Fig. 2

Percent cover of hard corals on breakwaters and surrounding natural reefs, and relationships among substrate type, research year, depth, and coral cover after bleaching. (a) Temporal dynamics in percent hard coral cover on breakwaters and surrounding natural reefs in Naha Port from 1989 to 2018. Black lines indicate the 1998 coral bleaching event. (b) Non-metric multidimensional scaling (nMDS) plots of coral communities of breakwater and surrounding natural reefs, based on coral cover and other benthic cover from 1989 to 2018. Grey vectors show coral taxa and other benthic substrates that correlate mostly with the change of communities. (c) Standardized effect size of explanatory variables of additive log-ratio (alr)-transformed coral cover after the 1998 bleaching event, from a Bayesian hierarchical model. White circles represent the median, and thin and thick horizontal lines represent the 95% and 80% highest density intervals (HDIs), respectively. Blue lines indicate that the 80% HDI does not overlap with 0, suggesting a credible trend, and grey lines indicate that the 80% HDI overlaps with 0, suggesting a less credible trend. For the effect of substrate (i.e., breakwaters or natural reefs), a positive effect size indicates a relatively positive effect on the coral cover on natural reefs and a negative effect size indicates a relatively positive effect on the coral cover on breakwaters. Please refer to Eq. (1) for a detailed explanation.