| Program | Site | Island | Depth (m) | Year added |
|---|---|---|---|---|
| TCRMP | Great Pond | STX | 4.0 | 2003 |
| Brewers Bay | STT | 6.0 | 2002 | |
| Fish Bay | STJ | 6.0 | 2002 | |
| Castle | STX | 7.0 | 2003 | |
| Coculus Rock | STT | 7.0 | 2002 | |
| Magens Bay | STT | 7.0 | 2002 | |
| Botany Bay | STT | 8.0 | 2002 | |
| Sprat Hole | STX | 8.0 | 2002 | |
| Black Point | STT | 9.0 | 2003 | |
| Savana | STT | 9.0 | 2003 | |
| Cane Bay | STX | 10.0 | 2002 | |
| Eagle Ray | STX | 10.0 | 2002 | |
| Salt River West | STX | 11.0 | 2002 | |
| Flat Cay | STT | 12.0 | 2003 | |
| Buck Island STT | STT | 14.0 | 2005 | |
| Jacks Bay | STX | 14.0 | 2002 | |
| Buck Island STX | STX | 15.0 | 2002 | |
| St James | STT | 15.0 | 2005 | |
| Seahorse Cottage Shoal | STT | 20.0 | 2003 | |
| South Water | STT | 20.0 | 2005 | |
| VINPS | VIIS-Newfound | STJ | 7.9 | 1999 |
| VIIS-Haulover | STJ | 8.2 | 2003 | |
| BUIS-Western Spur and Groove | STX | 9.4 | 2000 | |
| VIIS-Yawzi | STJ | 11.3 | 1999 | |
| BUIS-South Fore Reef | STX | 12.5 | 2002 | |
| VIIS-Mennebeck | STJ | 13.7 | 2000 | |
| VIIS-Tektite | STJ | 17.7 | 2005 | |
| CSUN | West Little Lameshur | STJ | 7.0 | 1992 |
| Yawzi | STJ | 9.0 | 1987 | |
| Cabritte Horn | STJ | 9.0 | 1992 | |
| East Tektite | STJ | 9.0 | 1992 | |
| Europa Bay | STJ | 9.0 | 1992 | |
| White Point | STJ | 9.0 | 1992 | |
| Tektite | STJ | 14.0 | 1987 |
benthic cover
about
2.1 Reformat raw benthic cover data
2.2 Cross-reference benthic codes
2.3 percentage cover of main benthic categories
2.4 percentage cover of coral genera
2.5 percentage cover of coral species
2.6 percentage cover of coral trait groups
2.7 percentage cover of algae taxa
2.8 percentage cover of sponge morphs
2.9 percentage cover of zoanthids and gorgonians
2.10 percentage cover of other benthic categories
VI Reef Resilience Study
(Any Others?)
Overview
About this study
Olinger LK, Edmunds PJ, Levitan D, Smith TB, Lasker H, Feeley M, Mahoney L, Dahl A. Reproductive mode, but not rarity, influences population trajectories in corals. In Review 2026.
About this study
This analysis accompanies the manuscript above on how reproductive mode and rarity relate to long term coral population trajectories in the U.S. Virgin Islands. It presents four analyses, one per monitoring program: TCRMP, VINPS, and CSUN track coral cover on the reef, and the octocoral program tracks octocoral colony density.
The coral-cover data behind the TCRMP, VINPS, and CSUN analyses comes from the Reef Code benthic cover section. A species-level file backs TCRMP and VINPS (coral species cover download); a genus-level file backs CSUN (coral genera cover download).
Two versions of each analysis
Each analysis appears in two versions. Open a program from the Publications menu to read the as submitted version, then use the toggle at the top of the page to switch to the updated version and back (as of July 2026, the two are the same).
The as submitted version reruns the analysis exactly as in the manuscript. TCRMP and VINPS clip to 2001–2023, CSUN to 1992–2023, and the octocoral program to 2014–2024.
