http://lod.bco-dmo.org/id/dataset/872285
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2022-03-23
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Percent cover of organisms within quadrats surveyed during surveys of 12 sites around St. Thomas and St. John, US Virgin Islands from 2011-2021
2022-03-25
publication
2022-03-25
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2022-03-29
publication
https://doi.org/10.26008/1912/bco-dmo.872285.1
Peter J. Edmunds
California State University Northridge
principalInvestigator
Tyler Smith
University of the Virgin Islands Center for Marine and Environmental Studies
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Edmunds, P. J., Smith, T. (2022) Percent cover of organisms within quadrats surveyed during surveys of 12 sites around St. Thomas and St. John, US Virgin Islands from 2011-2021. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2022-03-25 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.872285.1 [access date]
Methods and Sampling: <p>Location:&nbsp;St. John, US Virgin Islands (18.315°N, 64.716°W),&nbsp;Multiple field expeditions to the USVI between 2011 and 2021.</p>
<p>Material and methods</p>
<p>Sampling was accomplished photographically using digital cameras on a frame that held the camera perpendicular to the reef to record 0.5 × 0.5 m photoquadrats. Photographs were taken with a Nikon D90 camera in 2011 (12.3 MP, fitted with a Nikkor DX 18-70 lens), a Nikon D7000 in 2015 (16.2 MP, fitted with a Nikkor DX 18-70 lens), and a Nikon D810 in 2015–2021 (36.3 MP, fitted with a Nikkor FX 18-35 lens). Cameras were fitted with two strobes (Nikon SB105) and the pictures provided a resolution of objects &gt; 5 mm diameter.</p>
<p>Two sampling regimes were employed. First, sampling in the core area of the time-series project (1992-present on the south shore of St. John) took place between White Point and Cabritte Horn (1.3 km), and sampled 6 permanently marked sites (five at 9 m depth, one at 7 m depth) that were randomly selected in 1992. Along one 40 m transect at each site, photoquadrats were recorded at 40 positions that were randomized annually. Each sampling generated ~ 240 photoquadrats from which 40 were drawn randomly to characterize the fringing reefs along this stretch of shore (hereafter referred to as the Pooled Random Sites, PRS*) and support a balanced statistical contrast with the other 11 sites (described below). Sampling at the core sites in July/August 2011, 2015, 2019, and 2020 are used in the present analysis. Although the core sites were sampled in August 2020, they are contrasted with the January 2021 sampling of the other sites and considered together as “2021 sampling”.</p>
<p>In 2011, the sampling included 11 additional sites at 10 m depth that were scattered around St. John and St. Thomas to provide a contrast of shores (n = 3 sites shore-1) and islands (n = 6 sites island-1). These sites were selected haphazardly to sample fringing reefs at a landscape scale commensurate with the linear distance occupied by St. John and St. Thomas (~ 40 km). Logistical constraints prevented permanent marking of the sites, but they were relocated using GPS and landscape and seascape features. It therefore was possible to revisit the sites over time, but identical areas of reef were not sampled on each occasion. Sampling of the sites around both islands and their shores occurred in June 2011, June 2015, August 2019 (two sites on the south shore of St. John), and January 2021.</p>
<p>Coral reef benthic community structure was analyzed using CoralNet software with manual annotation of 200 dots randomly located on each image, and the results were expressed as percentage cover. Analyses resolved scleractinians to the lowest taxonomic level possible, macroalgae (mostly Dictyota, Lobophora, Padina, Sargassum, Halimeda, and peyssonellid algal crust), and crustose coralline algae, algal turf, and bare space combined (CTB) because they could not reliably be distinguished in photoquadrats. Scleractinians subsequently were pooled to Orbicella spp., Montastraea cavernosa, Agaricia spp., Colpophyllia natans, Pseudiploria spp., Diploria spp., Meandrina sp., Porites spp., Siderastrea spp, and “other” corals.<br />
<br />
See Edmunds &amp; Smith&nbsp;(2022) for statistical analyses that used these data.&nbsp; Statistical software used:&nbsp;Systat 13, PRIMER 6.<br />
<br />
Issue note:&nbsp;Some sampling non-consecutive in date columns.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2019992 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2019992
completed
Peter J. Edmunds
California State University Northridge
818-677-2502
Department of Biology 18111 Nordhoff Street
Northridge
CA
91330-8303
USA
peter.edmunds@csun.edu
pointOfContact
Tyler Smith
University of the Virgin Islands Center for Marine and Environmental Studies
1-340-693-1394
#2 John Brewers Bay
St. Thomas
U.S. Virgin Islands
00802
tsmith@uvi.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Quadrat_Number
