Based on Tsounis and Edmunds (In press), Ecosphere:\u00a0
\nAnalyses are based on ~ 1,600\u00a0photoquadrats\u00a0recorded annually since 1987. Photoquadrats were recorded with a Nikonos V camera fitted with Kodachrome 64 slide film from 1987-1999, but from 2000, digital cameras were used (2000-2006: Nikon Coolpix 990, 3.3 megapixels; 2007: Nikon D70, 6.1 megapixels; 2011, Nikon D90, 12.3 megapixels; and 2012-2013, Nikon D7000, 16.2 megapixels). Cameras were fitted with a strobe (Nikonos SB105) and mounted on a\u00a0quadrapod\u00a0holding them perpendicular to the substratum (Edmunds 2002, 2013). The camera\u00a0framer\u00a0remained identical throughout the study and together with the cameras, resolved objects greater than or equal to 10-mm diameter in a 1 \u00d7 1 m\u00a0framer. At each site,\u00a0photoquadrats\u00a0were recorded at ~ 10 contiguous locations along each of three transects that are parallel to one another at\u00a0constant\u00a0depth (+/- 2 meters), and 5-m apart (30 images y-1\u00a0at each site). The same transects were resampled every year. Sampling occurred in December 1987, March 1988, July 1988, December 1988, April 1989, October 1989, March 1991, May 1992, June 1993, August 1994, May 1995 to 1997, and July or August thereafter. Images are archived\u00a0online\u00a0(http://mcr.lternet.edu/vinp/overview/).
\nImages were analyzed for percentage cover of benthic organisms using CPCe version 3.6 software (Kohler and Gill 2006), or for\u00a0abundance\u00a0of octocoral colonies (number of colonies). First, percentage cover was determined using 200 dots randomly scattered on each image and scored by their occurrence on scleractinians, macroalgae (algae greater than or equal to 1 cm high, consisting mostly of\u00a0Halimeda, Lobophora, Padina,\u00a0and\u00a0Dictyota), and CTB. Scleractinians were scored as a single functional group as the fauna was dominated by\u00a0O.\u00a0annularis\u00a0(85 % at Yawzi; 58 % at Tektite, 1987), and resolution in the 1 x 1 m\u00a0photoquadrats\u00a0made it difficult to resolve small colonies such as those of\u00a0Agaricia\u00a0and juvenile\u00a0Porites\u00a0spp. Second, colony abundance of octocorals (individuals m-2) was quantified with annual resolution, and colonies were counted when their holdfasts were visible in the\u00a0photoquadrats\u00a0(Lenz et al. 2015).\u00a0Erythropodium\u00a0spp. and encrusting\u00a0Briareum\u00a0spp. were represented at low cover and abundance, and were quantified based on the number of discrete areas of colonies. Numerical abundance of octocorals was used at annual resolution. Cover data with 5-year resolution were included for comparison with other studies.
\nOctocorals are challenging to resolve to species underwater, because identification typically requires analysis of sclerites (Bayer 1961) in voucher specimens, the collection of which is restricted in the Virgin Islands National Park. Identification is even more challenging in\u00a0photoquadrats\u00a0where lighting and resolution can be limiting, and therefore our analysis focused on the 11 genera found at these sites:\u00a0Briareum, Erythropodium, Plexaura, Pseudoplexaura,\u00a0Eunicea, Plexaurella, Muriceopsis, Antillogorgia,\u00a0and\u00a0Gorgonia. Small colonies of\u00a0Eunicea,\u00a0Plexaurella,\u00a0Pseudoplexaura, and\u00a0Plexaura\u00a0spp. were scored as \u201cunknowns\u201d as they could not be distinguished in the photographs. The height of small colonies could not be determined in planar images, but they were ~ 12 cm tall.\u00a0Pterogorgia\u00a0and\u00a0Muricea\u00a0were found in the region, and either were not detected in the sampling areas, or could not be resolved in the photographs.
\nReferences:
\nEdmunds, P. J. 2002. Long-term dynamics of coral reefs in St. John US Virgin 827 Islands. Coral Reefs 21:357\u2212367.
Surveys of octocorals from 1987-2013
Based on Tsounis and Edmunds (In press), Ecosphere:\u00a0
\nCommunity structure was characterized for four assemblage constructs that employed annual means for dependent variables (cover or abundance). First, the scleractinian-focused assemblage was quantified using the percentage cover of scleractinians (pooled among taxa), macroalgae, and CTB. Second, the octocoral-focused assemblage was quantified using octocoral abundance (pooled among taxa) together with\u00a0cover\u00a0of macroalgae, and CTB. Third, the octocoral genus assemblage focused on octocoral abundance resolved to genus, or unknowns. Fourth, a complete assemblage was used, containing scleractinians (all taxa), octocorals (abundance by genus), macroalgae and CTB. Data for each benthic group were presented untransformed as means +/- SE by year on scatterplots.
