http://lod.bco-dmo.org/id/dataset/892258
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
2023-03-21
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Canopy closure values from photographs taken within octocoral forests in Lameshur Bay St. John, U.S. Virgin Islands from July 2019 to Jan 2020
2023-03-21
publication
2023-03-21
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2023-05-24
publication
https://doi.org/10.26008/1912/bco-dmo.892258.1
Peter J. Edmunds
California State University Northridge
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: Girard, J., Edmunds, P. J. (2023) Canopy closure values from photographs taken within octocoral forests in Lameshur Bay St. John, U.S. Virgin Islands from July 2019 to Jan 2020. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2023-03-21 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.892258.1 [access date]
Methods and Sampling: <p>Research was conducted from the University of the Virgin Islands Marine Station in Lameshure Bay during July – August 2019 and January 2020.<br />
<br />
Methods &amp; Sampling<br />
Quadrats were randomly placed along 20 m, non-overlapping transects that were positioned haphazardly along fringing reefs. Canopy closure was quantified using a modified method from (Jennings et. al. 1999) whereby a GoPro Hero 3+ camera with a 130° field of view (manufacturer’s specification, Go-Pro., Inc. San Mateo, CA) was used to record still images in the center, and at each of the four corners, of quadrats, with all five images quadrat-1 recorded within &lt; 5 minutes. To avoid biases in estimating canopy closure caused by adjacent non-living substrata (e.g., boulders and rock walls), images were excluded when they included these features. Images were analyzed using ImageJ software (v1.52a, Schneider et al., 2012), in which 300 randomly located dots (~ 0.5 pixel in diameter) were superimposed on each image. The number of dots on the octocoral canopy were counted and expressed as a percentage of the dot population. This metric was used to quantify canopy closure, and the results from the five images quadrat-1 were averaged to characterize each quadrat.</p>
<p>Instruments<br />
PVC Quadrats (1 m2)<br />
Transect tapes<br />
GoPro Hero 3+ camera</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1756678 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1756678
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
asNeeded
Dataset Version: 1
Unknown
Closure_Photo_ID
Site
lat
lon
Transect_Num
Quadrat_Number
Proportion_Closed
Box_1
Box_2
Box_3
Box_4
Box_5
Box_6
Box_7
Box_8
Box_9
Box_10
Box_11
Box_12
Box_13
Box_14
Box_15
Box_16
Box_17
Box_18
Box_19
Box_20
GoPro Hero 3+ camera
theme
None, User defined
sample description
site
latitude
longitude
transect
count
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.
Collaborative Research: Pattern and process in the abundance and recruitment of Caribbean octocorals
https://osprey.bco-dmo.org/project/752508
Collaborative Research: Pattern and process in the abundance and recruitment of Caribbean octocorals
<p><em>NSF Award Abstract:</em><br />
Coral reefs are exposed to a diversity of natural and anthropogenic disturbances, and the consequences for ecosystem degradation have been widely publicized. However, the reported changes have been biased towards fishes and stony corals, and for Caribbean reefs, the most notable example of this bias are octocorals ("soft corals"). Although they are abundant and dominate many Caribbean reefs, they are rarely included in studies due to the difficulty of both identifying them and in quantifying their abundances. In some places there is compelling evidence that soft corals have increased in abundance, even while stony corals have become less common. This suggests that soft corals are more resilient than stony corals to the wide diversity of disturbances that have been impacting coral corals. The best coral reefs on which to study these changes are those that have been studied for decades and can provide a decadal context to more recent events, and in this regard the reefs of St. John, US Virgin Islands are unique. Stony corals on the reefs have been studied since 1987, and the soft corals from 2014. This provides unrivalled platform to evaluate patterns of octocoral abundance and recruitment; identify the patterns of change that are occurring on these reefs, and identify the processes responsible for the resilience of octocoral populations. The project will extend soft coral monitoring from 4 years to 8 years, and within this framework will examine the roles of baby corals, and their response to seafloor roughness, seawater flow, and seaweed, in determining the success of soft corals. The work will also assess whether the destructive effects of Hurricanes Irma and Maria have modified the pattern of change. In concert with these efforts the project will be closely integrated with local high schools at which the investigators will host marine biology clubs and provide independent study opportunities for their students and teachers. Unique training opportunities will be provided to undergraduate and graduate students, as well as a postdoctoral researcher, all of whom will study and work in St. John, and the investigators will train coral reef researchers to identify the species of soft corals through a hands-on workshop to be conducted in the Florida Keys.</p>
