and Hillis-Starr, Zandy, 20220920, Experimental coral-growth data and time-series imagery for Acropora palmata and Pseudodiploria strigosa in St. Croix, U.S. Virgin Islands:.

    This is part of the following larger work.

    Kuffner, Ilsa B., Stathakopoulos, Anastasios, Ewen, Kristen A., Holloway, Nathaniel Hanna, Lyons, Erin O., Bartlett, Lucy A., Pollock, Clayton G., and Hillis-Starr, Zandy, 20220920, Experimental Coral-Growth Data and Time-Series Imagery for Acropora palmata and Pseudodiploria strigosa in St. Croix, U.S. Virgin Islands: U.S. Geological Survey data release doi:10.5066/P94BOI9T, U.S. Geological Survey - St. Petersburg Coastal and Marine Science Center, St. Petersburg, Florida.

    Online Links:

  2. What geographic area does the data set cover?
    West_Bounding_Coordinate: -64.62122
    East_Bounding_Coordinate: -64.61143
    North_Bounding_Coordinate: 17.79081
    South_Bounding_Coordinate: 17.78408
  3. What does it look like?
  4. Does the data set describe conditions during a particular time period?
    Beginning_Date: 19-Jun-2019
    Ending_Date: 20-Aug-2021
    Currentness_Reference:
    ground condition
  5. What is the general form of this data set?
    Geospatial_Data_Presentation_Form: raster digital data; tabular digital data
  6. How does the data set represent geographic features?
    1. How are geographic features stored in the data set?
      This is a Point data set. It contains the following vector data types (SDTS terminology):
      • Point (230)
    2. What coordinate system is used to represent geographic features?
      Horizontal positions are specified in geographic coordinates, that is, latitude and longitude. Latitudes are given to the nearest 0.000000001. Longitudes are given to the nearest 0.000000001. Latitude and longitude values are specified in Decimal Degrees. The horizontal datum used is WGS_1984.
      The ellipsoid used is WGS_84.
      The semi-major axis of the ellipsoid used is 6378137.0.
      The flattening of the ellipsoid used is 1/298.257223563.
  7. How does the data set describe geographic features?
    Palmata_growth_VI_USA.csv, Palmata_growth_VI_USA.xlsx
    These files contain attribute information for data describing the growth of corals of the species Acropora palmata, which were obtained from five legacy colonies (identified by NPS staff) within the Buck Island Reef National Monument and grown at three study sites within Buck Island Reef National Monument reefs during four time intervals: June 2019 to November 2019 (1), November 2019 to June 2020 (2), June 2020 to February 2021 (3), and February 2021 to August 2021 (4). Data includes coral identification number, latitude, longitude, colony identification label, site where they were deployed for growth, time interval, condition of coral colony at the end of time interval identified in “Time_interval”, calcification rate per coral-planar-footprint area per day, change in coral planar-footprint area per day, and change in coral height per day. The data is available as a comma-separated values (.csv) file and a Microsoft Excel (.xlsx) file. (Source: USGS)
    Site_ID
    A textual identifier of the site, assigned to locations where corals were deployed at Buck Island Reef National Monument and named by USGS personnel as follows: “NWR” indicates Northwest Reef (10 feet of seawater [fsw]), “NER” indicates Northeast Reef (16 fsw) and "SFR" indicates South Forereef (14 fsw). (Source: USGS) A textual description of the geographic site where coral growth data were collected.
    Latitude
    Latitudinal coordinate of the site locations where corals were deployed by USGS personnel. (Source: USGS)
    Range of values
    Minimum:17.78408
    Maximum:17.79081
    Units:decimal degrees
    Longitude
    Longitudinal coordinate of the site locations where corals were deployed by USGS personnel. (Source: USGS)
    Range of values
    Minimum:-64.62122
    Maximum:-64.61143
    Units:decimal degrees
    Coral_ID
    A numeric identifier for each coral colony in the study, assigned by USGS personnel. (Source: USGS) Non-sequential, increasing numerical identifiers ranging between 111 and 187.
    Genet_ID
    A textual identifier for each purportedly unique genetic strain (genet) of elkhorn coral in the study, as assigned by USGS and NPS personnel based upon the collection location of the original colony from which samples were taken. The two-letter code “BI” indicates “Buck Island”, and the numbers are sequentially assigned in their order of collection. Locations of the original legacy colonies are: BI1 at 17.78918, -64.60981, BI2 at 17.78850, -64.60872, BI3 at 17.79066, -64.62045, BI4 at 17.78830 N, -64.60998, and BI5 at 17.78425, -64.61414. (Source: USGS) A textual description of the geographic location where the original coral colony from which fragments were collected by USGS and NPS personnel.
    Time_interval
    A numerical identifier of the time interval during which the data were collected. Time “1” spans from June 2019 to November 2019, Time “2” spans from November 2019 to June 2020, Time “3” spans from June 2020 to Feb 2021, Time “4” spans from Feb 2021 to August 2021. (Source: USGS) Time intervals are not the same for each site, so data were normalized to the number of days between site visits (meaning, converted to rates) to reflect this source of variability in the data.
    Calcif_mg_cm2_d
    Dry mass of calcium carbonate gained during the time interval (Time_interval column) in the units of milligrams per square centimeter (planar-footprint area at start of time interval) per day. If the coral had died, or more than 50 percent of live tissue was lost in an earlier time interval, there is no value reported (data cell left blank). (Source: USGS)
    Range of values
    Minimum:-4.45
    Maximum:14.89
    Units:milligrams per square centimeter per day
    Calcif_del_SA_cm2_hy
    Change in planar-footprint area of the colony since the start of the time interval(Time_interval column) in units of square centimeters per half year (182.5 days). If the coral had died, or more than 50 percent of the tissue was lost in an earlier time interval, there is no value reported (data cell left blank). (Source: USGS)
    Range of values
    Minimum:-37.9
    Maximum:466.8
    Units:square centimeters per half year (182.5 days)
    Calcif_del_ht_mm_hy
