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Title Sum-
Institution Dataset ID
     data   graph     files  public Coral stereolithography files and sampling information for Acropora palmata, A. cervicornis,
and A. prolifera from St. Thomas U.S. Virgin Islands and Belize, 2015
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The Dataset's Variables and Attributes

Row Type Variable Name Attribute Name Data Type Value
attribute NC_GLOBAL access_formats String .htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson,.odvTxt
attribute NC_GLOBAL acquisition_description String Caribbean acroporids (Acropora palmata, A. cervicornis, and A. prolifera)
corals were photographed, measured, and collected and transported in coolers
of seawater to the laboratory for 3D scans. Corals were kept in a seawater
system or under the laboratory dock until scanning commenced.\u00a0 Corals
were first photographed, then landmarks (i.e., small balls of modeling clay)
were added to the corals to assist with alignments during post-scan analyses,
and the coral was scanned.

3D scans of corals were edited in Scan Studio software. Any unnecessary part
of the scan was trimmed off, such as the stand that corals were propped on.
Multiple scans were aligned using strategically placed markers that were
placed on the corals prior to scanning. After aligning the scans, markers were
trimmed off, and the image was fused in order to fill any existing holes.

Once .stl files were exported from the scanner software, files were uploaded
to Autodesk Meshmixer (Ver. 3.4.35). While in the Meshmixer software, most
files had the mesh repaired and filled in using the \u201cmake solid\u201d
tool in the \u201cedit\u201d tab. In the \u201cMake Solid tool \u201cSharp
Edge Preserve\u201d is to be selected for the \u201cSolid Type\u201d while
\u201cSolid Accuracy\u201d is set to 500, and \u201cMesh Density\u201d is set
to 420, all other settings remained the standard. However, prior to making it
solid the \u201cSculpt\u201d tool was used for the dense branched A.
prolifera. The \u201cInflate\u201d brush was used at various strength and
sizes to build in sections of branches what were not completely formed during
attribute NC_GLOBAL awards_0_award_nid String 663802
attribute NC_GLOBAL awards_0_award_number String OCE-1538469
attribute NC_GLOBAL awards_0_data_url String https://www.nsf.gov/awardsearch/showAward?AWD_ID=1538469 (external link)
attribute NC_GLOBAL awards_0_funder_name String NSF Division of Ocean Sciences
attribute NC_GLOBAL awards_0_funding_acronym String NSF OCE
attribute NC_GLOBAL awards_0_funding_source_nid String 355
attribute NC_GLOBAL awards_0_program_manager String Michael E. Sieracki
attribute NC_GLOBAL awards_0_program_manager_nid String 50446
attribute NC_GLOBAL cdm_data_type String Other
attribute NC_GLOBAL comment String Caribbean acroporids 3D scans and specimen metadata
PI: N. Fogarty (Nova U)
version: 2019-01-09
attribute NC_GLOBAL Conventions String COARDS, CF-1.6, ACDD-1.3
attribute NC_GLOBAL creator_email String info at bco-dmo.org
attribute NC_GLOBAL creator_name String BCO-DMO
attribute NC_GLOBAL creator_type String institution
attribute NC_GLOBAL creator_url String https://www.bco-dmo.org/ (external link)
attribute NC_GLOBAL data_source String extract_data_as_tsv version 2.3 19 Dec 2019
attribute NC_GLOBAL date_created String 2019-01-09T21:18:51Z
attribute NC_GLOBAL date_modified String 2019-03-14T19:46:22Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.752642.1
attribute NC_GLOBAL Easternmost_Easting double -64.902765
attribute NC_GLOBAL geospatial_lat_max double 18.404256
attribute NC_GLOBAL geospatial_lat_min double 16.917861
attribute NC_GLOBAL geospatial_lat_units String degrees_north
attribute NC_GLOBAL geospatial_lon_max double -64.902765
attribute NC_GLOBAL geospatial_lon_min double -87.768908
attribute NC_GLOBAL geospatial_lon_units String degrees_east
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/752642 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 752672
attribute NC_GLOBAL instruments_0_description String A 3D scan captures digital information about the shape of an object with equipment that uses a laser or light to measure the distance between the scanner and the object.
