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Title Sum-
Institution Dataset ID
     data   graph     files  public Data describing every diseased coral record from surveys in the Caribbean during
2012 (Contagious coral diseases project)
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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
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
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 (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 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/ (external link)
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 (external link)
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 (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/658275 (external link)
attribute NC_GLOBAL param_mapping String {'658275': {}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/658275/parameters (external link)
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/ (external link)
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/ (external link)
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.

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