From Edmunds et al (2015) Hydrobiologia:

The study exploited six sites between Cabritte Horn and White Point on the south shore of St. John that have been censused since 1992, and augments data from these sites with 11 new sites sampled in 2011. The six original sites were collapsed to provide a single sampling between Cabritte Horn and White Point, and together with the 11 new sites, an experimental design was created with three sites in each level of a two island x two shore analysis (i.e., with 12 sites). The original sites are at 7-9 m depth on fringing reefs, and since 2000, they have been sampled using ~40 photoquadrats (0.5 x 0.5 m) scattered randomly along a 40 m transect running parallel to the depth contour. To facilitate a comparison among sites on the two islands with similar sampling effort at each site (described below), photoquadrats recorded at the six original sites in 2011 were pooled (n ~ 240 quadrats), and 40 photoquadrats randomly selected for inclusion in the present analysis as representative of the single site between White Point and Cabritte Horn. The advantage of this approach is that it supported a balanced statistical design with ~40 quadrats at each of the 12 sites. Repeated random selections of 40 photoquadrats from the photoquadrats pooled among the original sites did not appreciably alter the mean estimates of coral abundance (data not shown). The 11 new sites were selected haphazardly to sample habitats similar to those evaluated at the original sites, and to sample the north and south shores (i.e., a contrast of exposure) of St. John and St. Thomas at the largest spatial scale that was possible to capture using the small boats available for this project. Sites were not selected with prior knowledge of the benthic communities, and the 40 m transects were placed along the depth contour of the first reef encountered after entering the water. The additional sites are not permanently marked (although the original sites are), but the GPS coordinates are reported in Fig. 1.

Photoquadrats were recorded with a digital camera (Nikon D90, 6.8 megapixels) fitted with an 18-70 mm lens, and two strobes (Nikonos SB 105). The camera was mounted on a framer to hold it perpendicular to the reef, and pictures were taken at random positions along each transect (images archived at http://mcr. lternet.edu/vinp). For scleractinians, images were analyzed for percentage cover by genus using CPCe software (Kohler & Gill, 2006), with 200 dots (10 pixel diameter) randomly placed on each image with the substratum beneath identified and scored. With this technique, ~8000 decisions characterized each site (~96,000 decisions for this study), and here we report analyses including a brief treatment of the cover of scleractinians, macroalgae, and crustose coralline algae, turf, and bare space [combined as CTB (Aronson & Precht, 2000)].

Measurements of planar area is the most widely used means of assessing abundance of benthic organisms on tropical reefs, but the biological interpretation of this metric is equivocal for branching organisms such as arborescent octocorals. Their soft and flexible branches create a canopy whose planar area varies depending on orientation, flow conditions, and height of branches. While percentage cover for such taxa evaluates their impact on the benthos, cover will vary depending on the conditions under which it is recorded, as well as the morphological strategies of the component taxa (e.g., candelabra versus fans), and it is related only loosely to the number of colonies producing the canopy [i.e., substratum occupancy Jackson, 1979)]. To avoid these challenges, we quantified octocoral densities (i.e., colonies 0.25 m-2), with colonies defined by the presence of their holdfast in the photoquadrat (Lenz et al., 2015), or contiguous encrusting colonies (for Erythropodium and encrusting Briareum). Photoquadrats provide an imperfect tool for quantifying arborescent colonies, but we have found densities determined in situ to be correlated with densities determined from photoquadrats, although analyses by photoquadrats are downwardly biased for octocoral density, with this effect intensifying at high densities (Lenz et al., 2015).

hydrobio_2015.csv