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Dataset Title:  Coral stereolithography files and sampling information for Acropora palmata,
A. cervicornis, and A. prolifera from St. Thomas U.S. Virgin Islands and
Belize, 2015
Institution:  BCO-DMO   (Dataset ID: bcodmo_dataset_752642)
Range: longitude = -87.768906 to -64.90276°E, latitude = 16.917862 to 18.404257°N
Information:  Summary ? | License ? | ISO 19115 | Metadata | Background (external link) | Data Access Form | Files
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Things You Can Do With Your Graphs

Well, you can do anything you want with your graphs, of course. But some things you might not have considered are:

The Dataset Attribute Structure (.das) for this Dataset

Attributes {
 s {
  scan_filename {
    String description "name of coral 3D scan CAD file";
    String ioos_category "Unknown";
    String long_name "Scan Filename";
    String units "unitless";
  Species {
    String description "taxonomic species name";
    String ioos_category "Taxonomy";
    String long_name "Species";
    String units "unitless";
  Coral_ID {
    Int16 _FillValue 32767;
    Int16 actual_range 320, 555;
    String description "unique identifier given in field";
    String ioos_category "Identifier";
    String long_name "Coral ID";
    String units "unitless";
  Genetics_ID {
    Int16 _FillValue 32767;
    Int16 actual_range 13698, 13827;
    String description "genetic identification identifier";
    String ioos_category "Identifier";
    String long_name "Genetics ID";
    String units "unitless";
  Location {
    String description "region where coral was collected";
    String ioos_category "Location";
    String long_name "Location";
    String units "unitless";
  Site {
    String description "local site name";
    String ioos_category "Unknown";
    String long_name "Site";
    String units "unitless";
  latitude {
    String _CoordinateAxisType "Lat";
    Float64 _FillValue NaN;
    Float64 actual_range 16.917861, 18.404256;
    String axis "Y";
    Float64 colorBarMaximum 90.0;
    Float64 colorBarMinimum -90.0;
    String description "gps coordinates";
    String ioos_category "Location";
    String long_name "Latitude";
    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";
    Float64 colorBarMaximum 180.0;
    Float64 colorBarMinimum -180.0;
    String description "gps coordinates";
    String ioos_category "Location";
    String long_name "Longitude";
    String standard_name "longitude";
    String units "degrees_east";
  Scan_Date {
    String description "Date the 3D scan was conducted";
    String ioos_category "Time";
    String long_name "Scan Date";
    String source_name "Scan_Date";
    String units "unitless";
  Collection_Depth_ft {
    Float64 _FillValue NaN;
    Float64 actual_range 4.0, 9.0;
    String description "depth in ft the coral was collected";
    String ioos_category "Location";
    String long_name "Collection Depth Ft";
    String units "feet";
  Current_Direction_from {
    Float64 colorBarMaximum 360.0;
    Float64 colorBarMinimum 0.0;
    String description "direction the prevailing current was coming from";
    String ioos_category "Currents";
    String long_name "Current Direction From";
    String units "unitless";
  Wave_Energy {
    String description "a relative description of wave energy at collection site (low/moderate/high)";
    String ioos_category "Surface Waves";
    String long_name "Wave Energy";
    String units "unitless";
  Benthic_Type {
    String description "brief description of substrate where colony was collected";
    String ioos_category "Unknown";
    String long_name "Benthic Type";
    String units "unitless";
  Length_cm {
    Byte _FillValue 127;
    Byte actual_range 23, 34;
    String description "size of collected colony";
    String ioos_category "Unknown";
    String long_name "Length Cm";
    String units "centimeters";
  Width_cm {
    Byte _FillValue 127;
    Byte actual_range 19, 25;
    String description "size of collected colony";
    String ioos_category "Unknown";
    String long_name "Width Cm";
    String units "centimeters";
  Height_cm {
    Float32 _FillValue NaN;
    Float32 actual_range 18.5, 21.0;
    String description "size of collected colony";
    String ioos_category "Unknown";
    String long_name "Height Cm";
    String units "centimeters";
  Volume {
    Int16 _FillValue 32767;
    Int16 actual_range 10488, 13875;
    String description "length x width x height";
    String ioos_category "Unknown";
    String long_name "Volume";
    String units "centimeters^3";
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson";
    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
    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 "Dr 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 2.2d  13 Jun 2019";
    String date_created "2019-01-09T21:18:51Z";
    String date_modified "2019-03-14T19:46:22Z";
    String defaultDataQuery "&time";
    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 
"2019-08-19T18:08:24Z (local files)
2019-08-19T18:08:24Z https://erddap.bco-dmo.org/tabledap/bcodmo_dataset_752642.das";
    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, currents, data, dataset, date, depth, direction, dmo, energy, erddap, filename, genetics, Genetics_ID, height, Height_cm, identifier, latitude, length, Length_cm, Location, longitude, management, oceanography, office, preliminary, scan, scan_filename, site, species, surface, surface waves, taxonomy, time, type, volume, wave, Wave_Energy, waves, width, Width_cm";
    String license 
"The data may be used and redistributed for free but is not intended
for legal use, since it may contain inaccuracies. Neither the data
Contributor, ERD, NOAA, nor the United States Government, nor any
of their employees or contractors, makes any warranty, express or
implied, including warranties of merchantability and fitness for a
particular purpose, or assumes any legal liability for the accuracy,
completeness, or usefulness, of this information.";
    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', '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 "Dr 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 "Collaborative research: Is hybridization among threatened Caribbean coral species the key to their survival or the harbinger of their extinction?";
    String projects_0_acronym "Coral Hybridization";
    String projects_0_description 
"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.";
    String projects_0_end_date "2018-09";
    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 "Nancy Copley";
    String publisher_role "BCO-DMO Data Manager(s)";
    String sourceUrl "(local files)";
    Float64 Southernmost_Northing 16.917861;
    String standard_name_vocabulary "CF Standard Name Table v29";
    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 title "Coral stereolithography files and sampling information for Acropora palmata, A. cervicornis, and A. prolifera from St. Thomas U.S. Virgin Islands and Belize, 2015";
    String version "1";
    Float64 Westernmost_Easting -87.768908;
    String xml_source "osprey2erddap.update_xml() v1.5-beta";


Using tabledap to Request Data and Graphs from Tabular Datasets

tabledap lets you request a data subset, a graph, or a map from a tabular dataset (for example, buoy data), via a specially formed URL. tabledap uses the OPeNDAP (external link) Data Access Protocol (DAP) (external link) and its selection constraints (external link).

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
For example,
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.

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