Data Management Plan

The coral reef benthic community data described here result from the annotation (classification) of benthic images collected during photoquadrat surveys conducted by the NOAA Pacific Islands Fisheries Science Center (PIFSC), Ecosystem Sciences Division (ESD, formerly the Coral Reef Ecosystem Division) as part of NOAA's ongoing National Coral Reef Monitoring Program (NCRMP). The photoquadrat surveys were conducted at coral reef sites according to protocols established by ESD and NCRMP during ESD-led NCRMP missions to the islands of the Mariana Archipelago in 2014, 2017, and 2022.

SCUBA divers conducted benthic photoquadrat surveys at permanent sites established in coral reef habitats by ESD. A select number of these sites were chosen in hard-bottom habitat at ~15-m depths, and a subset of the permanent sites (climate stations) were established at north, south, east, and west points around each of the islands. The divers estimated and delineated each site's rectangular perimeter by temporarily placing measuring tapes with 1-m markers starting from a permanently installed reference stake on the reef. Along the nearshore 10-m side of the survey site and the downslope 5-m side, the measuring tapes marked every meter of the L-shaped 15-m transect used for photoquadrat documentation. The divers photographed the reef at 1-m intervals on both sides of the 15-m tape, generating 20-30 photographs per survey site.

The benthic habitat images were quantitatively analyzed using Coral Point Count with Excel extensions (CPCe; Kohler and Gill, 2006) software from 2010-2014 and the web-based annotation tool, CoralNet (Beijbom et al. 2015), from 2015 to present. Ten points were randomly overlaid on each image and human analysts identified the organism or type of substrate beneath, with 300 annotations (points) generated per site. Benthic elements falling under each point were identified to genus/morphology for hard corals, and to genus/functional group for algae, invertebrates, and other taxa following Lozada-Misa et al. (2017). In general, the analysis resulted in three levels of benthic community data, including taxa group (Tier 1: hard coral, soft coral, macroalgae, turf algae, etc.), morphology (Tier 2: massive, branching, upright macroalgae, etc.), and genus (Tier 3). These benthic data can ultimately be used to produce estimates of relative abundance (percentage of benthic cover), frequency of occurrence, benthic community taxonomic composition, and relative generic richness.

Lineage Statement:
Benthic photographs were collected during photoquadrat surveys conducted at permanent sites and climate stations in coral reef habitats by the PIFSC Ecosystem Sciences Division. The imagery was later analyzed using Coral Point Count with Excel Extentions (CPCe; 2014 and prior) or CoralNet (starting in 2015) to generate benthic community data.

Process Steps:

• SCUBA divers conduct benthic photoquadrat surveys at permanent sites established in hard-bottom habitat at ~15-m depths. A subset of the permanent sites (climate stations) were established at north, south, east, and west points around the island/atoll. The divers estimate and delineate each site’s rectangular perimeter by temporarily placing measuring tapes with 1-m markers starting from a permanently installed reference stake on the reef. Along the nearshore 10-m side of the survey site and the downslope 5-m side, the measuring tapes mark every meter of the L-shaped 15-m transect used for photoquadrat documentation. Divers photograph the reef at 1-m intervals on both sides of the 15-m tape, generating 30 photographs per survey site. Photoquadrat images are organized by site, color-corrected (if necessary), and quality controlled to remove non-photoquadrat/poor quality images. An optical validation script is used to re-name photos and enforce several validation checks.
• Benthic habitat images collected during photoquadrat surveys at permanent sites and climate stations (30 images per site) were quantitatively analyzed using Coral Point Count with Excel extensions (CPCe; Kohler and Gill 2006) software through 2014 or by using the web-based annotation tool CoralNet (Beijbom et al. 2015) from 2015 to present. Ten points were randomly overlaid on each image by CPCe or CoralNet and human analysts identified the organism or type of substrate beneath, with 300 annotations (points) generated per site. Benthic elements falling under each point were identified to genus/morphology for hard corals, and to genus/functional group for algae, invertebrates, and other taxa following Lozada-Misa et al. (2017). The analysis resulted in three levels of benthic community data, including taxa group (Tier 1: hard coral, soft coral, macroalgae, turf algae, etc.), morphology (Tier 2: massive, branching, upright macroalgae, etc.), and genus (Tier 3). The detailed list of each functional group level or tier is included in the benthic image analysis classification scheme. (Citation: Lozada-Misa P, Schumacher BD, Vargas-Angel B. 2017. Analysis of benthic survey images via CoralNet : a summary of standard operating procedures and guidelines. Pacific Islands Fisheries Science Center, PIFSC Administrative Report, H-17-02, 169 p.)
• Raw survey data includes unique image name, individual point observations identified at three levels, and the corresponding physical data that reflect the description of the site. The physical data includes: region, island, site, date, latitude, longitude, reef zone, and depth.

Quality control is enforced by means of point-to-point, inter-observer calibration exercises that are conducted before each image analysis production series. Additionally, training modules and standard operating procedures have been developed and documented to ensure improved performance and consistent analysis results produced by multiple analysts.

Data can be accessed online via the NOAA National Centers for Environmental Information (NCEI) Ocean Archive.

Quality control is enforced by means of point-to-point, inter-observer calibration exercises that are conducted before each image analysis production series. Additionally, training modules and standard operating procedures have been developed and documented to ensure improved performance and consistent analysis results produced by multiple analysts.