DNA microsatellite markers for Mustard Hill Coral (Porites astreoides) from the Florida Keys Reef Tract

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Frequently anticipated questions:

What does this data set describe?

Title:
DNA microsatellite markers for Mustard Hill Coral (Porites astreoides) from the Florida Keys Reef Tract
Abstract:
This data set includes: (1) allele sizes of 11 previously published microsatellites (Kenkel and others, 2013; Shearer and Coffroth, 2004) for 39 individuals of mustard hill coral, Porites astreoides (mustard hill coralP. astreoides) collected in the Spring of 2017 from four locations in the Florida Keys Reef Tract (FKRT): Fowey Rocks, Crocker Reef, Sombrero Reef and Pulaski Shoal and (2) the deoxyribonucleic acid (DNA) concentration of the extracted DNA prior to polymerase chain reaction (PCR) reactions for the samples. These data were used in Gallery and others (2021) to evaluate the genetic diversity and connectivity of individuals among and between sites.
  1. How might this data set be cited?
    Gallery, Dominique N., Kuffner, Ilsa B., and Toth, Lauren T., 20210430, DNA microsatellite markers for Mustard Hill Coral (Porites astreoides) from the Florida Keys Reef Tract:.

    This is part of the following larger work.

    Gallery, Dominique N., Kuffner, Ilsa B., and Toth, Lauren T., 20210430, DNA microsatellite markers for Mustard Hill Coral (Porites astreoides) from the Florida Keys Reef Tract: U.S. Geological Survey data release doi:10.5066/P9R8NZ2J, 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: -82.77280
    East_Bounding_Coordinate: -80.09560
    North_Bounding_Coordinate: 25.59047
    South_Bounding_Coordinate: 24.62687
  3. What does it look like?
  4. Does the data set describe conditions during a particular time period?
    Calendar_Date: May-2017
    Currentness_Reference:
    Date of process steps
  5. What is the general form of this data set?
    Geospatial_Data_Presentation_Form: tabular digital data
  6. How does the data set represent geographic features?
    1. How are geographic features stored in the data set?
      Indirect_Spatial_Reference:
      GPS coordinates collected at the four study sites, Fowey Rocks, Crocker Reef, Sombrero Reef, Pulaski Shoal Light
      This is a Point data set.
    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 0.0197864699. Longitudes are given to the nearest 0.0228595953. Latitude and longitude values are specified in Decimal degrees. The horizontal datum used is D_WGS_1984.
      The ellipsoid used is WGS_1984.
      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?
    Porites astreoides Microsatellite Data.csv, Porites astreoides Microsatellite Data.xlsx
    Microsoft Excel comma-separated values (.csv) and worksheet (.xlsx) files containing data for the Microsatellite markers for Porites astreoides (Source: Authors)
    Sample Name
    This is a U.S. Geological Survey, Coastal and Marine Science Center numeric or alphanumeric label that uniquely identifies each sample. Three numbers identify the sample. Negative controls use the identifier "NEG". (Source: USGS) A unique identifier given tofor each sample. A three-digit number was given to a tested sample. Negative controls were given the alphanumeric identifier "NEGP#".
    Sample Type
    Identification of sample or negative control. (Source: USGS)
    ValueDefinition
    SampleSample of P. astreoides
    Negative ControlNegative controls were utilized to ensure there was no cross-contamination during PCR.
    Sample Location
    The study site at which the sample was collected. (Source: USGS)
    ValueDefinition
    PLSPulaski Shoal
    SMKSombrero Reef
    FWYFowey Rocks
    CRKCrocker Reef
    NegativeNegative control has no location of origin.
    Panel
    Microsatellite loci used for PCR amplification. Primers that begin with "Past_" are published in Kenkel and others (2013). Primers that begin with "PaGA" are published in Shearer and Coffroth (2004). (Source: USGS)
    ValueDefinition
    Past_2Primer "Past_2" as published in Kenkel and others (2013)
    Past_3Primer "Past_3" as published in Kenkel and others (2013)
    PaGA7Primer "PaGA7" as published in Shearer and Coffroth (2004)
    Past_8Primer "Past_8" as published in Kenkel and others (2013)
    Past_10Primer "Past_10" as published in Kenkel and others (2013)
    Past_13Primer "Past_13" as published in Kenkel and others (2013)
