**Based on Tsounis and Edmunds (In press), Ecosphere: **

Temporal trends of physical parameters were tested through linear regression using 3-year centered moving averages to address the lag of response of benthic community structure to environmental conditions (resulting in the loss of 2 y from the dataset).

Question 2. The seven physical environmental variables were tested for collinearity by screening variables by pairwise linear correlation. This procedure identified four variables that were independent, and these were used for subsequent analyses: hurricane index (Hindex), mean seawater temperature (deg C), rainfall (cm), and minimum seawater temperature (deg C). The physical variables were transformed using 3-year, centered moving averages of each dependent variable to smooth short-term fluctuations arising from stochastic effects, and to address delayed effects of environmental conditions on the communities. As physical conditions were measured on different scales, they were z-score standardized prior to analysis (Sokal and Rohlf 2012), and expressed as resemblance matrix based on Euclidean distances.

Each 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 correlations, and was followed with a 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]).

**References:**

Clarke, K. R., and M. Ainsworth. 1993. A method of linking multivariate community structure to environmental variables. Marine Ecology Progress Series 92:205-205.

Legendre, P., and L. Legendre. 1998. Numerical Ecology. 2nd English 918 Edition. Elsevier.

Oksanen, J., F. G. Blanchet, R. Kindt, P. Legendre, P. R. Minchin, R. B. O'Hara, G. L. Simpson, P. Solymos, M., H., H. Stevens, and H. Wagner. 2015. Vegan: Community Ecology Package. R package version 2.3-0. http://CRAN.R-project.org/package=vegan.

Sokal, R. R., and F. J. Rohlf. 2012. Biometry Fourth Edition. Freeman, New York.

**BCO-DMO Processing Notes:**

-Reformatted column names to comply with BCO-DMO standards.

-Replaced "no data" with "nd"