<p>Understanding how changing environmental conditions will affect the community structure of major biomes is the ecological objective defining the 21st century. The holistic effects of these conditions on coral reefs will be studied on shallow reefs within the Virgin Islands National Park in St. John, US Virgin Islands, which is the site of one of the longest-running, long-term studies of coral reef community dynamics in the region. With NSF-LTREB support, the investigators have been studying long-term changes in stony coral communities in this location since 1987, and in 2014 NSF-OCE support was used to build an octocoral "overlay" to this decadal perspective. The present project extends from this unique history, which has been punctuated by the effects of Hurricanes Irma and Maria, to place octocoral synecology in a decadal context, and the investigators exploit a rich suite of legacy data to better understand the present and immediate future of Caribbean coral reefs. This four-year project will advance on two concurrent fronts: first, to extend time-series analyses of octocoral communities from four to eight years to characterize the pattern and pace of change in community structure, and second, to conduct a program of hypothesis-driven experiments focused on octocoral settlement that will uncover the mechanisms allowing octocorals to more effectively colonize substrata than scleractinian corals on present day reefs. Specifically, the investigators will conduct mensurative and manipulative experiments addressing four hypotheses focusing on the roles of: (1) habitat complexity in distinguishing between octocoral and scleractinian recruitment niches, (2) the recruitment niche in mediating post-settlement success, (3) competition in algal turf and macroalgae in determining the success of octocoral and scleractian recruits, and (4) role of octocoral canopies in modulating the flux of particles and larvae to the seafloor beneath. The results of this study will be integrated to evaluate the factors driving higher ecological resilience of octocorals versus scleractinians on present-day Caribbean reefs.</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>
Octocoral Community Dynamics
largerWorkCitation
project
RUI: Pattern and process in four decades of change on Caribbean reefs
http://coralreefs.csun.edu/
RUI: Pattern and process in four decades of change on Caribbean reefs
<p><em>NSF Award Abstract:</em><br />
The coral reef crisis refers to the high rates of death affecting tropical reef-building corals throughout the world, and the strong likelihood that coral reefs will become functionally extinct within the current century. Knowledge of these trends comes from the monitoring of coral reefs to evaluate their health over time, with the most informative projects providing high-resolution information extending over decades. Such projects describe both how reefs are changing, and answer questions addressing the causes of the changes and the form in which reefs will persist in the future. This project focuses on coral reefs in United States waters, specifically around St. John in the US Virgin Islands. These reefs are protected within the Virgin Islands National Park, and have been studied more consistently and in greater detail than most reefs anywhere in the world. Building from 33 years of research, this project extends monitoring of these habitats by another five years, and uses the emerging base of knowledge, and the biological laboratory created by the reefs of St. John, to address the causes and consequences of the bottleneck preventing baby corals from repopulating the reefs. The work is accomplished with annual expeditions, staffed by faculty, graduate students, undergraduates, and teachers, coupled with analyses of samples at California State University, Northridge, and Florida State University, Tallahassee. The students and teachers assist with the research goals at the center of this project, but also engage in independent study and integrate with the rich and diverse societal context and natural history of the Caribbean. The scope of the science agenda extends to schools in California, where students are introduced to the roles played by marine animals in ecosystem health, concepts of long-term change in the biological world, and the role of science engagement in promoting positive environmental outcomes. In addition to generating a wide spectrum of project deliverables focusing on scientific discovery, the project promotes STEM careers and train globally aware scientists and educators capable of supporting the science agenda of the United States in the 21st Century.</p>
