ERDDAP > info > bcodmo_dataset_752642

Grid DAP Data	Sub- set	Table DAP Data	Make A Graph	W M S	Source Data Files	Acces- sible	Title	Sum- mary	FGDC, ISO, Metadata	Back- ground Info	RSS	E mail	Institution	Dataset ID
		data	graph		files	public	[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?)		F   I   M	background			BCO-DMO	bcodmo_dataset_752642

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 scanning.
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
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/
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
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
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/752642
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
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 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?)
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/
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/
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/
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/
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/
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/
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.