Accessing BCO-DMO data
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| Dataset Title: | Data describing interactions between neighboring coral colonies on St. John, Virgin Islands in 2014. 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_662791) |
| Information: | Summary
| License
| ISO 19115
| Metadata
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Attributes {
s {
site {
String bcodmo_name "site";
String description "Site where sampling occurred";
String long_name "Site";
String units "unitless";
}
latitude {
String _CoordinateAxisType "Lat";
Float64 _FillValue NaN;
Float64 actual_range 18.3166, 18.31685;
String axis "Y";
String bcodmo_name "latitude";
Float64 colorBarMaximum 90.0;
Float64 colorBarMinimum -90.0;
String description "Latitude; N is positive";
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 -64.72988, -64.72415;
String axis "X";
String bcodmo_name "longitude";
Float64 colorBarMaximum 180.0;
Float64 colorBarMinimum -180.0;
String description "Longitude; W is positve";
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";
}
colony {
Byte _FillValue 127;
Byte actual_range 1, 2;
String bcodmo_name "sample";
String description "PI issued colony ID";
String long_name "Colony";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
String units "unitless";
}
transect {
String bcodmo_name "transect";
String description "Transect where sampling occurred";
String long_name "Transect";
String units "unitless";
}
meter {
Byte _FillValue 127;
Byte actual_range 0, 9;
String bcodmo_name "transect";
String description "Meter on transect where sampling occurred";
String long_name "Meter";
String units "meters";
}
species {
String bcodmo_name "species";
String description "The octocoral colony closest to each sampling point was selected and identified.";
String long_name "Species";
String units "unitless";
}
height {
Byte _FillValue 127;
Byte actual_range 2, 120;
String bcodmo_name "height";
String description "Height of each colony was measured to the nearest centimeter.";
String long_name "Height";
String units "centimeters";
}
width {
Byte _FillValue 127;
Byte actual_range 1, 90;
String bcodmo_name "width";
String description "Width of each colony was measured to the nearest centimeter.";
String long_name "Width";
String units "centimeters";
}
thickness {
Byte _FillValue 127;
Byte actual_range 0, 55;
String bcodmo_name "length";
String description "Thickness of each colony was measured to the nearest centimeter.";
String long_name "Thickness";
String units "centimeters";
}
visibleInhibition {
Byte _FillValue 127;
Byte actual_range 0, 2;
String bcodmo_name "sample_descrip";
String description "Visible inhibition (1) denotes colony asymmetry or damage due to abrasion between colonies; (0) indicates no visible inhibition.";
String long_name "Visible Inhibition";
String units "unitless";
}
distance {
Byte _FillValue 127;
Byte actual_range 0, 48;
String bcodmo_name "unknown";
String description "The distance between the measured colony's base and the base of its nearest branching octocoral neighbor was measured to the nearest centimeter.";
String long_name "Distance";
String units "centimeters";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson";
String acquisition_description
"Methodology\\u00a0from\\u00a0Gambrel, B.\\u00a0and\\u00a0Lasker, H.R., 2016
To further examine the spatial distribution of colonies and potential
competition among them,\\u00a0nearest neighbor data\\u00a0were collected along
the belt\\u00a0transects from\\u00a0each site. Each transect had 20
sampling\\u00a0points arranged\\u00a0at the corners of every 1 m2
quadrat\\u00a0along the\\u00a0first 9 m of each transect. The
octocoral\\u00a0colony closest\\u00a0to each sampling point was selected,
identified,and the distance between its base and the\\u00a0base of\\u00a0its
nearest branching octocoral neighbor\\u00a0was measured\\u00a0to the nearest
centimeter (Fig. S1\\u00a0in the\\u00a0Supplement). The height, width, and
length\\u00a0of each\\u00a0colony was measured to the nearest\\u00a0centimeter
to\\u00a0calculate\\u00a0cross-sectional\\u00a0area (height \\u00d7
length)\\u00a0and volume\\u00a0(height \\u00d7 width \\u00d7 length), and
the\\u00a0proximity of\\u00a0the colony\\u2019s branches to nearby
octocorals\\u00a0was also\\u00a0noted. Due to the water flow and
the\\u00a0resulting oscillation\\u00a0of colony branches, measurements\\u00a0were
made\\u00a0when the branches were vertical in the\\u00a0water column\\u00a0to
optimize the precision of our measurements.To increase sample sizes, an
additional 9\\u00a0m transect\\u00a0parallel to the other 5 was sampled
at\\u00a0each site.