    Change in colony height since the start of the time interval (Time_interval column) in the units of millimeters per half year (182.5 days). If the coral was no longer in the study area during the specified time interval, or if more than 50 percent of the tissue had died in an earlier time interval, there is no value reported (data cell left blank). (Source: USGS)
    Range of values
    Minimum:-49.3
    Maximum:92.5
    Units:millimeters per half year (182.5 days)
    Condition
    A textual identifier assigned by USGS personnel as follows: “live” indicates that the coral gained mass and had live tissue during the entire time interval, “dead” indicates the coral had no live tissue remaining at the end of the time interval, and “broke” indicates that at least one coral branch had broken off during the time interval. In two cases for the last weighing interval, a branch broke but it did not affect the overall height of the colony; in this case, the condition was noted “broke_ht_ok”. (Source: USGS) A textual identifier assigned by USGS personnel describing the condition of the coral during the time interval.
    Strigosa_growth_VI_USA.csv, Strigosa_growth_VI_USA.xlsx
    These files contain attribute information for data describing the growth of corals of the species Pseudodiploria strigosa, which were obtained from either Northeast Reef (16 fsw) or South Forereef (14 fsw) at Buck Island Reef National Monument and grown at three study sites on Buck Island National Monument reefs during four time intervals: June 2019 to November 2019 (1), November 2019 to June 2020 (2), June 2020 to February 2021 (3), February 2021 to August 2021 (4). Data include coral identification numbers, latitude, longitude, site where they were deployed for growth, time interval, condition of coral colony at the end of time interval identified in “Time_interval”, calcification rate per planar area per day, change in coral planar-footprint surface area per day, and change in coral height per day. The data is available as a comma-separated values (.csv) file and a Microsoft Excel (.xlsx) file. (Source: USGS)
    Site_ID
    A textual identifier of the site, assigned by locations where corals were deployed and named by USGS personnel as follows: “NWR” indicates Northwest Reef (10 fsw), “NER” indicates Northeast Reef (16 fsw) and "SFR" indicates South Forereef (14 fsw) at Buck Island Reef National Monument. (Source: USGS) A textual description of the geographic site where data were collected.
    Latitude
    Latitudinal coordinate of the site locations where corals were deployed by USGS personnel. (Source: USGS)
    Range of values
    Minimum:17.78408
    Maximum:17.79081
    Units:decimal degrees
    Longitude
    Longitudinal coordinate of the site locations where corals were deployed by USGS personnel. (Source: USGS)
    Range of values
    Minimum:-64.62122
    Maximum:-64.61143
    Units:decimal degrees
    Coral_ID
    A numeric identifier for each coral colony in the study, assigned by USGS personnel. (Source: USGS) Non-sequential, increasing numerical identifiers ranging between 101-461.
    Time_interval
    A numerical identifier of the time interval during which the data were collected. Time “1” spans from June 2019 to November 2019, Time “2” spans from November 2019 to June 2020, Time “3” spans from June 2020 to Feb 2021, Time “4” spans from Feb 2021 to August 2021. (Source: USGS) Time intervals are not the same for each site, so data were normalized to the number of days between site visits (meaning, converted to rates) to reflect this source of variability in the data.
    Calcif_mg_cm2_d
    Dry mass of calcium carbonate gained during the time interval (Time_interval column) in the units of mg per square centimeter (planar area at start of time interval) per day. If the coral had died, or more than 50 percent of tissue was lost in an earlier time interval, there is no value reported (data cell left blank). (Source: USGS)
    Range of values
    Minimum:0.07
    Maximum:7.21
    Units:milligrams per square centimeter per day
    Calcif_del_SA_cm2_hy
    Change in planar-footprint surface area of the colony since the start of the time interval (Time_interval column) in the units of square centimeters per half year (182.5 days). If the coral had died or more than 50 percent of tissue was lost in an earlier time interval, there is no value reported (data cell left blank). (Source: USGS)
    Range of values
    Minimum:-14.9
    Maximum:32.8
    Units:square centimeters per half year (182.5 days)
    Calcif_del_ht_mm_hy
    Change in colony height since the start of the time interval (Time_interval column) in the units of millimeters per half year (182.5 days). If the coral had died, or more than 50 percent of tissue was lost in an earlier time interval, there is no value reported (data cell left blank). (Source: USGS)
    Range of values
    Minimum:-11.1
    Maximum:33.3
    Units:millimeters per half year (182.5 days)
    Condition
    A textual identifier assigned by USGS personnel as follows: “live” indicates that the coral gained mass and had live tissue during the entire study, “dead” indicates the coral had no live tissue remaining by the end of the study, and “partial” indicates at least 25 percent of the colony had died. (Source: USGS) A textual identifier assigned by USGS personnel describing the condition of the coral during the study.
    Entity_and_Attribute_Overview:
    VI_coral_photo_record.zip - This file contains time-series photographic images in Joint Photographic Experts Group (JPEG) format of experimental elkhorn (A. palmata) and symmetrical brain corals (P. strigosa) deployed at three sites throughout Buck Island Reef National Monument, U.S. Virgin Islands. The file names include the four-letter coral species code (APAL for Acropora palmata and PSTR for Pseudodiploria strigosa), the three-letter site identification code (NWR for Northwest Reef, NER for Northeast Reef and SFR for South Forereef), the three-number coral identification code, and indication if the time-series is from the side or top view. EXIF imagery headers were added using EXIFTool to include pertinent metadata for each image.
    Entity_and_Attribute_Detail_Citation:
    The entity and attribute information were generated by the individual and/or agency identified as the originator of the dataset. Please review the rest of the metadata record for additional details and information.