attribute NC_GLOBAL instruments_0_instrument_name String 3D scanner
attribute NC_GLOBAL instruments_0_instrument_nid String 752673
attribute NC_GLOBAL instruments_0_supplied_name String Next Engine Ultra HD 3D Scanner
attribute NC_GLOBAL keywords String bco, bco-dmo, benthic, Benthic_Type, biological, chemical, collection, Collection_Depth_ft, coral, Coral_ID, current, Current_Direction_from, data, dataset, date, depth, direction, dmo, energy, erddap, filename, genetics, Genetics_ID, height, Height_cm, latitude, length, Length_cm, Location, longitude, management, oceanography, office, preliminary, scan, scan_filename, site, species, time, type, volume, wave, Wave_Energy, width, Width_cm
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/752642/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/752642 (external link)
attribute NC_GLOBAL Northernmost_Northing double 18.404256
attribute NC_GLOBAL param_mapping String {'752642': {'Collection_Depth_ft': 'master - depth', 'latitude': 'master - latitude', 'Scan_Date': 'flag - time', 'longitude': 'master - longitude'}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/752642/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String Nova Southeastern University
attribute NC_GLOBAL people_0_person_name String Nicole Fogarty
attribute NC_GLOBAL people_0_person_nid String 663800
attribute NC_GLOBAL people_0_role String Principal Investigator
attribute NC_GLOBAL people_0_role_type String originator
attribute NC_GLOBAL people_1_affiliation String Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_1_affiliation_acronym String WHOI BCO-DMO
attribute NC_GLOBAL people_1_person_name String Nancy Copley
attribute NC_GLOBAL people_1_person_nid String 50396
attribute NC_GLOBAL people_1_role String BCO-DMO Data Manager
attribute NC_GLOBAL people_1_role_type String related
attribute NC_GLOBAL project String Coral Hybridization
attribute NC_GLOBAL projects_0_acronym String Coral Hybridization
attribute NC_GLOBAL projects_0_description String NSF Award Abstract:
Reef-building acroporid corals form the foundation of shallow tropical coral communities throughout the Caribbean. Yet, the once dominant staghorn coral (Acropora cervicornis) and the elkhorn coral (A. palmata) have decreased by more than 90% since the 1980s, primarily from disease. Their continuing decline jeopardizes the ability of coral reefs to provide numerous societal and ecological benefits, including economic revenue from seafood harvesting and tourism and shoreline protection from extreme wave events caused by storms and hurricanes. Despite their protection under the U.S. Endangered Species Act since 2006, threats to the survival of reef-building acroporid corals remain pervasive and include disease and warming ocean temperatures that may lead to further large-scale mortality. However, hybridization among these closely related species is increasing and may provide an avenue for adaptation to a changing environment. While hybrids were rare in the past, they are now thriving in shallow habitats with extreme temperatures and irradiance and are expanding into the parental species habitats. Additional evidence suggests that the hybrid is more disease resistant than at least one of the parental species. Hybridization may therefore have the potential to rescue the threatened parental species from extinction through the transfer of adapted genes via hybrids mating with both parental species, but extensive gene flow may alter the evolutionary trajectory of the parental species and drive one or both to extinction. This collaborative project is to collect genetic and ecological data in order to understand the mechanisms underlying increasing hybrid abundance. The knowledge gained from this research will help facilitate more strategic management of coral populations under current and emerging threats to their survival. This project includes integrated research and educational opportunities for high school, undergraduate and graduate students, and a postdoctoral researcher. Students in the United States Virgin Islands will take part in coral spawning research and resource managers will receive training on acroporid reproduction to apply to coral restoration techniques.