<p>This project leverages one of the longest time-series analyses of Caribbean coral reefs to extend the time-series from 33 to 38 years, and it tests hypotheses addressing the causes and consequences of changing coral reef community structure. The project focuses on reefs within the Virgin Islands National Park (VINP) and along the shore of St. John, US Virgin Islands, and is integrated with stakeholders working in conservation (VINP) and local academia (University of the Virgin Islands). Beginning in 1987, the project has addressed detail-oriented analyses within a small spatial area that complements the large-scale analyses conducted by the VINP. The results of these efforts create an unrivaled context within which ecologically relevant hypotheses can be tested to elucidate mechanisms driving ecological change. Building from image- and survey- based analyses, 33 years of data reveal the extent to which these reefs have transitioned to a low-abundance coral state, and the importance of the bottleneck preventing coral recruits from contributing to adult size classes. The intellectual merits of this project leverage these discoveries to address eight hypotheses: (H1) long-term changes are defining a cryptic regime change, with the low coral abundance reinforced by, (H2) enhanced community resilience, (H3) low post-settlement success, (H4) negative effects of peyssonnelid algal crusts (PAC) on juvenile corals, (H5) inability of juvenile corals to match their phenotypes to future conditions, (H6) impaired population growth caused by reduced genetic diversity, (H7) the premium placed on PAC-free halos around Diadema sea urchins for coral recruitment, and (H8) biotic homogenization occurring on a landscape-scale.</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>Related Projects:</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
-64.7314
-64.7218
18.3074
18.3147
2019-07-26
2020-01-27
From projects that focused on the following 2 locations: 1. St. John, US Virgin Islands 2. United States Virgin Islands, St. John: 18.318, -64.7253
0
BCO-DMO catalogue of parameters from Canopy closure values from photographs taken within octocoral forests in Lameshur Bay St. John, U.S. Virgin Islands from July 2019 to Jan 2020
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/895189.rdf
Name: Closure_Photo_ID
Units: unitless
Description: <p>ID of photograph analyzed (Filename without .JPG extension)</p>
http://lod.bco-dmo.org/id/dataset-parameter/895190.rdf
Name: Site
Units: unitless
Description: <p>Name of Site</p>
http://lod.bco-dmo.org/id/dataset-parameter/895191.rdf
Name: lat
Units: decimal degrees
Description: <p>Site latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/895192.rdf
Name: lon
Units: decimal degrees
Description: <p>Site longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/895193.rdf
Name: Transect_Num
Units: unitless
Description: <p>Transect number</p>
http://lod.bco-dmo.org/id/dataset-parameter/895194.rdf
Name: Quadrat_Number
Units: unitless
Description: <p>Quadrat number</p>
http://lod.bco-dmo.org/id/dataset-parameter/895195.rdf
Name: Proportion_Closed
Units: unitless
Description: <p>Closure measurment calculated from the sum of all the points scored in each of the twenty boxes divided by 300</p>
http://lod.bco-dmo.org/id/dataset-parameter/895196.rdf
Name: Box_1
Units: points
Description: <p>Number of points in Box 1 of the grid superimposed on the closure photograph that fell on octocoral branches</p>
http://lod.bco-dmo.org/id/dataset-parameter/895197.rdf
Name: Box_2
Units: points
Description: <p>Number of points in Box 2 of the grid superimposed on the closure photograph that fell on octocoral branches</p>
http://lod.bco-dmo.org/id/dataset-parameter/895198.rdf
Name: Box_3
Units: points
Description: <p>Number of points in Box 3 of the grid superimposed on the closure photograph that fell on octocoral branches</p>
http://lod.bco-dmo.org/id/dataset-parameter/895199.rdf
Name: Box_4
Units: points
Description: <p>Number of points in Box 4 of the grid superimposed on the closure photograph that fell on octocoral branches</p>
http://lod.bco-dmo.org/id/dataset-parameter/895200.rdf
Name: Box_5
Units: points
Description: <p>Number of points in Box 5 of the grid superimposed on the closure photograph that fell on octocoral branches</p>
http://lod.bco-dmo.org/id/dataset-parameter/895201.rdf
Name: Box_6
Units: points
Description: <p>Number of points in Box 6 of the grid superimposed on the closure photograph that fell on octocoral branches</p>
http://lod.bco-dmo.org/id/dataset-parameter/895202.rdf
Name: Box_7
Units: points
Description: <p>Number of points in Box 7 of the grid superimposed on the closure photograph that fell on octocoral branches</p>
http://lod.bco-dmo.org/id/dataset-parameter/895203.rdf
Name: Box_8
Units: points
Description: <p>Number of points in Box 8 of the grid superimposed on the closure photograph that fell on octocoral branches</p>
http://lod.bco-dmo.org/id/dataset-parameter/895204.rdf
Name: Box_9
Units: points
Description: <p>Number of points in Box 9 of the grid superimposed on the closure photograph that fell on octocoral branches</p>
http://lod.bco-dmo.org/id/dataset-parameter/895205.rdf
Name: Box_10
Units: points
Description: <p>Number of points in Box 10 of the grid superimposed on the closure photograph that fell on octocoral branches</p>
http://lod.bco-dmo.org/id/dataset-parameter/895206.rdf
Name: Box_11
Units: points
Description: <p>Number of points in Box 11 of the grid superimposed on the closure photograph that fell on octocoral branches</p>