Who produced the data set?

  1. Who are the originators of the data set? (may include formal authors, digital compilers, and editors)
    • Ilsa B. Kuffner
    • Anastasios Stathakopoulos
    • Kristen A. Ewen
    • Nathaniel Hanna Holloway
    • Erin O. Lyons
    • Lucy A. Bartlett
    • Clayton G. Pollock
    • Zandy Hillis-Starr
  2. Who also contributed to the data set?
    Acknowledgment of Ilsa B. Kuffner and the U.S. Geological Survey as data sources would be appreciated in products developed from these data, and such acknowledgment as is standard for citation and legal practices for data source is expected.
  3. To whom should users address questions about the data?
    Ilsa B. Kuffner
    U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center
    Research Marine Biologist
    600 4th Street South
    St. Petersburg, FL
    U.S.A.

    727-502-8048 (voice)
    ikuffner@usgs.gov

Why was the data set created?

These data were obtained to directly quantify rates of coral growth (calcification, height, and planar-area footprint) in Acropora palmata and Pseudodiploria strigosa corals grown at three sites at Buck Island Reef National Monument from June 2019 to August 2021. The data will be used to inform resource managers of the capacity for future restoration and growth of these two habitat-forming species on Buck Island reefs to guide coral-reef ecosystem and species-recovery plans. Some datasets included in this release were interpreted in Toth and others (2023).

How was the data set created?