Island
Site
Site_Code
Shore
lat
lon
Year
Taxon
Percent_Cover
Nikon D90 and Nikon D7000
theme
None, User defined
sample description
site description
site
latitude
longitude
year
taxon
percent coverage
featureType
BCO-DMO Standard Parameters
Underwater Camera
instrument
BCO-DMO Standard Instruments
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
RUI: Pattern and process in five decades of change on Caribbean reefs
http://coralreefs.csun.edu/
RUI: Pattern and process in five decades of change on Caribbean reefs
<p><strong>This project has been supported by continuing grants:</strong><br />
OCE-2019992 "RUI: Pattern and process in four decades of change on Caribbean reefs" (2020-2026)<br />
OCE-2546549 "RUI Pattern and process in five decades of change on Caribbean reefs" (2026-2029)</p>
<p><strong>NSF award OCE-2546549 project summary:</strong></p>
<p><strong>Overview</strong></p>
<p>This proposal focuses on American coral reefs in the United States Virgin Islands, most of which are trending towards persistent low coral colony abundances. This is a conspicuous aspect of the coral reef crisis, and while much is known of the disturbances causing corals to die, little is known about the ecological implications of low coral abundance. This project leverages four decades of research in St. John by using multiple sites to test five hypotheses addressing mechanisms preventing depleted coral populations from increasing in size, and they are developed in a hierarchical framework to advance basic ecology, and enhance understanding of coral reefs and the ecological processes structuring marine communities in the Anthropocene. The project is mensurative because it is conducted in an MPA, but its scope is broadened through: (a) analyses of algal symbionts (Symbiodiniaceae) with co PI, Cunning (Shedd Aquarium), (b) by extending the coral reef time-series from 40 to 43 yrs, and (c) applying wavelet analyses to the time-series. Three years of funding will support 1 mo/y of fieldwork, 11 mo/y of analysis, QA/QC, graduate training, a one year postdoc, outreach, and manuscript preparation. This RUI proposal is targeting the OCE call NSF PD 23-1650.</p>
<p><strong>Intellectual merit</strong></p>
<p>The intellectual merits lie in the <em>hypotheses</em> focused on the mechanisms leading to persistent low abundance coral communities. This project is<strong> </strong>designed around a conceptual model that preserves the integrity of a 43 yr time series and tests 5 integrated hypotheses addressing four science needs: (1) advancing basic ecology, (2) leveraging of existing data to realize emergent properties, (3) serving data to end users, and (4) outreach benefitting American stake holders. Over three years, fieldwork and analyses will address: H<sub>1 </sub>Coral reef community structure is converging to a stable low coral abundance state; <strong>H<sub>2</sub></strong>. The impact of disturbances is mediated by the spatial structuring of community dynamics, and the expression of portfolio effects<strong>; H<sub>3</sub> </strong>Intensification of the coral recruitment ‘bottleneck’ and its gradual transition to settlement failure; <strong>H<sub>4</sub></strong> Declining populations sizes of echinoids limit the formation of grazing halos in which corals settle; <strong>H<sub>5</sub></strong> Persistence of low abundance coral communities is favored by changes in the symbiodiniacaea complement.</p>
<p><strong>Broader impacts</strong></p>
<p>This project will advance discoverability of time-series data in the public domain, student mentoring and experiential fieldwork, research on the causes of changes affecting marine communities, and in-person outreach at schools in California an Illinois, the University of the Virgin Islands, and the Friends of the VI National Park. Open access to high resolution data quantifying coral reefs over five decades is a critical community need to which this project will respond by placing in > 14,000 photoquadrats in the public domain (1987-present). Up to five graduate (MS) students will be mentored in marine science through fieldwork and lab analysis, and one REU students will be supported in a graduate mentoring framework. At middle schools, an “aquarium library” program will place marine animals in classrooms for 2–3 weeks in collaboration with the non-profit organization, ‘Underwater Zoo’. At high schools, ‘marine biology clubs’ will address project themes, provide research opportunities, and entrain teachers in field trips. In the field, teachers will conduct research leading to publications and will lead outreach activities with children in the junior ranger program administered by the Friends of the VI National Park. The efficacy of outreach tasks will be assessed through pre/post surveys and questionnaires administered using Google forms by teachers at partner schools. The results of assessment will be used to tune project deliverable to better meet the needs of the outreach audience.</p>
