Table of Contents

• Coverage
• Dataset Description
  • Methods & Sampling
  • Data Processing Description
• Data Files
• Supplemental Files
• Related Publications
• Related Datasets
• Parameters
• Instruments
• Project Information
• Funding

Location: St. John, US Virgin Islands (18.315°N, 64.716°W), Multiple field expeditions to the USVI between 2011 and 2021.

Material and methods

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 > 5 mm diameter.

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”.

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.

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.

See Edmunds & Smith (2022) for statistical analyses that used these data.  Statistical software used: Systat 13, PRIMER 6.

Issue note: Some sampling non-consecutive in date columns.

Image processing in CoralNET (Chen et al., 2021).

BCO-DMO Data Manager Processing Notes:

* Data from source file "Data in paper 4 March 2022_Marine_Biology copy.xls" Sheet1 were imported into the BCO-DMO data system.

* Percent cover values imported from Excel were 16 decimal places long. Rounded them to 2.

* Parameters (column names) renamed to comply with BCO-DMO naming conventions. See https://www.bco-dmo.org/page/bco-dmo-data-processing-conventions

* Site list extracted from Table 1 of publication Edmunds (2014).  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.

* Site list joined into this dataset to add additional columns lat,lon, site_code from Edmunds (2014).

* Checked organism taxon names using World Register of Marine Species taxa match tool on 2022-03-25.  Taxon list with the names used in the dataset and the matched accepted name and IDs added to supplemental files for this dataset.  
* Unmatched taxon names in dataset changed accepted taxon names after discussion with data submitter (Mycetopohyllia changed to Mycetophyllia , M. cavernosa changed to Montastraea cavernosa ). Supplemental species list updated.
* 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.  These sites between the two references were the same sites:
"Cow and Calf", "Cow and Calves"
"Flat Cay","south Flat Cay"
"Inner Brass","north Inner Brass Cay"
"Waterlemon Cay","north Waterlemon Cay"
* site lat,lon and site codes extracted from Edmunds, P. (2014) and added to this dataset (site list verified by submitter).
* site list added as a supplemental file.

NSF Award Abstract:
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.

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.

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.

Related Projects:

• Affiliated with MCR-LTER - https://www.bco-dmo.org/project/2222
• 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 - https://www.bco-dmo.org/project/734983
• 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 - https://www.bco-dmo.org/project/752508
• LTREB Long-term coral reef community dynamics in St. John, USVI: 1987-2019 - https://www.bco-dmo.org/project/2272
• RUI: Pattern and process in four decades of change on Caribbean reefs - https://www.bco-dmo.org/project/835192
• RAPID: Hurricane Irma: Effects of repeated severe storms on shallow Caribbean reefs and their changing ecological resilience - https://www.bco-dmo.org/project/722163