  1. From what previous works were the data drawn?
  2. How were the data generated, processed, and modified?
    Date: Aug-2021 (process 1 of 3)
    Acropora palmata growth: Acropora palmata coral fragments were obtained from five colonies at Buck Island Reef National Monument chosen based upon historical knowledge of their condition over time, referred to as “legacy colonies”, as expressed by Zandy Hillis-Starr of the National Park Service (NPS). On June 24, 2019, USGS and NPS personnel collected 6 small branch tips each from these five distinctive, large colonies of A. palmata. A pneumatically powered, reciprocating saw attached to a Self-Contained Underwater Breathing Apparatus (SCUBA) tank was used to cleanly cut the branch tips from the colonies, and then the corals were mounted on plastic (polyvinyl chloride) PVC disks with epoxy and fitted with stainless-steel bolts as described in Morrison and others (2013). Pseudodiploria strigosa growth: On June 26 and 27, 2019, ten small Pseudodiploria strigosa colonies each were collected from the south forereef (SFR) and northeast reef (NER) at Buck Island Reef National Monument, respectively, and mounted to plastic discs as described above. Because of inclement weather, P. strigosa deployed to the northwest reef (NWR) site were not collected until November 2019, and because there were no colonies found at that site, colonies deployed there were collected from the SFR site. The 30 P. strigosa colonies were stained with alizarin-red on the day they were deployed for later sectioning and use for measurement of linear extension and development and calibration of the Strontium/Calcium (Sr/Ca) temperature proxy. The 60 prepared coral colonies were deployed to the field sites to grow for a total of two years at the south forereef (SFR), northeast reef (NER), and northwest reef (NWR) sites. The corals were reversibly attached with a washer and wingnut to concrete blocks secured to the substratum. At the start of the experiment and during the four subsequent sampling visits, all corals were photographed, measured with calipers (length x width x height), and weighed using the buoyant-weight method (Jokiel and others, 1978). For more details about the methods used, refer to Morrison and others (2013). For the final sampling, because the caliper measurements performed by volunteers in July 2021 showed an unlikely average loss of coral planar area and height signifying insufficient training, USGS personnel remeasured the colonies in August 2021 and report these measurements in lieu of those made in July. Corals that died during the experiment were not included in further assessments of growth metrics (missing data are left blank). Calcification rates were normalized to the planar-footprint area of the colony at the beginning of each weighing interval as determined using calipers and the formula for the area of an ellipse. Person who carried out this activity:
    Ilsa B. Kuffner
    Southeast Region
    Research Marine Biologist
    600 4th Street South
    St. Petersburg, FL
    United States

    727-502-8048 (voice)
    ikuffner@usgs.gov
    Date: 2021 (process 2 of 3)
    Photography: The photographs of the corals were taken by USGS personnel (E. Lyons and A. Stathakopoulos) or by NPS personnel (K. Ewen and Nathaniel Hanna Holloway) using a Nikon COOLPIX camera mounted on a tripod. The digital photographs were taken in the field of each colony with a ruler for scale. The images were subsequently used to create a time-series montage for each coral (L. Bartlett). Images were color corrected as needed and stitched together in chronological order using Adobe Photoshop CC version 23.3.2 to adjust for light regime and enhance contrast and brightness. Additionally, text indicating the coral identification number (if not handwritten on the photo stand with red-waxed pencil), the sampling season, and year were added to each image using Photoshop. The digital images are included in the data release download file, VI_coral_photo_record.zip. Person who carried out this activity:
    Ilsa B. Kuffner
    Southeast Region
    Research Marine Biologist
    600 4th Street South
    St. Petersburg, FL
    United States

    727-502-8048 (voice)
    ikuffner@usgs.gov
    Date: 25-Aug-2022 (process 3 of 3)
    Populating the image headers: Credit, contact information, copyright, usage terms, image descriptions, attribution url, metadata link, and georeferencing information were added to the exchangeable image file format (EXIF) header of each image using Phil Harvey’s ExifTool (version 12.44). Each coral species (APAL for Acropora palmata and PSTR for Pseudodiploria strigosa) and sample site (SFR, NER, NWR) were grouped together and the command was run on each group of images. The image groupings were as follows: APAL SFR, PSTR SFR, APAL NER, PSTR NER, APAL NWR, and PSTR NWR. All information in the script were the same among all images, aside from the EXIF:ImageDescription, EXIF:GPSLatitude and EXIF:GPSLongtitude information, as that information varied between the grouped site and coral species images. First, the following command was run on the grouped images to preserve filenames: exiftool -P "-XMP:PreservedFileName<Filename" *.JPG. Second, the following command was run on the grouped images to populate the image headers. This example command was run on the APAL SFR images: exiftool -IPTC:Credit="U.S. Geological Survey" -IPTC:Contact="gs-g-spcmsc_data_inquiries@usgs.gov" -EXIF:Copyright="Public Domain" -XMP:UsageTerms="Unless otherwise stated, all data, metadata and related materials are considered to satisfy the quality standards relative to the purpose for which the data were collected. Although these data and associated metadata have been reviewed for accuracy and completeness and approved for release by the U.S. Geological Survey (USGS), no warranty expressed or implied is made regarding the display or utility of the data for other purposes, nor on all computer systems, nor shall the act of distribution constitute any such warranty." -EXIF:ImageDescription="Time-series photographs taken of colonies of the elkhorn coral, Acropora palmata, grown at south forereef at Buck Island Reef National Monument from June 2019 to July 2021." -XMP:AttributionURL="https://doi.org/10.5066/P94BOI9T" -EXIF:GPSAreaInformation="Location of collection site, GPS coordinates are approximate" -XMP:ExternalMetadataLink="https://data.usgs.gov/datacatalog/metadata/USGS.d5b888e0-7781-44a0-8802-48c240a5cc00.xml" -EXIF:GPSLatitude="17.78408" -EXIF:GPSLatitudeRef="N" -EXIF:GPSLongitude="64.61416" -EXIF:GPSLongitudeRef="W" *.JPG To extract the information from the image headers using ExifTool, run the following command after connecting to the unzipped folder containing the images (VI_coral_photo_record): exiftool a.jpg, where 'a' is replaced with the filename. Example: exiftool APAL_NER_113_SideView.jpg Person who carried out this activity:
    Heather A. Schreppel
    Southeast Region
    Geographer (Data Management Specialist
    600 4th Street South
    St. Petersburg, FL
    United States

