ERDDAP > info > bcodmo_dataset_658275

Grid DAP Data	Sub- set	Table DAP Data	Make A Graph	W M S	Source Data Files	Acces- sible	Title	Sum- mary	ISO, Metadata	Back- ground Info	RSS	E mail	Institution	Dataset ID
		data	graph		files	public	Data describing every diseased coral record from surveys in the Caribbean during 2012 (Contagious coral diseases project)		I   M	background			BCO-DMO	bcodmo_dataset_658275

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
attribute	NC_GLOBAL	acquisition_description	String	[Adapted from: Randall et al. 2014 Ecology 95(7) 1981-1994]\u00a0\u00a0 \u00a0 To assess the prevalence of coral diseases at each location, a survey area (1-10 km^2 depending on the region\u2019s geographic features) of hard-bottom habitat was visually defined using [Google Earth](\\"http://earth.google.com/\\"). The survey area was divided into 100 by 100 meter cells (using Google Earth Path 1.4.4). Within each location, twenty-five 100 by 100 meter cells were randomly selected as sites. These sites were defined as the primary sampling units. A single 10 by 10 meterquadrat was haphazardly placed within each site, for field-data collection. To maintain consistency across locations and to minimize potential effects of coral-assemblage differences, three criteria had to be met for a site to be surveyed: (1) the depth averaged between 5 and 10 meters, (2) the substrate was hard bottom, and (3) corals were present. If any one of these criteria was not met at a given site, it was rejected and the next randomly generated site was selected. In total, twenty-five, 10 by 10 meter quadrats were sampled at each location, for a total of 50 quadrats across two frequent- anomaly locations and 50 quadrats across two reference locations, for a total survey area of 10,000 m^2.\u00a0 All four locations were surveyed between 2 July and 1 September 2012. At each site, divers surveyed each 100 m^2\u00a0quadrat by systematically laying ten contiguous 1 x 10 m belt transects onto the reef substrate. Each coral colony with a disease sign was identified in situ and the species and disease signs were recorded. Four disease signs were identified: (1) white sign was defined as a bright, white band or patch of recent mortality adjacent to healthy- appearing tissue (i.e., the tissue bordered a well-defined edge of exposed skeleton not yet colonized by algae or other biofouling organisms) (sensu Bythell et al. 2004) , (2) dark spot was defined as tissue with purple, brown or black lesions, forming spots of irregular shapes (sensu Goreau et al. 1998), (3) black band was defined as a black band over the coral tissue exposing white skeleton with different stages of biofouling (sensu Richardson 2004), and (4) yellow sign was defined as a yellow discoloration of tissue forming a band or blotches (sensu Santavy et al. 1999). White signs and black bands were associated with recent tissue loss; yellow signs and dark spots were usually, but not always, associated with recent tissue loss. Notably, very few yellow bands were observed that followed the classical description (Reeves 1994). Instead, most coral colonies presented a patchy, non-uniform yellowing of the tissue; therefore the condition was termed \u2018yellow sign.\u2019 Additionally, any area of recently exposed white skeleton, which was not clearly caused by predation or a competitive interaction, was recorded as a white sign, including white plagues, white bands and white pox. The white-sign diseases were not differentiated because of similar- or identical- appearing signs, unknown etiologies for several diseases, and the possibility that the diseases were caused by the same pathogens (Bythell et al. 2004, Ainsworth et al. 2007). Coral colonies were occasionally recorded with two or more signs of disease, when those signs appeared to be spatially independent. Disease mapping: Four 100 m^2 quadrats per location were mapped in their entirety, for a total of eight 100 m^2 quadrats per temperature-stress level. Approximately 50 digital images were captured from each video-transect file using Free Video to JPG Converter v. 5.0.58 build 324. The digital images were stitched together using Adobe Photoshop\u00a0CS5 v. 12.0, and ten 1\u2013m by 10\u2013m image mosaics were created for each 10 m by 10 m site. Each photo-mosaic was printed and, with the aid of the digital images and videos, the following data were measured and recorded for every coral colony within each site: (1) species, (2) spatial coordinates, (3) maximum diameter, (4) perpendicular diameter, (5) an estimate of percent partial mortality (0, <5, 25, 50, 75, or >95 %), and (6) \u2018health\u2019 status. Corals were identified as either healthy, or as having white signs, dark spots, black bands, yellow signs, or unknown signs of disease (as described above). Bleached or pale colonies also were recorded, and when multiple disease signs were present on an individual colony, both signs were recorded. Data from each site that was mapped are found in individual excel files in the folder called Disease mapping site data files.\u00a0
attribute	NC_GLOBAL	awards_0_award_nid	String	562562
attribute	NC_GLOBAL	awards_0_award_number	String	OCE-1219804
attribute	NC_GLOBAL	awards_0_data_url	String	http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1219804
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	All Raw Mapping Data R. van Woesik, PI Version 2 September 2016
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	2016-09-06T20:16:14Z