\nAll analyses of scleractinian-focused, octocoral-focused, octocoral\u00a0genera,\u00a0and complete assemblages were based on resemblance matrices using Bray-Curtis similarities. Data for the scleractinian-focused assemblage consisted of percent cover and were square root transformed; data for the octocoral-focused and complete assemblage consisted of both percent cover and numerical abundance, and therefore were z-score standardized (Sokal and Rohlf 2012); and data for the octocoral genera were z-score standardized to optimize the performance of PCoA for the zero-inflated data. A dummy value of 3 was added to z-score standardized data to create positive values that could\u00a0analyzed\u00a0in this statistical framework.
\nNon-metric multidimensional scaling (nMDS) was used to visualize multivariate trends in community structure for the four assemblages. To prepare nMDS plots, multiple restarts of 999 iterations were used until stress stabilized and ordinations were repeatable (after Clarke and Warwick 2001). In these plots, years were represented as circles scaled to scleractinian cover in the scleractinian-focused analysis, and to pooled abundance of octocorals in the octocoral focused and octocoral\u00a0genera\u00a0analyses. Sampling years were clustered using the SIMPROF routine in PRIMER-E, with 999 permutations and significant clusters identified at an alpha of 0.05. SIMPROF results were displayed as similarity contours on the respective nMDS plots visualizing hierarchical similarity among years (after Clarke and Warwick 2001). To evaluate similarities between two groupings of years that became apparent during initial analysis (as in Edmunds 2013; Edmunds and Lasker 2016), we used an iterative procedure for each graph to determine the highest value of dissimilarity percentage that would describe the groups of years separated in nMDS state space. To identify the contribution of each benthic group to inter-annual variability, a principal coordinate analysis (PCoA) was performed using the\u00a0cmdscale\u00a0function in the R statistical package (R Development Core Team 2008). Loading scores were calculated as the Pearson correlations of each dependent variable (i.e., benthic group) against PCO1 and PCO2, and were displayed when significant (P less than 0.05) as vectors scaled to a maximum length of 1. The PCoA were based on Bray-Curtis similarities that were produced using the vegan package for R (Oksanen et al. 2015).
\nQuestion 1.\u00a0To test whether the description of community dynamics differ when described with the four assemblages constructs, we used a multivariate correlation procedure with significance determined within a permutational framework using a Mantel test (Legendre and Legendre 1998). First we compared the scleractinian-focused assemblage with the octocoral-focused assemblage; second, we compared the scleractinian-focused assemblage with the octocoral\u00a0genera\u00a0assemblage; and third, we tested whether the scleractinian-focused assemblage differed from the complete assemblage. The Mantel test was performed using the Vegan package in R [Oksanen et al. 2015; R Development Core Team 2008]).
\nEach of the four assemblages was tested for associations with all combinations of the four measures of physical conditions, using Spearman rank correlation (Clarke and Ainsworth 1993). The Bioenv function (Clarke and Ainsworth 1993) was used for\u00a0correlations,\u00a0and was followed\u00a0with\u00a0a Mantel procedure (Legendre and Legendre 1998) to identify the set of physical variables most strongly associated with the biological variables, with significance evaluated in a permutational framework. The Bioenv function was performed using the vegan package for R (R Development Core Team 2008 [Oksanen et al. 2015]).
\nAnalysis of general implications
\nTo address general implications of our findings, the Yawzi Point versus Tektite contrast was interpreted as a comparison of a reef dominated by living\u00a0Orbicella\u00a0annularis\u00a0(i.e., Tektite), with one dominated by antecedent (but dead) colonies of\u00a0O.\u00a0annularis\u00a0with the decline in cover of this species having taken place since 1987. In this format, the contrast has utility in evaluating how the regional trend for declining cover of\u00a0O.\u00a0annularis\u00a0(e.g., Hughes and Tanner 2000, Edmunds 2015) is likely to influence the community dynamics of octocorals. Central to this interpretation was an inferential test of octocoral community dynamics at Yawzi Point versus Tektite, and this was accomplished using the Mantel test to compare all four assemblages as described above.
\nBCO-DMO Processing Notes:
\n-Reformatted column names to comply with BCO-DMO standards.
\n-Replaced \"no data\" with \"nd\"
\n-Changed significant figures to reflect the accuracy of the measuring system.