The updated version reruns the identical analysis: same code, same site and taxon scoping. Only the year range changes. Comparing the two side by side shows whether the pattern reported in the paper is holding, strengthening, or shifting as the record grows.
The monitoring programs
Our study used time-series analyses on the fringing reefs of St. John, St. Thomas, and St. Croix, US Virgin Islands (Figure 1, Table 1). Each program has been established for at least two decades, and each involves annual transect and quadrat surveys at permanent sites across the USVI with different taxonomic foci, resolution, methods, and spatial extent. While combining studies introduces limitations with respect to the contrasts that can be supported, as we show, independent analyses combine to create emergent properties when common results are obtained. For stony corals, the study conducted at the largest spatial scale was completed at 20 sites around all three islands since 2001 by the Territorial Coral Reef Monitoring Program (hereafter “TCRMP”; (1, 2)). The study with most extensive sampling (n = 20 transects / site) was completed at 7 sites since 2001 by the VI National Park Service (hereafter “VINPS”; (3, 4)). The longest study comes from 8 sites (7–14 m depth) between White Point and Cabritte Horn, St. John, that have been studied since 1992 by California State University Northridge (hereafter “CSUN”; (5)).
The Territorial Coral Reef Monitoring Program (TCRMP)
The Territorial Coral Reef Monitoring Program (TCRMP) was established in 2001 (1). Sites were selected to represent a range of reef types and depths across the US Virgin Islands. This analysis focuses on 20 shallow (0-20m) sites. At each site, benthic cover surveys are conducted annually along six 10 m long permanent transects marked with steel or brass rods. Video are recorded along transects with a high definition digital video recorder (most recently a Sony a6500 with Sola Video 3800 lights) located approximately 40 cm above the reef contour. After taping, non-overlapping images from each transect are captured and superimposed with randomly placed dots (380 points/transect). Living and non-living substrate are identified and used to calculate percent cover. Coral and some algae are identified to genera or species when possible, and sponges and gorgonians are identified by morphology. The video and images are permanently stored as a historical record of reef condition and are available for more detailed analyses (2).
The Virgin Islands National Park (VINPS)
The Virgin Islands National Park Service (VINPS) monitoring program data used here (3, 4) focuses on 7 reefs (see Figure 1) around St. John and within Virgin Islands National Park, and within Buck Island Reef National Monument on St. Croix at 4 to 20 meters depth. Sites were chosen for their historical high coral cover, physical complexity, species diversity and high-relief, rugose habitat (linear reef) and well defined boundaries. The sampling employs 20 permanent marked and randomly selected 10 m transects that are recorded with a digital video camera (Panasonic DMC-GH4 fitted with two Light & Motion Sola Video 3800, and a 14 - 42 mm F/3.5-5.6 Olympus M.Zuiko lens) (3). The transects are marked by copper-clad start and end pins. The videos are analysed as sequential still “frames” and 10 dots are randomly placed upon each image and the substratum on which they occur is categorized as coral (by species), algae (macroalgae, turf, or crustose coralline), octocorals (sea fans, etc.), sponges, and bare substratum. The sites are typically surveyed annually in February to April in St. Croix and September to October in St. John.
The California State University Northridge (CSUN)
The California State University Northridge (CSUN) program data (5) come from an analysis of 8 sites that were established in 1992 on hard substrata at 7-9 m depth on the fringing reefs between White Point and Cabritte Horn. Sites were permanently marked with stainless steel poles, and each consisted of a single 20 m transect from 1992 to 2000, and thereafter were increased to 40 m. Transects were oriented along the isobath, and annually were sampled (mostly in July) using photoquadrats (0.5 \(\times\) 0.5 m) placed at random positions every year. There were 18 photoquadrats/site from 1992 to 2000, and 40 photoquadrats/site thereafter. From 1992-2001 photoquadrats were recorded on color slide film in a Nikonos V camera, and thereafter were recorded digitally with cameras increasing from 3.3 megapixels (Nikon Coolpix 990) to 45.7 megapixels (Nikon D850). Cameras were fitted to a rigid framer that held them perpendicular to the reef, and images were illuminated with two strobes (Nikonos SB105). Color slides were digitized and all images were analyzed for benthic space holders using CPCe or CoralNET software. Images were overlaid with a grid of 200 randomly-located dots that were manually annotated by functional group and to the lowest taxonomic level possible for scleractinians. For this analysis, 8 sites were utilized and results are reported for scleractinians with genus resolution because of limited resolution on some of the images and the low coral cover encountered.