<p>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.</p>
<p><strong>Related Projects:</strong></p>
<ul>
<li>Affiliated with MCR-LTER - <a href="https://www.bco-dmo.org/project/2222">https://www.bco-dmo.org/project/2222</a></li>
<li>Serves as a new project that builds on NSF DEB-1350146 - RUI-LTREB Renewal: Three decades of coral reef community dynamics in St. John, USVI: 2014-2019 - <a href="https://www.bco-dmo.org/project/734983">https://www.bco-dmo.org/project/734983</a></li>
<li>Overlaps with OCE 17-56678 (which focuses on soft corals with H. Lasker) - Collaborative Research: Pattern and process in the abundance and recruitment of Caribbean octocorals - <a href="https://www.bco-dmo.org/project/752508">https://www.bco-dmo.org/project/752508</a></li>
<li>LTREB Long-term coral reef community dynamics in St. John, USVI: 1987-2019 - <a href="https://www.bco-dmo.org/project/2272">https://www.bco-dmo.org/project/2272</a></li>
<li>RUI: Pattern and process in four decades of change on Caribbean reefs - <a href="https://www.bco-dmo.org/project/835192">https://www.bco-dmo.org/project/835192</a></li>
<li>RAPID: Hurricane Irma: Effects of repeated severe storms on shallow Caribbean reefs and their changing ecological resilience - <a href="https://www.bco-dmo.org/project/722163">https://www.bco-dmo.org/project/722163</a></li>
</ul>
St John Coral Reefs
largerWorkCitation
project
eng; USA
oceans
-65.0343
-64.0199
18.3028
18.3832
2011-06-01
2021-01-01
United States Virgin Islands, St. John: 18.318, -64.7253
0
BCO-DMO catalogue of parameters from Percent cover of organisms within quadrats surveyed during surveys of 12 sites around St. Thomas and St. John, US Virgin Islands from 2011-2021
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/872438.rdf
Name: Quadrat_Number
Units: unitless
Description: <p>Arbitary number of photograph recording each quadrat</p>
http://lod.bco-dmo.org/id/dataset-parameter/872439.rdf
Name: Island
Units: unitless
Description: <p>Island code. STJ = St. John, STT = St. Thomas</p>
http://lod.bco-dmo.org/id/dataset-parameter/872440.rdf
Name: Site
Units: unitless
Description: <p>Site around St. John and St. Thomas where surveys were completed. (PRS*=Pooled Random Sites)</p>
http://lod.bco-dmo.org/id/dataset-parameter/872441.rdf
Name: Site_Code
Units: unitless
Description: <p>Site code around St. John and St. Thomas where surveys were completed as used in Edumnds (2014). (PRS=Pooled Random Sites)</p>
http://lod.bco-dmo.org/id/dataset-parameter/872442.rdf
Name: Shore
Units: unitless
Description: <p>Shore. S = south. N = north</p>
http://lod.bco-dmo.org/id/dataset-parameter/872443.rdf
Name: lat
Units: decimal degrees
Description: <p>Site latitude from Edmunds (2014).</p>
http://lod.bco-dmo.org/id/dataset-parameter/872444.rdf
Name: lon
Units: decimal degrees
Description: <p>Site longitude from Edmunds (2014).</p>
http://lod.bco-dmo.org/id/dataset-parameter/872445.rdf
Name: Year
Units: unitless
Description: <p>Year of survey</p>
http://lod.bco-dmo.org/id/dataset-parameter/872446.rdf
Name: Taxon
Units: unitless
Description: <p>Benthic group quantified, genus of coral, other coral, macroalgae, CTB (combined category, see methodology)</p>
http://lod.bco-dmo.org/id/dataset-parameter/872447.rdf
Name: Percent_Cover
Units: percent (%)
Description: <p>Percentage cover of floor in quadrat</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
4467005
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/6dcabc9b-8adf-5774-baaf-1f4f3fbb5ff2/content
download
https://doi.org/10.26008/1912/bco-dmo.872285.1
download
onLine
dataset
<p>Location:&nbsp;St. John, US Virgin Islands (18.315°N, 64.716°W),&nbsp;Multiple field expeditions to the USVI between 2011 and 2021.</p>
<p>Material and methods</p>
<p>Sampling was accomplished photographically using digital cameras on a frame that held the camera perpendicular to the reef to record 0.5 × 0.5 m photoquadrats. Photographs were taken with a Nikon D90 camera in 2011 (12.3 MP, fitted with a Nikkor DX 18-70 lens), a Nikon D7000 in 2015 (16.2 MP, fitted with a Nikkor DX 18-70 lens), and a Nikon D810 in 2015–2021 (36.3 MP, fitted with a Nikkor FX 18-35 lens). Cameras were fitted with two strobes (Nikon SB105) and the pictures provided a resolution of objects &gt; 5 mm diameter.</p>
<p>Two sampling regimes were employed. First, sampling in the core area of the time-series project (1992-present on the south shore of St. John) took place between White Point and Cabritte Horn (1.3 km), and sampled 6 permanently marked sites (five at 9 m depth, one at 7 m depth) that were randomly selected in 1992. Along one 40 m transect at each site, photoquadrats were recorded at 40 positions that were randomized annually. Each sampling generated ~ 240 photoquadrats from which 40 were drawn randomly to characterize the fringing reefs along this stretch of shore (hereafter referred to as the Pooled Random Sites, PRS*) and support a balanced statistical contrast with the other 11 sites (described below). Sampling at the core sites in July/August 2011, 2015, 2019, and 2020 are used in the present analysis. Although the core sites were sampled in August 2020, they are contrasted with the January 2021 sampling of the other sites and considered together as “2021 sampling”.</p>