attribute	NC_GLOBAL	date_modified	String	2019-05-13T20:42:07Z
attribute	NC_GLOBAL	defaultDataQuery	String	&amp;time&lt;now
attribute	NC_GLOBAL	doi	String	10.1575/1912/bco-dmo.658275.1
attribute	NC_GLOBAL	infoUrl	String	https://www.bco-dmo.org/dataset/658275
attribute	NC_GLOBAL	institution	String	BCO-DMO
attribute	NC_GLOBAL	keywords	String	bco, bco-dmo, biological, chemical, data, dataset, depth, depth_max, dmo, erddap, genus, level, management, meter, number, oceanography, office, preliminary, reef, sign, sign_1, sign_2, sign_3, sign_4, site, site_number, species, temp_level, temperature, uin
attribute	NC_GLOBAL	license	String	https://www.bco-dmo.org/dataset/658275/license
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/658275
attribute	NC_GLOBAL	param_mapping	String	{'658275': {}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/658275/parameters
attribute	NC_GLOBAL	people_0_affiliation	String	Florida Institute of Technology
attribute	NC_GLOBAL	people_0_affiliation_acronym	String	FIT
attribute	NC_GLOBAL	people_0_person_name	String	Robert van Woesik
attribute	NC_GLOBAL	people_0_person_nid	String	562565
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	Florida Institute of Technology
attribute	NC_GLOBAL	people_1_affiliation_acronym	String	FIT
attribute	NC_GLOBAL	people_1_person_name	String	Dr Carly J. Randall
attribute	NC_GLOBAL	people_1_person_nid	String	657875
attribute	NC_GLOBAL	people_1_role	String	Contact
attribute	NC_GLOBAL	people_1_role_type	String	related
attribute	NC_GLOBAL	people_2_affiliation	String	Florida Institute of Technology
attribute	NC_GLOBAL	people_2_affiliation_acronym	String	FIT
attribute	NC_GLOBAL	people_2_person_name	String	Robert van Woesik
attribute	NC_GLOBAL	people_2_person_nid	String	562565
attribute	NC_GLOBAL	people_2_role	String	Contact
attribute	NC_GLOBAL	people_2_role_type	String	related
attribute	NC_GLOBAL	people_3_affiliation	String	Woods Hole Oceanographic Institution
attribute	NC_GLOBAL	people_3_affiliation_acronym	String	WHOI BCO-DMO
attribute	NC_GLOBAL	people_3_person_name	String	Hannah Ake
attribute	NC_GLOBAL	people_3_person_nid	String	650173
attribute	NC_GLOBAL	people_3_role	String	BCO-DMO Data Manager
attribute	NC_GLOBAL	people_3_role_type	String	related
attribute	NC_GLOBAL	project	String	Contagious coral diseases?
attribute	NC_GLOBAL	projects_0_acronym	String	Contagious coral diseases?
attribute	NC_GLOBAL	projects_0_description	String	Diseases are one of the greatest threats to corals in the Caribbean. Yet, very little is known about marine diseases in general and coral diseases in particular.  Although some pathogens have been acknowledged, identifying coral pathogens has proven difficult and evasive. Presently, coral diseases are assumed to be both infectious and contagious, suggesting that infection is caused by pathogens being passed from colony to colony through a vector. However, few studies have tested this assumption. Spatial epidemiology, or disease mapping, can provide insight into whether diseases cluster and follow a contagious-disease model. In this study we will take a two tiered approach. First, we will use a hierarchical sampling design to test whether coral diseases follow a contagious-disease model over two spatial scales in the Caribbean. We will also undertake this study in locations with and without a recent history of frequent thermal stress to test the alternate hypothesis that coral diseases are not infectious and contagious but are instead the result of compromised coral hosts that have undergone thermal stress. Second, we will undertake transmission experiments to examine whether coral diseases are indeed transmissible. The research will take place in the Caribbean, at four locations: (1) Mahahual, Mexico (latitude  18"42’N, longitude  87"42’W) and (2) Tuxpan, Mexico (latitude  21"01’N, longitude  97"11'W), (3) Bocas del Toro, Panama (latitude  9"12’N, longitude  82"09’W) and (4) St. John, United States Virgin Islands (USVI) (latitude  18"18’N, longitude  64"45’W). Intellectual merit There is a certain urgency to identify coral diseases, predict their prevalence, and determine whether they are infectious and contagious or non-communicable. By understanding the etiology of coral diseases, we can determine whether human intervention will help reduce their prevalence. Without understanding these processes, we will merely continue to measure disease, continue to look for pathogens that may not exist, and watch coral populations continue to deteriorate. Although microbes play a role in disease infection, many coral diseases might not be transmissible. Therefore, we may need to incorporate environmental threshold parameters, which may be more likely the underlying mechanisms driving coral-disease dynamics. The results will have important implications for modeling diseases and predicting contemporary and future coral disease outbreaks.   Broader Impact The underlying assumption of most disease models is contagion, which is the transmission of pathogens from infected to susceptible hosts. This study will examine this basic assumption. If it turns out that coral diseases are a consequence of a two-step process, and the corals that are tolerant to temperature stress are also resistant to diseases, then making predictions based on temperature trends will be transformational, especially in rapidly warming, yet heterogeneous, oceans. The study will train students in the field of spatial epidemiology of coral diseases.