Octocorals
As a comparison to the scleractinian coral data, another dataset of octocoral surveys was subjected to identical analyses. Octocoral data come from three sites (Grootpan Bay, Europa Bay, and Tektite) at 7–9 m depth on the southern shore of St. John, from 2014 (described in (6) and (7)). Briefly, octocorals are counted by species in 1 m\(^2\) quadrats, randomly placed on each of 6 parallel, 10 m long transects, with surveys completed in July and August of each year. Censuses were not conducted in 2021 and 2023 due to logistical constraints, but event sampling was conducted in November 2017, shortly after Hurricanes Irma and Maria struck St. John. The number of quadrats sampled differed among transects based on the abundance of octocorals at each site, with sites having the fewest octocoral colonies sampled most intensively. The number of quadrats increased at all sites over the 10-year period to enhance resolution of the study. Quadrats were positioned randomly with respect to position along, and side of, the transect. Colonies were identified to species, or to a species group of 2 or 3 congeners.
Reproductive mode and rarity
The following was repeated independently for each program. First, the highest taxonomic resolution of benthic cover data were aggregated for each site and year. For each taxon, we retained site-taxon combinations where the taxon was observed at least once during the study period, assuming that if a taxon was never observed at a site, that site lay outside the taxon’s range. The first five years of the data were aggregated (2001-2005 for TCRMP and VINPS; 1992-1996 for CSUN) and taxa were sorted and categorized as common (representing the top 90% of cumulative cover) or rare (representing the bottom 10% of cumulative cover). Taxa not recorded during the baseline period were excluded from subsequent trend analyses, so that modeled slopes reflect only species present at the outset of each monitoring program (each program’s excluded taxa are listed on its analysis page). A sliding window sensitivity analysis, in which the cumulative cover threshold was systematically varied across the species rank distribution, identified the 90% cumulative cover threshold as the strictest definition of rarity (i.e., the smallest rare group) at which temporal slope estimates remained insensitive to the reclassification of individual species between groups. Taxa were also categorized as broadcast spawners or brooding spawners (Table 2). For genera-level data in CSUN, the genus was assigned the reproductive mode that is most common in the genus, or most common in the subspecies found in the region.
The ‘baseline abundance’ for coral taxa in each project was defined as the mean percentage cover across the first five years of sampling (starting 1992 for CSUN and 2001 for TCRMP and VINPS), and it was evaluated after the onset of regional coral mortality that commenced in the 1980s (8–10). The determinations of rare and common are therefore not relative to a ‘natural’ reef (sensu 11), but our baseline abundance ranks are similar to those prepared for Caribbean reefs in the 1950s and 1960s (12) as well as the fossil record for at least 95,000 years (13). Orbicella spp., for example, has remained one of the most abundant broadcasting corals in the present projects and has been recorded as a dominant reef-builder throughout the region in the fossil record from the Pleistocene (14). Populations of O. annularis and O. faveolata increased in abundance and spatial extent around 2–1 million years ago (MYA) following the Pliocene-Pleistocene extinction of the sister species O. nancyi (15).