    Past_16Primer "Past_16" as published in Kenkel and others (2013)
    Past_17Primer "Past_17" as published in Kenkel and others (2013)
    Past_21Primer "Past_21" as published in Kenkel and others (2013)
    PaGA24Primer "PaGA24" as published in Shearer and Coffroth (2004)
    PaGA63Primer "PaGA63" as published in Shearer and Coffroth (2004)
    Run Date
    The date the run was processed by UIUC Core Sequencing Facility. (Source: USGS)
    Range of values
    Minimum:08/15/2019
    Maximum:11/13/2019
    Units:Dates in MM/DD/YYYY format
    Allele 1
    The first allele called from Gene-Mapper program. An integer value for called alleles. "NP" indicates there was no product visible in Gene-Mapper to call. "?" indicates there was product visible, but the result was not strong enough to definitively call the allele. (Source: USGS)
    ValueDefinition
    NPNP indicates there was no product visible in Gene-Mapper to call.
    ?"?" indicates there was product visible, but the result was not strong enough to definitively call the allele.
    Range of values
    Minimum:139
    Maximum:463
    Units:Base pairs
    Allele 2
    The second allele called from Gene-Mapper program. An integer value for called alleles. "NP" indicates there was no product visible in Gene-Mapper to call. "?" indicates there was product visible, but the result was not strong enough to definitively call the allele. Homozygous alleles have the same value from Allele 1 repeated in Allele 2. (Source: USGS)
    ValueDefinition
    NPIndicates there was no product visible in Gene-Mapper to call.
    ?? indicates there was product visible, but the result was not strong enough to definitively call the allele.
    Range of values
    Minimum:141
    Maximum:463
    Units:Base pairs
    Size 1
    A non-integer number that is the exact number of base pairs determined by Gene-Mapper based on Rox1000 dye size standard. NP indicates there was no product visible in Gene-Mapper. (Source: USGS)
    ValueDefinition
    NPIndicates there was no product visible in Gene-Mapper to call.
    Range of values
    Minimum:139.02
    Maximum:462.80
    Units:Base pairs
    Size 2
    A non-integer number that is the exact number of base pairs determined by Gene-Mapper based on Rox1000 dye size standard. NP indicates there was no product visible in Gene-Mapper. Homozygous alleles have the same value from Size 1 repeated in Size 2 (Source: USGS)
    ValueDefinition
    NPNP indicates there was no product visible in Gene-Mapper.
    Range of values
    Minimum:141.18
    Maximum:463.80
    Units:Base pairs
    Porites_astreoides_DNA_concentration.csv, Porites_astreoides_DNA_concentration.xlsx
    Microsoft Excel comma-separated values (.csv) and worksheet (.xlsx) files containing data for the concentration of DNA from Porites astreoides samples as determined by Qubit 3.0. These values were used to determine the volume of DNA added to PCR. (Source: USGS)
    Run Date
    The date the run was processed by USGS researchers. (Source: USGS)
    Range of values
    Minimum:05/5/2019
    Maximum:05/15/2019
    Units:Dates in MM/DD/YYYY format
    Test Name
    Unique alpha-numeric identifier assigned to each sample by Qubit 3.0 (Source: USGS)
    Range of values
    Minimum:Sample_#190505-174736
    Maximum:Sample_#190515-170555
    Units:N/A
    Sample Number
    This is a U.S. Geological Survey, Coastal and Marine Science Center alphanumeric label that uniquely identifies each sample. Three numbers identify the sample. (Source: USGS)
    Range of values
    Minimum:207
    Maximum:497
    Units:N/A
    Sample Location
    The is the study site at which the sample was collected. (Source: USGS)
    ValueDefinition
    CRKCrocker Reef
    FWYFowey Rocks
    SMKSombrero Reef
    PLSPulaski Shoal
    Qubit tube concentration (ng/mL)
    The concentration of double-stranded DNA in the assay tube in nanograms per milliliter (ng/mL). (Source: USGS)
    Range of values
    Minimum:0.93
    Maximum:495
    Units:ng/mL
    Original sample concentration (ng/mL)
    The concentration of the original sample DNA as calculated by Qubit 3.0 in nanograms per milliliter (ng/mL). (Source: USGS)
    Range of values
    Minimum:186
    Maximum:99000
    Units:ng/mL
    Sample volume (μL)
    The volume of original sample used in the assay in microliters (μL). (Source: USGS)
    Range of values
    Minimum:1
    Maximum:1
    Units:μL

Who produced the data set?

