Accessing BCO-DMO data
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| Dataset Title: | [Coral 3D scans] - Coral stereolithography files and sampling information for Acropora palmata, A. cervicornis, and A. prolifera from St. Thomas U.S. Virgin Islands and Belize, 2015 (Collaborative research: Is hybridization among threatened Caribbean coral species the key to their survival or the harbinger of their extinction?) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_752642) |
| Information: | Summary
| License
| FGDC
| ISO 19115
| Metadata
| Background
| Files
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Attributes {
s {
scan_filename {
String bcodmo_name "file_name";
String description "name of coral 3D scan CAD file";
String long_name "Scan Filename";
String units "unitless";
}
Species {
String bcodmo_name "species";
String description "taxonomic species name";
String long_name "Species";
String units "unitless";
}
Coral_ID {
Int16 _FillValue 32767;
Int16 actual_range 320, 555;
String bcodmo_name "sample";
String description "unique identifier given in field";
String long_name "Coral ID";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
String units "unitless";
}
Genetics_ID {
Int16 _FillValue 32767;
Int16 actual_range 13698, 13827;
String bcodmo_name "sample";
String description "genetic identification identifier";
String long_name "Genetics ID";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
String units "unitless";
}
Location {
String bcodmo_name "region";
String description "region where coral was collected";
String long_name "Location";
String units "unitless";
}
Site {
String bcodmo_name "site";
String description "local site name";
String long_name "Site";
String units "unitless";
}
latitude {
String _CoordinateAxisType "Lat";
Float64 _FillValue NaN;
Float64 actual_range 16.917861, 18.404256;
String axis "Y";
String bcodmo_name "latitude";
Float64 colorBarMaximum 90.0;
Float64 colorBarMinimum -90.0;
String description "gps coordinates";
String ioos_category "Location";
String long_name "Latitude";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LATX/";
String standard_name "latitude";
String units "degrees_north";
}
longitude {
String _CoordinateAxisType "Lon";
Float64 _FillValue NaN;
Float64 actual_range -87.768908, -64.902765;
String axis "X";
String bcodmo_name "longitude";
Float64 colorBarMaximum 180.0;
Float64 colorBarMinimum -180.0;
String description "gps coordinates";
String ioos_category "Location";
String long_name "Longitude";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LONX/";
String standard_name "longitude";
String units "degrees_east";
}
time {
String _CoordinateAxisType "Time";
Float64 actual_range 1.445904e+9, 1.4470272e+9;
String axis "T";
String bcodmo_name "date";
String description "Date the 3D scan was conducted";
String ioos_category "Time";
String long_name "Scan Date";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/";
String source_name "Scan_Date";
String standard_name "time";
String time_origin "01-JAN-1970 00:00:00";
String time_precision "1970-01-01";
String units "seconds since 1970-01-01T00:00:00Z";
}
Collection_Depth_ft {
Float64 _FillValue NaN;
Float64 actual_range 4.0, 9.0;
String bcodmo_name "depth";
String description "depth in ft the coral was collected";
String long_name "Collection Depth Ft";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/DEPH/";
String units "feet";
}
Current_Direction_from {
String bcodmo_name "brief_desc";
String description "direction the prevailing current was coming from";
String long_name "Current Direction From";
String units "unitless";
}
Wave_Energy {
String bcodmo_name "brief_desc";
String description "a relative description of wave energy at collection site (low/moderate/high)";
String long_name "Wave Energy";
String units "unitless";
}
Benthic_Type {
String bcodmo_name "site_descrip";
String description "brief description of substrate where colony was collected";
String long_name "Benthic Type";
String units "unitless";
}
Length_cm {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 23, 34;
String bcodmo_name "length";
String description "size of collected colony";
String long_name "Length Cm";
String units "centimeters";
}
Width_cm {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 19, 25;
String bcodmo_name "width";
String description "size of collected colony";
String long_name "Width Cm";
String units "centimeters";
}
Height_cm {
Float32 _FillValue NaN;
Float32 actual_range 18.5, 21.0;
String bcodmo_name "height";
String description "size of collected colony";
String long_name "Height Cm";
String units "centimeters";
}
Volume {
Int16 _FillValue 32767;
Int16 actual_range 10488, 13875;
String bcodmo_name "volume";
String description "length x width x height";
String long_name "Volume";
String units "centimeters^3";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson,.odvTxt";
String acquisition_description