Abundance was measured as percentage cover, a standard metric for colonial organisms (10, 16), and we applied a \(\log_{10}\) transformation to produce slope estimates representing annual proportional rates of change (17, 18).
| Taxon | Repro. mode | TCRMP | VINPS | CSUN |
|---|---|---|---|---|
| Acropora | Broadcaster | - | - | Rare |
| Acropora cervicornis | Broadcaster | Rare | Rare | - |
| Acropora palmata | Broadcaster | Rare | - | - |
| Agaricia | Brooder | - | - | Rare |
| Agaricia agaricites | Brooder | Common | Rare | - |
| Agaricia fragilis | Brooder | Rare | - | - |
| Agaricia grahamae | Brooder | Rare | - | - |
| Agaricia humilis | Brooder | Rare | - | - |
| Agaricia lamarcki | Brooder | Rare | - | - |
| Agaricia tenuifolia | Brooder | Rare | - | - |
| Colpophyllia | Broadcaster | - | - | Rare |
| Colpophyllia natans | Broadcaster | Rare | Rare | - |
| Dendrogyra | Broadcaster | - | - | Rare |
| Dendrogyra cylindrus | Broadcaster | Rare | Rare | - |
| Dichocoenia | Broadcaster | - | - | Rare |
| Dichocoenia stokesii | Broadcaster | Rare | Rare | - |
| Diploria | Broadcaster | - | - | Rare |
| Diploria labyrinthiformis | Broadcaster | Rare | Rare | - |
| Eusmilia | Broadcaster | - | - | Rare |
| Eusmilia fastigiata | Broadcaster | Rare | Rare | - |
| Favia | Brooder | - | - | Rare |
| Favia fragum | Brooder | Rare | Rare | - |
| Helioseris cucullata | Brooder | - | Rare | - |
| Isophyllia sinuosa | Brooder | Rare | Rare | - |
| Isopyhyllastrea rigida | Brooder | Rare | - | - |
| Madracis | Brooder | - | - | Rare |
| Madracis decactis | Brooder | Rare | Rare | - |
| Madracis formosa | Brooder | Rare | - | - |
| Madracis mirabilis | Brooder | Common | Rare | - |
| Manicina | Brooder | - | - | Rare |
| Manicina areolata | Brooder | Rare | - | - |
| Meandrina | Broadcaster | - | - | Rare |
| Meandrina meandrites | Broadcaster | Rare | Rare | - |
| Montastraea | Broadcaster | - | - | Rare |
| Montastraea cavernosa | Broadcaster | Common | Common | - |
| Mussa | Brooder | - | - | Rare |
| Mycetophyllia aliciae | Brooder | Rare | Rare | - |
| Mycetophyllia daniana | Brooder | Rare | - | - |
| Mycetophyllia ferox | Brooder | Rare | Rare | - |
| Mycetophyllia lamarckiana | Brooder | Rare | Rare | - |
| Orbicella | Broadcaster | - | - | Common |
| Orbicella annularis | Broadcaster | Common | Common | - |
| Orbicella faveolata | Broadcaster | Common | Rare | - |
| Orbicella franksi | Broadcaster | Common | Common | - |
| Porites | Brooder | - | - | Common |
| Porites astreoides | Brooder | Common | Common | - |
| Porites divaricata | Brooder | Rare | - | - |
| Porites furcata | Brooder | Rare | Rare | - |
| Porites porites | Brooder | Common | Common | - |
| Pseudodiploria clivosa | Broadcaster | Rare | Rare | - |
| Pseudodiploria strigosa | Broadcaster | Common | Common | - |
| Siderastrea | Broadcaster | - | - | Common |
| Siderastrea radians | Brooder | Rare | Rare | - |
| Siderastrea siderea | Broadcaster | Common | Common | - |
| Solenastrea bournoni | Broadcaster | Rare | - | - |
| Solenastrea hyades | Broadcaster | Rare | - | - |
| Stephanocoenia | Broadcaster | - | - | Rare |
| Stephanocoenia intercepta | Broadcaster | Rare | Rare | - |
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