The nature of the spatial distribution of\\u00a0octocorals at\\u00a0each site
was determined from the nearest-neighbor data\\u00a0following Clark & Evans
(1954).\\u00a0Observed and\\u00a0expected mean distances between
the\\u00a0octocoral neighbors\\u00a0were calculated using the
total\\u00a0distance between\\u00a0neighbors, sample size (120 pairs
of\\u00a0octocorals per\\u00a0site) and the density of octocorals at each
site(calculated from the belt transect data). The ratio (R)of the observed and
expected (given a randomly\\u00a0distributed octocoral\\u00a0community) mean
distances between octocoral neighbors describes the\\u00a0octocoral
distribution\\u00a0at each site, where R = 1 denotes a\\u00a0random
distribution, R < 1, an aggregated distribution,and R > 1, a uniform
distribution (Clark & Evans1954). The significance of R was determined
by\\u00a0analyzing the\\u00a0standard variate of the normal curve (c), since the
measured distances between neighbors in\\u00a0a randomly\\u00a0dispersed
community are expected to\\u00a0follow a\\u00a0normal distribution.
The effects of colony\\u2212colony proximity on colony size were assessed by
correlating the distance\\u00a0between\\u00a0neighbors at the base with the sum
of\\u00a0their sizes\\u00a0(Pielou 1962). If competition affects growth, then
the closer\\u00a0the organisms\\u00a0are, the smaller their expected sizes will
be (Pielou 1962). Implicit in these analyses is the notion that size is both
an indicator of resource use and of success in acquiring resources.
The relationships among the distance between octocoral neighbors at the base
(divided into 3 distance groups to make the data categorical: 5\\u221214 cm,
15\\u221224\\u00a0cm\\u00a0and 25\\u221234 cm), branch proximity and site were
analyzed using a hierarchical log-linear test in SPSS. The relationship
between the distance between neighbors and branch proximity was further
analyzed in a separate log-linear test in SPSS.";
String awards_0_award_nid "562090";
String awards_0_award_number "OCE-1334052";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1334052";
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 "David L. Garrison";
String awards_0_program_manager_nid "50534";
String cdm_data_type "Other";
String comment
"Nearest Neighbor Survey
Howard Lasker, PI
Version 14 October 2016";
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 "2016-10-25T21:41:41Z";
String date_modified "2019-04-18T17:39:09Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.662791.1";
Float64 Easternmost_Easting -64.72415;
Float64 geospatial_lat_max 18.31685;
Float64 geospatial_lat_min 18.3166;
String geospatial_lat_units "degrees_north";
Float64 geospatial_lon_max -64.72415;
Float64 geospatial_lon_min -64.72988;
String geospatial_lon_units "degrees_east";
String history
"2024-04-19T07:38:53Z (local files)
2024-04-19T07:38:53Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_662791.html";
String infoUrl "https://www.bco-dmo.org/dataset/662791";
String institution "BCO-DMO";
String keywords "bco, bco-dmo, biological, chemical, colony, data, dataset, distance, dmo, erddap, height, inhibition, latitude, longitude, management, meter, oceanography, office, preliminary, site, species, thickness, transect, visible, visibleInhibition, width";
String license "https://www.bco-dmo.org/dataset/662791/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/662791";
Float64 Northernmost_Northing 18.31685;
String param_mapping "{'662791': {'lat': 'master - latitude', 'lon': 'master - longitude'}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/662791/parameters";
String people_0_affiliation "State University of New York at Buffalo";
String people_0_affiliation_acronym "SUNY Buffalo";
String people_0_person_name "Howard Lasker";
String people_0_person_nid "562092";
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 "Hannah Ake";
String people_1_person_nid "650173";
String people_1_role "BCO-DMO Data Manager";
String people_1_role_type "related";
String project "St. John LTREB,VI Octocorals";
String projects_0_acronym "St. John LTREB";
String projects_0_description
"Long Term Research in Environmental Biology (LTREB) in US Virgin Islands:
From the NSF award abstract:
In an era of growing human pressures on natural resources, there is a critical need to understand how major ecosystems will respond, the extent to which resource management can lessen the implications of these responses, and the likely state of these ecosystems in the future. Time-series analyses of community structure provide a vital tool in meeting these needs and promise a profound understanding of community change. This study focuses on coral reef ecosystems; an existing time-series analysis of the coral community structure on the reefs of St. John, US Virgin Islands, will be expanded to 27 years of continuous data in annual increments. Expansion of the core time-series data will be used to address five questions: (1) To what extent is the ecology at a small spatial scale (1-2 km) representative of regional scale events (10's of km)? (2) What are the effects of declining coral cover in modifying the genetic population structure of the coral host and its algal symbionts? (3) What are the roles of pre- versus post-settlement events in determining the population dynamics of small corals? (4) What role do physical forcing agents (other than temperature) play in driving the population dynamics of juvenile corals? and (5) How are populations of other, non-coral invertebrates responding to decadal-scale declines in coral cover? Ecological methods identical to those used over the last two decades will be supplemented by molecular genetic tools to understand the extent to which declining coral cover is affecting the genetic diversity of the corals remaining. An information management program will be implemented to create broad access by the scientific community to the entire data set.