attribute	NC_GLOBAL	projects_0_end_date	String	2016-05
attribute	NC_GLOBAL	projects_0_geolocation	String	Caribbean
attribute	NC_GLOBAL	projects_0_name	String	Are coral diseases contagious?
attribute	NC_GLOBAL	projects_0_project_nid	String	562563
attribute	NC_GLOBAL	projects_0_start_date	String	2012-06
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	standard_name_vocabulary	String	CF Standard Name Table v55
attribute	NC_GLOBAL	summary	String	Data describing every diseased coral record from surveys in the Caribbean during 2012 (Contagious coral diseases project)
attribute	NC_GLOBAL	title	String	Data describing every diseased coral record from surveys in the Caribbean during 2012 (Contagious coral diseases project)
attribute	NC_GLOBAL	version	String	1
attribute	NC_GLOBAL	xml_source	String	osprey2erddap.update_xml() v1.3
variable	temp_level		String
attribute	temp_level	bcodmo_name	String	temperature
attribute	temp_level	description	String	Temperature stress level.
attribute	temp_level	long_name	String	Temp Level
attribute	temp_level	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P01/current/TEMPP901/
attribute	temp_level	units	String	unitless
variable	location		String
attribute	location	bcodmo_name	String	site
attribute	location	description	String	Location where coral was located.
attribute	location	long_name	String	Location
attribute	location	units	String	unitless
variable	reef		String
attribute	reef	bcodmo_name	String	site
attribute	reef	description	String	Reef where coral was located.
attribute	reef	long_name	String	Reef
attribute	reef	units	String	unitless
variable	site_number		byte
attribute	site_number	_FillValue	byte	127
attribute	site_number	actual_range	byte	1, 25
attribute	site_number	bcodmo_name	String	site
attribute	site_number	colorBarMaximum	double	100.0
attribute	site_number	colorBarMinimum	double	0.0
attribute	site_number	description	String	Site ID number.
attribute	site_number	long_name	String	Site Number
attribute	site_number	units	String	unitless
variable	depth_max		float
attribute	depth_max	_FillValue	float	NaN
attribute	depth_max	actual_range	float	4.6, 12.2
attribute	depth_max	bcodmo_name	String	depth_max
attribute	depth_max	colorBarMaximum	double	8000.0
attribute	depth_max	colorBarMinimum	double	-8000.0
attribute	depth_max	colorBarPalette	String	TopographyDepth
attribute	depth_max	description	String	Maximum depth of site.
attribute	depth_max	long_name	String	Depth
attribute	depth_max	standard_name	String	depth
attribute	depth_max	units	String	meters
variable	meter		String
attribute	meter	bcodmo_name	String	site
attribute	meter	description	String	Meter along 10 meter transect.
attribute	meter	long_name	String	Meter
attribute	meter	units	String	unitless
variable	genus		String
attribute	genus	bcodmo_name	String	genus
attribute	genus	description	String	Genus of coral sampled.
attribute	genus	long_name	String	Genus
attribute	genus	units	String	unitless
variable	species		String
attribute	species	bcodmo_name	String	species
attribute	species	description	String	Species of coral sampled.
attribute	species	long_name	String	Species
attribute	species	units	String	unitless
variable	UIN		short
attribute	UIN	_FillValue	short	32767
attribute	UIN	actual_range	short	1, 6599
attribute	UIN	bcodmo_name	String	sample
attribute	UIN	description	String	Individual coral ID number.
attribute	UIN	long_name	String	UIN
attribute	UIN	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P02/current/ACYC/
attribute	UIN	units	String	unitless
variable	sign_1		String
attribute	sign_1	bcodmo_name	String	brief_desc
attribute	sign_1	description	String	First disease sign identified.
attribute	sign_1	long_name	String	Sign 1
attribute	sign_1	units	String	unitless
variable	sign_2		String
attribute	sign_2	bcodmo_name	String	brief_desc
attribute	sign_2	description	String	Second disease sign identified.
attribute	sign_2	long_name	String	Sign 2
attribute	sign_2	units	String	unitless
variable	sign_3		String
attribute	sign_3	bcodmo_name	String	brief_desc
attribute	sign_3	description	String	Third disease sign identified.
attribute	sign_3	long_name	String	Sign 3
attribute	sign_3	units	String	unitless
variable	sign_4		String
attribute	sign_4	bcodmo_name	String	brief_desc
attribute	sign_4	description	String	Fourth disease sign identified.
attribute	sign_4	long_name	String	Sign 4
attribute	sign_4	units	String	unitless

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.