"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
scanning.";
String awards_0_award_nid "663802";
String awards_0_award_number "OCE-1538469";
String awards_0_data_url "https://www.nsf.gov/awardsearch/showAward?AWD_ID=1538469";
String awards_0_funder_name "NSF Division of Ocean Sciences";
String awards_0_funding_acronym "NSF OCE";
String awards_0_funding_source_nid "355";
String awards_0_program_manager "Michael E. Sieracki";
String awards_0_program_manager_nid "50446";
String cdm_data_type "Other";
String comment
"Caribbean acroporids 3D scans and specimen metadata
PI: N. Fogarty (Nova U)
version: 2019-01-09";
String Conventions "COARDS, CF-1.6, ACDD-1.3";
String creator_email "info@bco-dmo.org";
String creator_name "BCO-DMO";
String creator_type "institution";
String creator_url "https://www.bco-dmo.org/";
String data_source "extract_data_as_tsv version 2.3 19 Dec 2019";
String date_created "2019-01-09T21:18:51Z";
String date_modified "2019-03-14T19:46:22Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.752642.1";
Float64 Easternmost_Easting -64.902765;
Float64 geospatial_lat_max 18.404256;
Float64 geospatial_lat_min 16.917861;
String geospatial_lat_units "degrees_north";
Float64 geospatial_lon_max -64.902765;
Float64 geospatial_lon_min -87.768908;
String geospatial_lon_units "degrees_east";
String history
"2024-11-08T05:58:15Z (local files)
2024-11-08T05:58:15Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_752642.html";
String infoUrl "https://www.bco-dmo.org/dataset/752642";
String institution "BCO-DMO";
String instruments_0_dataset_instrument_nid "752672";
String instruments_0_description "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.";
String instruments_0_instrument_name "3D scanner";
String instruments_0_instrument_nid "752673";
String instruments_0_supplied_name "Next Engine Ultra HD 3D Scanner";
String keywords "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";
String license "https://www.bco-dmo.org/dataset/752642/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/752642";
Float64 Northernmost_Northing 18.404256;
String param_mapping "{'752642': {'Collection_Depth_ft': 'master - depth', 'latitude': 'master - latitude', 'Scan_Date': 'flag - time', 'longitude': 'master - longitude'}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/752642/parameters";
String people_0_affiliation "Nova Southeastern University";
String people_0_person_name "Nicole Fogarty";
String people_0_person_nid "663800";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "Woods Hole Oceanographic Institution";
String people_1_affiliation_acronym "WHOI BCO-DMO";
String people_1_person_name "Nancy Copley";
String people_1_person_nid "50396";
String people_1_role "BCO-DMO Data Manager";
String people_1_role_type "related";
String project "Coral Hybridization";
String projects_0_acronym "Coral Hybridization";
String projects_0_description
"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.";
String projects_0_end_date "2020-09";
String projects_0_geolocation "Caribbean and North-West Atlantic";
String projects_0_name "Collaborative research: Is hybridization among threatened Caribbean coral species the key to their survival or the harbinger of their extinction?";
String projects_0_project_nid "663794";
String projects_0_start_date "2015-10";
String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
String publisher_type "institution";
String sourceUrl "(local files)";
Float64 Southernmost_Northing 16.917861;
String standard_name_vocabulary "CF Standard Name Table v55";
String summary "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.";
String time_coverage_end "2015-11-09";
String time_coverage_start "2015-10-27";
String title "[Coral 3D scans] - Coral stereolithography files and sampling information for Acropora palmata, A. cervicornis, and A. prolifera from St. Thomas U.S. Virgin Islands and Belize, 2015 (Collaborative research: Is hybridization among threatened Caribbean coral species the key to their survival or the harbinger of their extinction?)";
String version "1";
Float64 Westernmost_Easting -87.768908;
String xml_source "osprey2erddap.update_xml() v1.3";
}
}
Data Access Protocol (DAP) and its
selection constraints.
The URL specifies what you want: the dataset, a description of the graph or the subset of the data, and the file type for the response.
Tabledap request URLs must be in the form
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/datasetID.fileType{?query}
For example,
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/pmelTaoDySst.htmlTable?longitude,latitude,time,station,wmo_platform_code,T_25&time>=2015-05-23T12:00:00Z&time<=2015-05-31T12:00:00Z
Thus, the query is often a comma-separated list of desired variable names,
followed by a collection of
constraints (e.g., variable<value),
each preceded by '&' (which is interpreted as "AND").
For details, see the tabledap Documentation.