  1. Who are the originators of the data set? (may include formal authors, digital compilers, and editors)
    • Gallery, Dominique N.
    • Kuffner, Ilsa B.
    • Toth, Lauren T.
  2. Who also contributed to the data set?
  3. To whom should users address questions about the data?
    Lauren T. Toth
    U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center
    Physical Scientist
    600 4Th Street South
    St. Petersburg, Florida
    United States

    727-502-8029 (voice)
    ltoth@usgs.gov

Why was the data set created?

Microsatellites were used to determine the genetic relatedness of the sampled Porites astreoides in the Florida Keys.

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: May-2017 (process 1 of 10)
    Porites astreoides samples were obtained from four locations along the FKRT using a Global Positioning System (GPS): Fowey Rocks in Biscayne National Park (25.59047, -80.09560), Crocker Reef in the Upper Florida Keys (24.90908, -80.52665), Sombrero Reef in the Middle Florida Keys (24.62687, -81.10893), and Pulaski Shoal in the Dry Tortugas National Park (24.69355, -82.77280). The corals were collected within a 100 to 200 square meter area at each site, and colonies selected for sampling were no closer than approximately 20 meters (Lenz and others, 2021; compare with Kuffner and others, 2013). After collection, the corals were grown for two years (from 2015 to 2017) on cinderblocks installed on the reef as part of the U.S. Geological Survey calcification assessment project (Kuffner and others 2013; Morrison and others 2013). Coral colony condition was assessed, and growth rates were monitored every six months during the study using the methods outlined in Kuffner and others (2013; data presented in Lenz and others, 2021). At the end of the two-year period, several 4 millimeter thick slabs were cut from the center of the colonies. One slab was used for host tissue sampling in this study as well as symbiont sampling and histological examination in an associated study (Lenz and others, 2021). The rest of the colonies were outplanted onto the reefs. Person who carried out this activity:
    Ilsa B.Kuffner
    U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center
    600 4th Street South
    St. Petersburg, Florida
    United States

    727-502-8048 (voice)
    ikuffner@usgs.gov
    Date: May-2019 (process 2 of 10)
    DNA Extraction: Preparation of cetyltrimethylammonium bromide (CTAB) mixture (Baker and Cunning 2016). Person who carried out this activity:
    Dominique N. Gallery
    University of South Florida, U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center
    600 4th Street South
    St. Petersburg, Florida
    United States

    727-502-8000 (voice)
    dgallery@mail.usf.edu
    Date: May-2019 (process 3 of 10)
    Quibit 3.0 analysis to quantify DNA extracted. Person who carried out this activity:
    Dominique N. Gallery
    University of South Florida, U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center
    600 4th Street South
    St. Petersburg, Florida
    United States

    727-502-8000 (voice)
    dgallery@mail.usf.edu
    Date: May-2019 (process 4 of 10)
    Run electrophoresis gel using a 1.5% agarose gel suspension to visualize DNA extraction. Person who carried out this activity:
    Dominique N. Gallery
    University of South Florida, U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center
    600 4th Street South
    St. Petersburg, Florida
    United States

    727-502-8000 (voice)
    dgallery@mail.usf.edu
    Date: Aug-2019 (process 5 of 10)
    Amplified DNA using PCR in 10 microliter (μL) reactions with 10 nanograms (ng) DNA, 1 micromole (μM) fluorescently-labeled forward primer, 1 μM reverse primer, 0.2 millimole (mM) deoxynucleoside triphosphate (dNTP) (Promega), 2μL 5 times (5x) PCR GoTaq Flexi buffer (Promega), 0.25 units (0.05 μL) GoTaq Flexi polymerase (Promega), 2 mM MgCl2 (Promega). The PCR procedure was based on the protocols of Davies and others (2013), but was modified as follows: (1) increased to 1 μM fluorescently-labeled forward primer and 1 μM reverse primer, (2) modified to 2 μL 5X PCR GoTaq Flexi buffer (Promega). Increased 0.25 U GoTaq Flexi polymerase (Promega), (3) added 2 mM magnesium chloride (MgCl2) (Promega), and (4) thermocycler protocol modifications: Increased initial denaturing temperature 95 degrees Celsius (˚C). Increased number of cycles to 40 at (95˚C for 40 seconds, 58–60˚C for 60 seconds, 72˚C for 60 seconds). Person who carried out this activity:
    Dominique N. Gallery
    University of South Florida, U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center
    600 4th Street South
    St. Petersburg, Florida
    United States