The importance of this study lies in the extreme longevity of the data describing coral reefs in a unique ecological context, and the immense potential that these data possess for understanding both the patterns of comprehensive community change (i.e., involving corals, other invertebrates, and genetic diversity), and the processes driving them. Importantly, as this project is closely integrated with resource management within the VI National Park, as well as larger efforts to study coral reefs in the US through the NSF Moorea Coral Reef LTER, it has a strong potential to have scientific and management implications that extend further than the location of the study.
The following publications and data resulted from this project:
2015 Edmunds PJ, Tsounis G, Lasker HR (2015) Differential distribution of octocorals and scleractinians around St. John and St. Thomas, US Virgin Islands. Hydrobiologia. doi: 10.1007/s10750-015-2555-zoctocoral - sp. abundance and distributionDownload complete data for this publication (Excel file)
2015 Lenz EA, Bramanti L, Lasker HR, Edmunds PJ. Long-term variation of octocoral populations in St. John, US Virgin Islands. Coral Reefs DOI 10.1007/s00338-015-1315-xoctocoral survey - densitiesoctocoral counts - photoquadrats vs. insitu surveyoctocoral literature reviewDownload complete data for this publication (Excel file)
2015 Privitera-Johnson, K., et al., Density-associated recruitment in octocoral communities in St. John, US Virgin Islands, J.Exp. Mar. Biol. Ecol. DOI 10.1016/j.jembe.2015.08.006octocoral recruitmentDownload complete data for this publication (Excel file)
2014 Edmunds PJ. Landscape-scale variation in coral reef community structure in the United States Virgin Islands. Marine Ecology Progress Series 509: 137–152. DOI 10.3354/meps10891.
Data at MCR-VINP.
Download complete data for this publication (Excel file)
2014 Edmunds PJ, Nozawa Y, Villanueva RD. Refuges modulate coral recruitment in the Caribbean and Pacific. Journal of Experimental Marine Biology and Ecology 454: 78-84. DOI: 10.1016/j.jembe.2014.02.00
Data at MCR-VINP.Download complete data for this publication (Excel file)
2014 Edmunds PJ, Gray SC. The effects of storms, heavy rain, and sedimentation on the shallow coral reefs of St. John, US Virgin Islands. Hydrobiologia 734(1):143-148.
Data at MCR-VINP.Download complete data for this publication (Excel file)
2014 Levitan, D, Edmunds PJ, Levitan K. What makes a species common? No evidence of density-dependent recruitment or mortality of the sea urchin Diadema antillarum after the 1983-1984 mass mortality. Oecologia. DOI 10.1007/s00442-013-2871-9.
Data at MCR-VINP.Download complete data for this publication (Excel file)
2014 Lenz EA, Brown D, Didden C, Arnold A, Edmunds PJ. The distribution of hermit crabs and their gastropod shells on shallow reefs in St. John, US Virgin Islands. Bulletin of Marine Science 90(2):681-692. https://dx.doi.org/10.5343/bms.2013.1049
Data at MCR-VINP.Download complete data for this publication (Excel file)
2013 Edmunds PJ. Decadal-scale changes in the community structure of coral reefs in St. John, US Virgin Islands. Marine Ecology Progress Series 489: 107-123.
Data at MCR-VINP.Download complete data for this publication (zipped Excel files)
2013 Brown D, Edmunds PJ. Long-term changes in the population dynamics of the Caribbean hydrocoral Millepora spp. J. Exp Mar Biol Ecol 441: 62-70. doi: 10.1016/j.jembe.2013.01.013Millepora colony sizeMillepora cover - temps - storms 1992-2008Millepora cover 1992-2008seawater temperature USVI 1992-2008storms USVI 1992-2008Download complete data for this publication (Excel file)
2012 Brown D, Edmunds PJ. The hermit crab Calcinus tibicen lives commensally on Millepora spp. in St. John, United States Virgin Islands. Coral Reefs 32: 127-135. doi: 10.1007/s00338-012-0948-2crab abundance and coral sizecrab displacement behaviorcrab nocturnal surveyscrab predator avoidanceDownload complete data for this publication (Excel file)
2011 Green DH, Edmunds PJ. Spatio-temporal variability of coral recruitment on shallow reefs in St. John, US Virgin Islands. Journal of Experimenal Marine Biology and Ecology 397: 220-229.