http://lod.bco-dmo.org/id/dataset-parameter/895207.rdf
Name: Box_12
Units: points
Description: <p>Number of points in Box 12 of the grid superimposed on the closure photograph that fell on octocoral branches</p>
http://lod.bco-dmo.org/id/dataset-parameter/895208.rdf
Name: Box_13
Units: points
Description: <p>Number of points in Box 13 of the grid superimposed on the closure photograph that fell on octocoral branches</p>
http://lod.bco-dmo.org/id/dataset-parameter/895209.rdf
Name: Box_14
Units: points
Description: <p>Number of points in Box 14 of the grid superimposed on the closure photograph that fell on octocoral branches</p>
http://lod.bco-dmo.org/id/dataset-parameter/895210.rdf
Name: Box_15
Units: points
Description: <p>Number of points in Box 15 of the grid superimposed on the closure photograph that fell on octocoral branches</p>
http://lod.bco-dmo.org/id/dataset-parameter/895211.rdf
Name: Box_16
Units: points
Description: <p>Number of points in Box 16 of the grid superimposed on the closure photograph that fell on octocoral branches</p>
http://lod.bco-dmo.org/id/dataset-parameter/895212.rdf
Name: Box_17
Units: points
Description: <p>Number of points in Box 17 of the grid superimposed on the closure photograph that fell on octocoral branches</p>
http://lod.bco-dmo.org/id/dataset-parameter/895213.rdf
Name: Box_18
Units: points
Description: <p>Number of points in Box 18 of the grid superimposed on the closure photograph that fell on octocoral branches</p>
http://lod.bco-dmo.org/id/dataset-parameter/895214.rdf
Name: Box_19
Units: points
Description: <p>Number of points in Box 19 of the grid superimposed on the closure photograph that fell on octocoral branches</p>
http://lod.bco-dmo.org/id/dataset-parameter/895215.rdf
Name: Box_20
Units: points
Description: <p>Number of points in Box 20 of the grid superimposed on the closure photograph that fell on octocoral branches</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
28599
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/a3a1c7ba-b91b-42bb-a29d-4f48ac18420f/content
download
https://doi.org/10.26008/1912/bco-dmo.892258.1
download
onLine
dataset
<p>Research was conducted from the University of the Virgin Islands Marine Station in Lameshure Bay during July – August 2019 and January 2020.<br />
<br />
Methods &amp; Sampling<br />
Quadrats were randomly placed along 20 m, non-overlapping transects that were positioned haphazardly along fringing reefs. Canopy closure was quantified using a modified method from (Jennings et. al. 1999) whereby a GoPro Hero 3+ camera with a 130° field of view (manufacturer’s specification, Go-Pro., Inc. San Mateo, CA) was used to record still images in the center, and at each of the four corners, of quadrats, with all five images quadrat-1 recorded within &lt; 5 minutes. To avoid biases in estimating canopy closure caused by adjacent non-living substrata (e.g., boulders and rock walls), images were excluded when they included these features. Images were analyzed using ImageJ software (v1.52a, Schneider et al., 2012), in which 300 randomly located dots (~ 0.5 pixel in diameter) were superimposed on each image. The number of dots on the octocoral canopy were counted and expressed as a percentage of the dot population. This metric was used to quantify canopy closure, and the results from the five images quadrat-1 were averaged to characterize each quadrat.</p>
<p>Instruments<br />
PVC Quadrats (1 m2)<br />
Transect tapes<br />
GoPro Hero 3+ camera</p>
Specified by the Principal Investigator(s)
<p>Data processing<br />
To calculate canopy closure images were analyzed using ImageJ software (v1.52a, Schneider et al., 2012), in which 300 randomly located dots (~ 0.5 pixel in diameter) were superimposed on each image. The number of dots on the octocoral canopy were counted and expressed as a proportion of the dot population. To aid in the quantification of dots a grid of twenty squares was superimposed on the image. Each "box" was scored for the number of points in it that fell on the octocoral canopy. All twenty boxes for each image were summed for the total points out of 300 falling on the octocoral canopy.</p>
<p>BCO-DMO Data Manager Processing Notes:<br />
* File "St.John_Octocoral Forest Closure Photo Analysis for Community Quadrats.csv" imported as the primary table for this dataset.<br />
* Supplemental files shared with other related datasets also added here (site list, photo inventory, photos).<br />
* Photo ID transformed to be uppercase in this data table to match the actual file names.<br />
* lat lon values added into the table by joining with the site list.<br />
*&nbsp;Proportion_Closed rounded to three decimal places.<br />
* Column names adjusted to conform to BCO-DMO naming conventions designed to support broad re-use by a variety of research tools and scripting languages. [Only numbers, letters, and underscores.&nbsp; Can not start with a number]</p>
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
GoPro Hero 3+ camera
GoPro Hero 3+ camera
PI Supplied Instrument Name: GoPro Hero 3+ camera 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/