    727-502-8000 (voice)
    hschreppel@usgs.gov
  3. What similar or related data should the user be aware of?
    Toth, L.T., Storlazzi, C.D., Kuffner I.B., Quataert, E., Reyns, J., McCall, R., Stathakopoulos, A., Hillis-Starr, Z., Hanna Holloway, N., Ewen, K.A., Pollock, C.G., Code, T., and Aronson, R.B., 20230421, The potential for coral reef restoration to mitigate coastal flooding as sea levels rise: Nature Communications 14, Article number: 2313.

    Online Links:

    Jokiel, P.L., Maragos, J.E., and Franzisket, L., 1978, Coral growth: buoyant weight technique: UNESCO, Paris, France.

    Other_Citation_Details: Editors Stoddart, D.R. and Johannes, pages 529-541
    Morrison, J.M., Kuffner, I.B., and Hickey, T.D., 2013, Methods for monitoring corals and crustose coralline algae to quantify in-situ calcification rates: U.S. Geological Survey Open-File Report 2013-1159, U.S. Geological Survey, Reston, Virginia.

    Online Links:

    Other_Citation_Details: 11 pages

How reliable are the data; what problems remain in the data set?

  1. How well have the observations been checked?
    No formal attribute accuracy tests were conducted.
  2. How accurate are the geographic locations?
    No formal positional accuracy tests were conducted.
  3. How accurate are the heights or depths?
    No formal positional accuracy tests were conducted.
  4. Where are the gaps in the data? What is missing?
    Dataset is considered complete for the information presented, as described in the abstract. Users are advised to read the rest of the metadata record carefully for additional details.
  5. How consistent are the relationships among the observations, including topology?
    No formal logical accuracy tests were conducted.

How can someone get a copy of the data set?

Are there legal restrictions on access or use of the data?
Access_Constraints None
Use_Constraints Public domain data from the U.S. Government are freely redistributable with proper metadata and source attribution. The U.S. Geological Survey requests to be acknowledged as originator of these data in future products or derivative research.
  1. Who distributes the data set? (Distributor 1 of 1)
    Ilsa B. Kuffner
    U.S. Geological Survey
    600 4th Street South
    Saint Petersburg, FL
    U.S.A.

    727-502-8048 (voice)
    ikuffner@usgs.gov
  2. What's the catalog number I need to order this data set?
  3. What legal disclaimers am I supposed to read?
    This publication was prepared by an agency of the United States Government. Although these data have been processed successfully on a computer system at the U.S. Geological Survey, no warranty expressed or implied is made regarding the display or utility of the data on any other system, nor shall the act of distribution imply any such warranty. The U.S. Geological Survey shall not be held liable for improper or incorrect use of the data described and (or) contained herein. Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise does not constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof.
  4. How can I download or order the data?

Who wrote the metadata?

Dates:
Last modified: 26-May-2023
Metadata author:
Ilsa B. Kuffner
U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center
Research Marine Biologist
600 4th Street South
St. Petersburg, FL
U.S.A.

727-502-8048 (voice)
ikuffner@usgs.gov
Metadata standard:
Content Standard for Digital Geospatial Metadata (FGDC-STD-001-1998)
This page is <https://cmgds.marine.usgs.gov/catalog/spcmsc/Coral_growth_VI_USA_metadata.faq.html>
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