Data at MCR-VINP.Download complete data for this publication (Excel file)
2011 Colvard NB, Edmunds PJ. (2011) Decadal-scale changes in invertebrate abundances on a Caribbean coral reef. Journal of Experimental Marine Biology and Ecology. 397(2): 153-160. doi: 10.1016/j.jembe.2010.11.015benthic invert codesinverts - Tektite and Yawzi Ptinverts - pooledDownload complete data for this publication (Excel file)";
String projects_0_end_date "2014-04";
String projects_0_geolocation "St. John, U.S. Virgin Islands; California State University Northridge";
String projects_0_name "LTREB Long-term coral reef community dynamics in St. John, USVI: 1987-2019";
String projects_0_project_nid "2272";
String projects_0_project_website "http://coralreefs.csun.edu/";
String projects_0_start_date "2009-05";
String projects_1_acronym "VI Octocorals";
String projects_1_description
"The recent past has not been good for coral reefs, and journals have been filled with examples of declining coral cover, crashing fish populations, rising cover of macroalgae, and a future potentially filled with slime. However, reefs are more than the corals and fishes for which they are known best, and their biodiversity is affected strongly by other groups of organisms. The non-coral fauna of reefs is being neglected in the rush to evaluate the loss of corals and fishes, and this project will add on to an on-going long term ecological study by studying soft corals. This project will be focused on the ecology of soft corals on reefs in St. John, USVI to understand the Past, Present and the Future community structure of soft corals in a changing world. For the Past, the principal investigators will complete a retrospective analysis of octocoral abundance in St. John between 1992 and the present, as well as Caribbean-wide since the 1960's. For the Present, they will: (i) evaluate spatio-temporal changes between soft corals and corals, (ii) test for the role of competition with macroalgae and between soft corals and corals as processes driving the rising abundance of soft corals, and (iii) explore the role of soft corals as \"animal forests\" in modifying physical conditions beneath their canopy, thereby modulating recruitment dynamics. For the Future the project will conduct demographic analyses on key soft corals to evaluate annual variation in population processes and project populations into a future impacted by global climate change.
This project was funded to provide and independent \"overlay\" to the ongoing LTREB award (DEB-1350146, co-funded by OCE, PI Edmunds) focused on the long-term dynamics of coral reefs in St. John.
Note: This project is closely associated with the project \"RAPID: Resilience of Caribbean octocorals following Hurricanes Irma and Maria\". See: https://www.bco-dmo.org/project/749653.
The following publications and data resulted from this project:
2017 Tsounis, G., and P. J. Edmunds. Three decades of coral reef community dynamics in St. John, USVI: a contrast of scleractinians and octocorals. Ecosphere 8(1):e01646. DOI: 10.1002/ecs2.1646Rainfall and temperature dataCoral and macroalgae abundance and distributionDescriptions of hurricanes affecting St. John
2016 Gambrel, B. and Lasker, H.R. Marine Ecology Progress Series 546: 85–95, DOI: 10.3354/meps11670Colony to colony interactionsEunicea flexuosa interactionsGorgonia ventalina asymmetryNearest neighbor surveys
2015 Lenz EA, Bramanti L, Lasker HR, Edmunds PJ. Long-term variation of octocoral populations in St. John, US Virgin Islands. Coral Reefs DOI 10.1007/s00338-015-1315-xoctocoral survey - densitiesoctocoral counts - photoquadrats vs. insitu surveyoctocoral literature reviewDownload complete data for this publication (Excel file)
2015 Privitera-Johnson, K., et al., Density-associated recruitment in octocoral communities in St. John, US Virgin Islands, J.Exp. Mar. Biol. Ecol. DOI: 10.1016/j.jembe.2015.08.006octocoral density dependenceDownload complete data for this publication (Excel file)
Other datasets related to this project:octocoral transects - adult colony height";
String projects_1_end_date "2016-08";
String projects_1_geolocation "St. John, US Virgin Islands: 18.3185, 64.7242";
String projects_1_name "Ecology and functional biology of octocoral communities";
String projects_1_project_nid "562086";
String projects_1_project_website "http://coralreefs.csun.edu/";
String projects_1_start_date "2013-09";
String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
String publisher_type "institution";
String sourceUrl "(local files)";
Float64 Southernmost_Northing 18.3166;
String standard_name_vocabulary "CF Standard Name Table v55";
String summary "Data describing interactions between neighboring coral colonies on St. John, Virgin Islands in 2014.";
String title "Data describing interactions between neighboring coral colonies on St. John, Virgin Islands in 2014.";
String version "1";
Float64 Westernmost_Easting -64.72988;
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.