Current models predict the demise of reefs in the next 200 years due to increasing sea surface temperatures and ocean acidification. It is thus essential to identify habitats, taxa and evolutionary mechanisms that will allow some coral species to maintain their role as foundation fauna. Hybridization can provide an avenue for adaptation to changing conditions. Corals hybridize with some frequency and results may range from the introduction of a few alleles into existing parent species via introgression, to the birth of a new, perhaps better adapted genetic lineage. The only widely accepted coral hybrid system consists of the once dominant but now threatened Caribbean species, Acropora cervicornis and A. palmata. In the past, hybrid colonies originating from natural crosses between elkhorn and staghorn corals were rare, and evidence of hybrid reproduction was limited to infrequent matings with the staghorn coral. Recent field observations suggest that the hybrid is increasing and its ecological role is changing throughout the Caribbean. These hybrids appear to be less affected by the disease that led to the mass mortality of their parental species in recent decades. Hybrids are also found thriving in shallow habitats with high temperatures and irradiance suggesting they may be less susceptible to future warming scenarios. At the same time, they are expanding into the deeper parental species habitats. Preliminary genetic data indicate that hybrids are now mating with each other, demonstrating the potential for the formation of a new species. Further, hybrids appear to be capable of mating with both staghorn and elkhorn coral, perhaps leading to gene flow between the parent species via the hybrid. Research is proposed to address how the increase in hybridization and perhaps subsequent introgression will affect the current ecological role and the future evolutionary trajectory of Caribbean acroporids. Specifically, this collaborative project aims to answer the following questions: 1) What is the historic rate, direction, and degree of introgression across species ranges and genomes? Linkage block analysis based on genome-wide SNP genotyping across three replicate hybrid zones will answer this question. 2) What is the current extent and future potential of later generation hybrid formation? Morphometric and genetic analyses combined with in vitro fertilization assays will be used. 3) What mechanisms allow hybrids to thrive in hot, shallow waters? A series of manipulative in situ and ex situ experiments will determine whether biotic or abiotic factors favor hybrid survival in shallow waters. 4) Are hybrids more disease resistant than the parentals species? Disease transmission assays in reciprocal transplant experiments and histological analysis to determine the extent of disease will be conducted. A multidisciplinary approach will be taken that combines traditional and cutting edge technology to provide a detailed analysis of the evolutionary ecology of Caribbean corals.
Note: PI Nicole Fogarty's original award OCE-1538469 was issued while at Nova Southeastern University. This was replaced by OCE-1929979 upon moving to the University of North Carolina Wilmington.
attribute NC_GLOBAL projects_0_end_date String 2020-09
attribute NC_GLOBAL projects_0_geolocation String Caribbean and North-West Atlantic
attribute NC_GLOBAL projects_0_name String Collaborative research: Is hybridization among threatened Caribbean coral species the key to their survival or the harbinger of their extinction?
attribute NC_GLOBAL projects_0_project_nid String 663794
attribute NC_GLOBAL projects_0_start_date String 2015-10
attribute NC_GLOBAL publisher_name String Biological and Chemical Oceanographic Data Management Office (BCO-DMO)
attribute NC_GLOBAL publisher_type String institution
attribute NC_GLOBAL sourceUrl String (local files)
attribute NC_GLOBAL Southernmost_Northing double 16.917861
attribute NC_GLOBAL standard_name_vocabulary String CF Standard Name Table v55
attribute NC_GLOBAL summary String Coral specimens collected in the St. Thomas, U.S. Virgin Islands and Belize were 3-dimensionally scanned. This dataset includes metadata on the coral samples such as the collection location and conditions, and the dimensions of the samples. The STL files are available for download in the Supplemental Documentation section below.
attribute NC_GLOBAL time_coverage_end String 2015-11-09
attribute NC_GLOBAL time_coverage_start String 2015-10-27
attribute NC_GLOBAL title String Coral stereolithography files and sampling information for Acropora palmata, A. cervicornis, and A. prolifera from St. Thomas U.S. Virgin Islands and Belize, 2015
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL Westernmost_Easting double -87.768908
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.3
variable scan_filename   String  
attribute scan_filename bcodmo_name String file_name
attribute scan_filename description String name of coral 3D scan CAD file
attribute scan_filename long_name String Scan Filename
attribute scan_filename units String unitless
variable Species   String  
attribute Species bcodmo_name String species
attribute Species description String taxonomic species name
attribute Species long_name String Species
attribute Species units String unitless
variable Coral_ID   short  
attribute Coral_ID _FillValue short 32767
attribute Coral_ID actual_range short 320, 555
attribute Coral_ID bcodmo_name String sample
attribute Coral_ID description String unique identifier given in field
attribute Coral_ID long_name String Coral ID
attribute Coral_ID nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute Coral_ID units String unitless
variable Genetics_ID   short  
attribute Genetics_ID _FillValue short 32767
attribute Genetics_ID actual_range short 13698, 13827