    727-502-8000 (voice)
    dgallery@mail.usf.edu
    Date: Aug-2019 (process 6 of 10)
    Sent select samples to the University of Illinois Urbana-Champagne (UIUC) Core Sequencing Facility for fragment analysis of dilution sets to determine optimum dilution for each primer set. Person who carried out this activity:
    Unknown
    University of Illinois Urbana-Champagne Core Sequencing Facility
    334 Edward R. Madigan Laboratory, 1201 W. Gregory Drive
    Urbana, Illinois
    United States

    217-333-9520 (voice)
    dna-seq@illinois.edu
    Date: Sep-2019 (process 7 of 10)
    Sent samples to the UIUC Core Sequencing Facility for fragment analysis using Applied Biosystems 3730x1 DNA Analyzer and ROX1000 standards. Person who carried out this activity:
    Unknown
    University of Illinois Urbana-Champagne Core Sequencing Facility
    334 Edward R. Madigan Laboratory, 1201 W. Gregory Drive
    Urbana, Illinois
    United States

    217-333-9520 (voice)
    dna-seq@illinois.edu
    Date: Oct-2019 (process 8 of 10)
    USGS researchers worked with collaborators at University of South Florida (USF), Saint Petersburg to analyze microsatellites using GeneMapper 5.0 to determine microsatellite calls. Micro-Checker (version 2.2.3) was used to confirm that calls were accurate (for example, correct number of bases between calls). Allele bins were assigned by rounding observed size to the closest integer, except when Micro-Checker indicated that the bins should be adjusted due to errors with nucleotide repeats (for example, only 2 base pairs [bp] difference for trinucleotide repeats). In those cases, alleles were marked as unknown "?" instead of called. Person who carried out this activity:
    Dominique N. Gallery
    University of South Florida, U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center
    600 4th Street South
    St. Petersburg, Florida
    United States

    727-502-8000 (voice)
    dgallery@mail.usf.edu
    Date: Nov-2019 (process 9 of 10)
    Reran PCR for samples that failed to amplify well or indicated potential null alleles. Person who carried out this activity:
    Dominique N. Gallery
    University of South Florida, U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center
    600 4th Street South
    St. Petersburg, Florida
    United States

    727-502-8000 (voice)
    dgallery@mail.usf.edu
    Date: Nov-2019 (process 10 of 10)
    Sent rerun samples to the UIUC Core Sequencing Facility for fragment analysis using Applied Biosystems 3730x1 DNA Analyzer and ROX1000 standards. "GeneScan™ 1000 ROX™ Size Standard is an internal lane size standard developed for use with Applied Biosystems® fluorescence-based DNA electrophoresis systems. The use of an internal lane size standard during electrophoresis enables automated data analysis and precise DNA fragment size comparisons between electrophoresis runs. GeneScan™ 1000 ROX™ Size Standard is designed for sizing DNA fragments in the 47–946 bp range and provides labeled fragments of 47, 51, 55, 82, 85 93 99, 126, 136, 262, 293, 317, 439, 557, 692, 695 and 946 bases. Each of the DNA fragments is labeled with ROX™ fluorophore, which results in a single peak when run under non-denaturing conditions." Quotation is from the ThermoFisher Catalog # 401098 Person who carried out this activity:
    Unknown
    University of Illinois Urbana-Champagne Core Sequencing Facility
    334 Edward R. Madigan Laboratory, 1201 W. Gregory Drive
    Urbana, Illinois
    United States

    217-333-9520 (voice)
    dna-seq@illinois.edu
  3. What similar or related data should the user be aware of?
    Gallery, D.N., Green, M.L., Kuffner, I.B., Lenz, E.A., and Toth, L.T., 20210709, Genetic structure and diversity of the mustard hill coral Porites astreoides along the Florida Keys reef tract: Marine Biodiversity, Springer Nature, Berlin, Germany.

