Dataset: Octocoral Sensus Data for Light Quadrats at Yawzi Point and East Cabritte sites in St. John, U.S. Virgin Islands

Name: Octocoral canopy metrics (mean height, density, and closure) in St. John, US Virgin Islands in March of 2019
Published: 2023-03-21
Keywords: oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.892293.1

Spatial Extent: N:18.3154 E:-64.7186 S:18.3096 W:-64.7252

Temporal Extent: 2019-03-09 - 2019-03-11

Project:

Collaborative Research: Pattern and process in the abundance and recruitment of Caribbean octocorals (Octocoral Community Dynamics)

RUI: Pattern and process in four decades of change on Caribbean reefs (St John Coral Reefs)

Principal Investigator:

Peter J. Edmunds (California State University Northridge, CSUN)

Student:

John Girard (California State University Northridge, CSUN)

BCO-DMO Data Manager:

Amber D. York (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2023-03-21

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Octocoral canopy metrics (mean height, density, and closure) in St. John, US Virgin Islands in March of 2019

Abstract:

These data represent the octocoral canopy metrics (mean height, density, and closure) in quadrats (1 m2) where light regimes were quantified. Surveys took place at the Yawzi Point (~8-m depth) and East Cabritte (~9-m depth) sites in St. John, U.S. Virgin Islands during March of 2019. These data were collected as part of an NSF Coral Reef Time Series, Virgin Islands: Long-term coral reef community dynamics in the Virgin Islands National Park and were published in Girard and Edmunds (2023).

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2023-03-21	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.892293.1	2023-05-24

Methods & Sampling

Location:
Yawzi Point and East Cabritte sites along the south shore of St. John, U.S. Virgin Islands at ~8–9-m depth
Research conducted from the University of the Virgin Islands Marine Station in Lameshur Bay during March 2019.

Methods & Sampling:

Quadrats (1m2) were placed such that the light logger was at its center. Octocorals were counted and measured if their holdfasts were present within the quadrat. Height was measured as the distance from the holdfast to the most distal branch relatively perpendicular to the benthos.

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 < 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.

Instruments:
Quadrat (1m2)
Ribbon Tape with mm graduations
GoPro Hero 3+

Data Processing Description

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 percentage 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.

BCO-DMO Data Manager Processing Notes:
* File "St.John_Octocoral Forest Metrics for Light Data_March2019.csv" imported as the primary table for this dataset.
* lat lon values added into the table by joining with the site list.
* site name added to data table
* Date converted to ISO 8601 format
* Mean_Closure rounded to three decimal places
* 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. Can not start with a number]

Data Files

File
canopy_metrics.csv (Comma Separated Values (.csv), 846 bytes) MD5:6484efaa50b8fc9fdd1ce5ba03dd934f Primary data table for dataset 892293.

Supplemental Files

File

Site List
filename: site_list.csv

(Comma Separated Values (.csv), 192 bytes)
MD5:4415feb2d663fc251a671a2a7c5cac04

Site list for all dataset related to the results publication Girard and Edmunds (2023). 

Parameters (column names, descriptions, and units): 

Site, Site name used in dataset related to Girard and Edmunds (2023),unitless
lat, Site latitude,decimal degrees
lon,Site longitude,decimal degrees
Alternate_name, Alternate name for the site,unitless

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1756678
NSF Division of Ocean Sciences	OCE-2019992

Deployments

None available yet

Instruments

Camera

Supplied Name: GoPro Hero 3+

Supplied Description:

Instrument Type

Generic Name: Camera

Acronym: camera

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/311/

Generic Description:

All types of photographic equipment including stills, video, film and digital systems.

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
Date	Date of octocoral survey Format: %Y-%m-%d	unitless	date
Site	Name of site	unitless	site
lat	Site latitude	decimal degrees	lat
lon	Site longitude	decimal degrees	lon
Canopy_State	Broad Canopy Classification of quadrat placement	unitless	sample_descrip
Depth	Depth of quadrat	meters (m)	depth
Quadrat_ID	Number given to quadrat, in sequence, at a particular site as an identifyer	unitless	sample_descrip
Mean_Octocoral_Height	Mean height of ocotocoral within a quadrat	centimeters (cm)	height
Density	Density of octocorals within a quadra	individuals/m2	density
Mean_Closure	Proportion of sky obscured by the octocoral canopy	unitless	no_bcodmo_term
HOBO_ID	Recorded identifying number of the HOBO data logger at the center of the quadrat	unitless	Sensor_Id

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Database

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Dataset: Octocoral Sensus Data for Light Quadrats at Yawzi Point and East Cabritte sites in St. John, U.S. Virgin Islands