Table of Contents

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

Features of Millepora species are examined along with environmental parameters to determine what affects morphology. 

This study was undertaken at Cabritte Horn on the south shore of St. John, US Virgin Islands across three decades. 

Photographic quadrat sampling
Photographic sampling of quadrats (0.5 meters x 0.5 meters) was performed annually from 1992 to 2021 using cameras mounted on a framer at a fixed height above the reef.  Color slide film was used from 1992–2000 (and digitized at 4000 dpi), with digital photography implemented in 2001. Photoquadrats were recorded at random positions along the transect, which was 20 meters long from 1992–1999 and 40 meters long from 2000 onward when the sample size was increased to ~40 photoquadrats per year.   

The photoquadrats were used to quantify Millepora abundance using ImageJ software (Abràmoff et al., 2004), and taxa were resolved to the M. alcicornis/M. complanata complex (hereafter described as M. alcicornis). As 99.8% of colonies were M. alcicornis, all colonies were considered to be a single species and described as Millepora sp. Areas of encrusting Millepora sp. were located in each photoquadrat, and outlined and measured for area with all pieces of encrusting sheets quantified separately. Because Millepora species’ sheet forms meander across the substratum and are prone to fission, it was not always clear where colonies began or ended within photoquadrats. Colonies therefore were defined as areas of autonomous tissue, so portions of colonies that were partially within the photoquadrats were scored as separate colonies (although such cases were relatively uncommon).

To access images, see Related Publications section below for Coral Image Downloads and Viewer link (Cabritte Horn images under "Random Sites")   

Morphology
Branches on each sheet were quantified as the number of proximal “roots” where they attached to the encrusting sheet, and as the number of distal growing points on each root. Branch fragments lying on the benthos were not counted. The size of Millepora sp. colonies was determined from the mean planar area of autonomous portions of sheets (cm²), and roots and growing points were normalized to the sheet (Roots 100 cm² and Growing Points 100 cm²) and colony (Roots per colony and growing points per colony); growing points were also expressed per root (Growing Points per root). The area of sheets were summed by quadrat and used to calculate the percentage cover of Millepora sp. (%).  Occasionally Millepora sp. was found encrusting octocoral colonies on which they appeared as long branches with miniscule sites of basal attachment; such colonies were excluded from analyses of roots and growing points.

The capacity of Millepora species to exploit a sheet-tree morphology was quantified through the quotient of roots and growing points to the area of the sheet (Roots 100 cm-2 and Growing Points 100 cm-2). Quotients quantified the exploitation of  “trees” relative to “sheets”, but they have the limitation of not being able to distinguish between effects caused by the growth of new roots or growing points versus changes in absolute area of the sheets. The relationships between these quotients and environmental conditions (rainfall, seawater temperature, hurricanes) were evaluated using generalized additive models (GAMs) that supported tests for complex non-linear relationships with multiple predictors. GAMs were prepared using the mgcv package (version 1.8-34) (Wood, 2011; Wood, 2017) in R (version 4.0.5), accessed through the XLSTAT (version 2021.2.1, Addinsoft, Paris) add-in to Excel16.54 (Microsoft). Models were run using Gaussian errors, cubic splines, and variance components estimated by REML. Restricted Maximum Likelihood Models were restricted to three quantitative effects to enhance interpretation (Fisher et al., 2018), and the best model was identified from the lowest corrected Akaike Information Criterion (AICc) (Burnham & Anderson, 2004). Summary of model selection using GAMs is detailed in Table S2 of Edmunds (2022).

Environmental parameters
Rainfall values from thirty years of monthly rainfall measurements (in centimeters) are presented in a supplemental document.  From 1991 to 2011 rainfall values were obtained from the Southeastern Regional Climate Center (www.sercc.com), which compiled data from a rain gauge in Cruz Bay, St. John (Station 671980). Where this record was incomplete, values were obtained from Catherinburg (Station 671348), East End (Station 672551), or through interpolation. From 2012 onward, rainfall was measured using a Standard Rain Gauge (NOAA, National Weather Service) deployed on the north shore of St. John (18.3558°N, -64.7660° W) at Station VI-SJ-3 (https://wys.cocorahs.org). 

Seawater temperature was measured with loggers (primarily Onset Computer Corp., Hobo U22-001, ± 0.2°C) sampling at 0.0011Hz and located ~ 900 m from Cabritte Horn at Yawzi Point (Edmunds & Gray, 2014). Temperature was averaged by day and month to characterize the mean of the hottest three months prior to each sampling (“Temperature1”, August–October, mean ± SE, n = 3), and between 31 July and the previous 1 August by study year (“Temperature2”, mean ± SE, n = 12 months).  Mean seawater temperatures can be accessed here: https://www.bco-dmo.org/dataset/875694, and in the Related Datasets section.

Hurricanes and intensity were evaluated as a qualitative effect. Ranks were assigned based on hurricane tracks (https://www.nhc.noaa.gov) in conjunction with local knowledge of wind speeds and impact.  Years of major hurricanes were assigned a rank of one (1), and all other years a rank of zero (0).  Major storms affecting the St.John study area include Hurricanes Marilyn (1995), Georges (1998), Lenny (1999), Earl (2010), Irma (2017) and Maria (2017) which occurred in the Fall (Sep-Nov). Since ecological sampling was performed in July/August, the impact of these Fall storms was first recorded in the photoquadrat images taken 8-10 months later (in the following calendar year). For example, Hurricanes Irma and Maria occurred in September 2017, but any effect on the Millepora at Cabritte Horn was not detected until  sampling took place in Summer of the subsequent year.  Please refer to the "Hurricane ranking" file in the Supplemental Files section for additional details.  

Statistical analyses
The morphology of Millepora sp. (log transformed), macroalgal cover (arcsine transformed), and temperature were compared among years using one way ANOVAs with Bonferonni post hoc analyses to compare between years (using Systat 13 software).

BCO-DMO processing
- converted Date to YMD format
- added columns for latitude and longitude
- added columns for location and camera type
- added conventional header with dataset name, PI name, version date
- modified parameter names to conform with BCO-DMO naming conventions

This project has been supported by continuing grants:
OCE-2019992 "RUI: Pattern and process in four decades of change on Caribbean reefs"  (2020-2026)
OCE-2546549 "RUI Pattern and process in five decades of change on Caribbean reefs" (2026-2029)

NSF award OCE-2546549 project summary:

Overview

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.

Intellectual merit

The intellectual merits lie in the hypotheses focused on the mechanisms leading to persistent low abundance coral communities. This project is 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: H₁ Coral reef community structure is converging to a stable low coral abundance state; H₂. The impact of disturbances is mediated by the spatial structuring of community dynamics, and the expression of portfolio effects; H₃ Intensification of the coral recruitment ‘bottleneck’ and its gradual transition to settlement failure; H₄ Declining populations sizes of echinoids limit the formation of grazing halos in which corals settle; H₅ Persistence of low abundance coral communities is favored by changes in the symbiodiniacaea complement.

Broader impacts

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.

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