    Online Links:

    Kenkel, C.D., Goodbody-Gringley, G., Caillaud, D., Davies, S.W., Bartels, E., and Matz, M.V., 20130730, Evidence for a host role in thermotolerance divergence between populations of the mustard hill coral (Porites astreoides) from different reef environments: Molecular Ecology, Wiley, Hoboken, New Jersey.

    Online Links:

    Shearer, T.L., and Coffroth, M.A., 20040608, Isolation of microsatellite loci from the scleractinian corals, Montastraea cavernosa and Porites astreoides: Molecular Ecology Notes, Wiley, Hoboken, New Jersey.

    Online Links:

    Oosterhout, C. van, Hutchinson, W.F., Wills, D.P.M., and Shipley, P., 20040608, Micro-Checker: software for identifying and correcting genotyping errors in microsatellite data: Molecular Ecology Notes, Wiley, Hoboken, New Jersey.

    Online Links:

    Davies, S.W., Rahman, M., Meyer, E., Green, E.A., Buschiazzo, E., Medina, M., and Matz, M.V., 20121031, Novel polymorphic microsatellite markers for population genetics of the endangered Caribbean star coral, Montastraea faveolata: Marine Biodiversity, Springer, Berlin, Germany.

    Online Links:

    Baker, A., and Cunning, R., 20160304, Bulk gDNA extraction from coral samples: protocols.io, Online.

    Online Links:

    Kuffner, I.B., Hickey, T.D., and Morrison, J.M., 20130608, Calcification rates of the massive coral Siderastrea siderea and crustose coralline algae along the Florida Keys (USA) outer-reef tract: Coral Reefs, Springer, Berlin, Germany.

    Online Links:

    Morrison, J.M., Kuffner, I.B., and Hickey, T.D., 20130730, Methods for monitoring corals and crustose coralline algae to quantify in-situ calcification rates: U.S. Geological Survey, Reston, VA.

    Online Links:

    Lenz, E.A., Bartlett, L.A., Stathakopoulos, A., and Kuffner, I.B., 20210622, Physiological differences in bleaching response of the coral Porites astreoides along the Florida Keys reef tract during high-temperature stress: Frontiers in Marine Science, Frontiers, Lausanne, Switzerland.

    Online Links:

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

  1. How well have the observations been checked?
    Individual sample ID's were cross-checked and verified in Microsoft Excel Version 2002 worksheets for extraction, PCR, and placement into plates sent for data analysis. For quality control, all samples were run on an agarose gel to ensure DNA extraction was successful prior to running PCR. Microsatellite marker calls were processed through Micro-Checker V. 2.2.3 (van Oosterhout and others 2004) to detect errors in data interpretation.
  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?
    Any data omissions for entities are explained in the Entity and Attribute definition section below. Blank data indicates data was homozygous for that allele. Attribute data equaling “NP” in a cell of the data set refers to a sample that did not amplify or show any product (“no product”). Attribute data equaling "?" refers to a sample with product not sufficient (DNA concentration too low) to call the allele.
  5. How consistent are the relationships among the observations, including topology?
    Reported allele sizes were reviewed to confirm they conform to expected distributions using Micro-Checker V. 2.2.3 (van Oosterhout and others 2004).

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: none
  1. Who distributes the data set? (Distributor 1 of 1)
    Lauren T. Toth
    U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center
    Research Physical Scientist
    600 4Th Street South
    St. Petersburg, FL
    US

    727-502-8029 (voice)
    ltoth@usgs.gov
  2. What's the catalog number I need to order this data set?
  3. What legal disclaimers am I supposed to read?
    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 on any other system or for general or scientific purposes, nor shall the act of distribution constitute any such warranty.
  4. How can I download or order the data?

Who wrote the metadata?

Dates:
Last modified: 13-Jul-2021
Metadata author:
Lauren T. Toth
U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center
Research Physical Scientist
600 4Th Street South
St. Petersburg, Florida
United States

727-502-8029 (voice)
ltoth@usgs.gov
Metadata standard:
Content Standard for Digital Geospatial Metadata (FGDC-STD-001-1998)
This page is <https://cmgds.marine.usgs.gov/catalog/spcmsc/Porites_astreoides_metadata.faq.html>
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