Statistical analyses
We compared the richness of coral-associated macrofauna on live and dead
corals over time, first of all surveyed macrofauna, as well as each for
fishes and mobile macroinvertebrates, separately. We calculated
randomized observed species richness (‘observed species richness’) of
the community associated with finger coral heads by constructing
randomized Species Accumulation Curves (SACs), calculating the mean SAC
and its standard deviation from random permutations of the data, or
subsampling without replacement (Gotelli & Colwell 2001). We also
calculated Chao 1 estimated species richness (‘Chao 1 estimated
richness’) for the entire community, fishes and mobile invertebrates, of
coral heads using the Chao 1 estimator, a non-parametric species
estimator for abundance data (Chao et al. 2009), including 95%
confidence intervals based on the actual Chao estimator (Colwell &
Elsensohn 2014).
We also compared the composition of coral-associated macrofauna on live
and dead corals over time by performing a Principal Components Analysis
(PCA) using raw abundances of coral-associated macrofauna as the
response variables and treating each individual coral head in each
survey as an individual sample. The PCA algorithm used unweighted
singular value decomposition on values fitted using unweighted linear
regression of chi-transformed data (Legendre and Legendre 2012). We then
calculated Euclidean dissimilarities in composition using multiscale
bootstrapped resampling.
Finally, we assessed the attributes that predicted associated richness
by constructing linear mixed effects models of associated richness per
coral head, first for all macrofauna, and then each for fishes and
mobile macroinvertebrates. Overhead surface area of the coral colonies
and maximum coral branch length were treated as fixed effects,
individual coral heads and sites included in the model as random
intercepts, and time was treated as a random slope.
We ran mixed effects models using the lme4 R package (Bates et al.
2015), we ran rarefaction (species accumulation curves) and principal
components analysis using the vegan R package (Oksanen et al. 2020), and
we calculated Chao 1 total estimated richness using the SpadeR package
(Chao et al. 2016). All statistical analyses were conducted using R
software (version 3.6.2, R Core Development Team 2017).