<p>In 2011, the sampling included 11 additional sites at 10 m depth that were scattered around St. John and St. Thomas to provide a contrast of shores (n = 3 sites shore-1) and islands (n = 6 sites island-1). These sites were selected haphazardly to sample fringing reefs at a landscape scale commensurate with the linear distance occupied by St. John and St. Thomas (~ 40 km). Logistical constraints prevented permanent marking of the sites, but they were relocated using GPS and landscape and seascape features. It therefore was possible to revisit the sites over time, but identical areas of reef were not sampled on each occasion. Sampling of the sites around both islands and their shores occurred in June 2011, June 2015, August 2019 (two sites on the south shore of St. John), and January 2021.</p>
<p>Coral reef benthic community structure was analyzed using CoralNet software with manual annotation of 200 dots randomly located on each image, and the results were expressed as percentage cover. Analyses resolved scleractinians to the lowest taxonomic level possible, macroalgae (mostly Dictyota, Lobophora, Padina, Sargassum, Halimeda, and peyssonellid algal crust), and crustose coralline algae, algal turf, and bare space combined (CTB) because they could not reliably be distinguished in photoquadrats. Scleractinians subsequently were pooled to Orbicella spp., Montastraea cavernosa, Agaricia spp., Colpophyllia natans, Pseudiploria spp., Diploria spp., Meandrina sp., Porites spp., Siderastrea spp, and “other” corals.<br />
<br />
See Edmunds &amp; Smith&nbsp;(2022) for statistical analyses that used these data.&nbsp; Statistical software used:&nbsp;Systat 13, PRIMER 6.<br />
<br />
Issue note:&nbsp;Some sampling non-consecutive in date columns.</p>
Specified by the Principal Investigator(s)
<p>Image processing in CoralNET (Chen et al., 2021).</p>
<div>BCO-DMO Data Manager Processing Notes:</div>
<div>* Data from source file "Data in paper 4 March 2022_Marine_Biology copy.xls" Sheet1 were imported into the BCO-DMO data system.</div>
<div>* Percent cover values imported from Excel were 16 decimal places long. Rounded them to 2.</div>
<div>* Parameters (column names) renamed to comply with BCO-DMO naming conventions. See https://www.bco-dmo.org/page/bco-dmo-data-processing-conventions</div>
<div>* Site list extracted from Table 1 of publication Edmunds (2014).&nbsp; Since there were site name discrepancies between that table and this dataset, a list of site names, lat, lons was sent to the submitter for verification they were correct for this dataset.</div>
<div>* Site list joined into this dataset to add additional columns lat,lon, site_code from Edmunds (2014).</div>
<div>* Checked organism taxon names using World Register of Marine Species taxa match tool on 2022-03-25.&nbsp; Taxon list with the names used in the dataset and the matched accepted name and IDs&nbsp;added to supplemental files for this dataset.&nbsp;&nbsp;<br />
* Unmatched taxon names in dataset changed&nbsp;accepted taxon names after discussion with data submitter (Mycetopohyllia changed to Mycetophyllia ,&nbsp;M. cavernosa changed to Montastraea cavernosa ). Supplemental species list updated.<br />
* Verified with the submitter that the site name differences between this dataset and the Edmunds, P. (2014) reference provided for the site list were in fact the same sites.&nbsp; These sites between the two references were the same sites:<br />
"Cow and Calf", "Cow and Calves"<br />
"Flat Cay","south Flat Cay"<br />
"Inner Brass","north Inner Brass Cay"<br />
"Waterlemon Cay","north Waterlemon Cay"<br />
* site lat,lon and site codes extracted from&nbsp;Edmunds, P. (2014) and added to this dataset (site list verified by submitter).<br />
* site list added as a supplemental file.</div>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
Nikon D90 and Nikon D7000
Nikon D90 and Nikon D7000
PI Supplied Instrument Name: Nikon D90 and Nikon D7000 PI Supplied Instrument Description:DSLR camera for underwater images.
Photographs were taken with a Nikon D90 camera in 2011 (12.3 MP, fitted with a Nikkor DX 18-70 lens), a Nikon D7000 in 2015 (16.2 MP, fitted with a Nikkor DX 18-70 lens), and a Nikon D810 in 2015–2021 (36.3 MP, fitted with a Nikkor FX 18-35 lens). Cameras were fitted with two strobes (Nikon SB105) and the pictures provided a resolution of objects > 5 mm diameter. Instrument Name: Underwater Camera Instrument Short Name: Instrument Description: All types of photographic equipment that may be deployed underwater including stills, video, film and digital systems. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/180/