attribute Genetics_ID bcodmo_name String sample
attribute Genetics_ID description String genetic identification identifier
attribute Genetics_ID long_name String Genetics ID
attribute Genetics_ID nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute Genetics_ID units String unitless
variable Location   String  
attribute Location bcodmo_name String region
attribute Location description String region where coral was collected
attribute Location long_name String Location
attribute Location units String unitless
variable Site   String  
attribute Site bcodmo_name String site
attribute Site description String local site name
attribute Site long_name String Site
attribute Site units String unitless
variable latitude   double  
attribute latitude _CoordinateAxisType String Lat
attribute latitude _FillValue double NaN
attribute latitude actual_range double 16.917861, 18.404256
attribute latitude axis String Y
attribute latitude bcodmo_name String latitude
attribute latitude colorBarMaximum double 90.0
attribute latitude colorBarMinimum double -90.0
attribute latitude description String gps coordinates
attribute latitude ioos_category String Location
attribute latitude long_name String Latitude
attribute latitude nerc_identifier String https://vocab.nerc.ac.uk/collection/P09/current/LATX/ (external link)
attribute latitude standard_name String latitude
attribute latitude units String degrees_north
variable longitude   double  
attribute longitude _CoordinateAxisType String Lon
attribute longitude _FillValue double NaN
attribute longitude actual_range double -87.768908, -64.902765
attribute longitude axis String X
attribute longitude bcodmo_name String longitude
attribute longitude colorBarMaximum double 180.0
attribute longitude colorBarMinimum double -180.0
attribute longitude description String gps coordinates
attribute longitude ioos_category String Location
attribute longitude long_name String Longitude
attribute longitude nerc_identifier String https://vocab.nerc.ac.uk/collection/P09/current/LONX/ (external link)
attribute longitude standard_name String longitude
attribute longitude units String degrees_east
variable time   double  
attribute time _CoordinateAxisType String Time
attribute time actual_range double 1.445904E9, 1.4470272E9
attribute time axis String T
attribute time bcodmo_name String date
attribute time description String Date the 3D scan was conducted
attribute time ioos_category String Time
attribute time long_name String Scan Date
attribute time nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/ (external link)
attribute time source_name String Scan_Date
attribute time standard_name String time
attribute time time_origin String 01-JAN-1970 00:00:00
attribute time time_precision String 1970-01-01
attribute time units String seconds since 1970-01-01T00:00:00Z
variable Collection_Depth_ft   double  
attribute Collection_Depth_ft _FillValue double NaN
attribute Collection_Depth_ft actual_range double 4.0, 9.0
attribute Collection_Depth_ft bcodmo_name String depth
attribute Collection_Depth_ft description String depth in ft the coral was collected
attribute Collection_Depth_ft long_name String Collection Depth Ft
attribute Collection_Depth_ft nerc_identifier String https://vocab.nerc.ac.uk/collection/P09/current/DEPH/ (external link)
attribute Collection_Depth_ft units String feet
variable Current_Direction_from   String  
attribute Current_Direction_from bcodmo_name String brief_desc
attribute Current_Direction_from description String direction the prevailing current was coming from
attribute Current_Direction_from long_name String Current Direction From
attribute Current_Direction_from units String unitless
variable Wave_Energy   String  
attribute Wave_Energy bcodmo_name String brief_desc
attribute Wave_Energy description String a relative description of wave energy at collection site (low/moderate/high)
attribute Wave_Energy long_name String Wave Energy
attribute Wave_Energy units String unitless
variable Benthic_Type   String  
attribute Benthic_Type bcodmo_name String site_descrip
attribute Benthic_Type description String brief description of substrate where colony was collected
attribute Benthic_Type long_name String Benthic Type
attribute Benthic_Type units String unitless
variable Length_cm   byte  
attribute Length_cm _FillValue byte 127
attribute Length_cm actual_range byte 23, 34
attribute Length_cm bcodmo_name String length
attribute Length_cm description String size of collected colony
attribute Length_cm long_name String Length Cm
attribute Length_cm units String centimeters
variable Width_cm   byte  
attribute Width_cm _FillValue byte 127
attribute Width_cm actual_range byte 19, 25
attribute Width_cm bcodmo_name String width
attribute Width_cm description String size of collected colony
attribute Width_cm long_name String Width Cm
attribute Width_cm units String centimeters
variable Height_cm   float  
attribute Height_cm _FillValue float NaN
attribute Height_cm actual_range float 18.5, 21.0
attribute Height_cm bcodmo_name String height
attribute Height_cm description String size of collected colony
attribute Height_cm long_name String Height Cm
attribute Height_cm units String centimeters
variable Volume   short  
attribute Volume _FillValue short 32767
attribute Volume actual_range short 10488, 13875
attribute Volume bcodmo_name String volume
attribute Volume description String length x width x height
attribute Volume long_name String Volume
attribute Volume units String centimeters^3

The information in the table above is also available in other file formats (.csv, .htmlTable, .itx, .json, .jsonlCSV1, .jsonlCSV, .jsonlKVP, .mat, .nc, .nccsv, .tsv, .xhtml) via a RESTful web service.

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