*3.2. Prevalence of Coral Disease and Indicators of Compromised Health*

Overall, most hard corals at the sites surveyed appeared healthy as recorded on the belt transects. Those categorized as "healthy" made up 65.7 ± 2.9% of corals surveyed averaged over both years, with a low (<1%) prevalence of diseases and a 33.7 ± 1.7% prevalence of other compromised states. In 2015, there was 0.9 ± 0.2% prevalence of WS at Rural-N on *Acropora* spp., which made up 44.9% of all diseases recorded (Figure 5). In the same year, Rural-N also had the highest prevalence of Growth Anomalies (GAs; 0.6 ± 0.2%). There was one case of unconfirmed Trematodiasis, which requires microscopic confirmation of the larval trematode. In 2017, disease prevalence was lower with the highest prevalence of WS (0.5 ± 0.1%) at Rural-N again but Urban-W recording the most GAs (0.6 ± 0.3%). All cases of WS were documented on acroporids in 2017, while GAs were less host-specific and found on nine genera across the two years. In 2015, the number of branching acroporids was comparable between depths at each site while in 2017 the overall number of this coral morphology decreased, more branching acroporids were found at 10 m (Figure S3).

**Figure 5.** Prevalence of disease and states of compromised health on corals recorded in 15 × 2 m belt transect surveys at four sites (Rural-N, Rural-E, Urban-W, Urban-E), pooled by depth in Timor-Leste from November 2015 and June 2017. Abbreviations as follows: All Algae—combined macroalgae, turf, and cyanobacteria overgrowth; BL—Bleaching; CCA—Crustose coralline algae overgrowth; Other: combined pigmentation, predation, invertebrate infestation/overgrowth, burrowing invertebrates; TL—Unexplained tissue loss; WS—White Syndrome.

Prevalence of disease and compromised health categories from belt transects varied significantly by two interactions: year and site [three-way repeated measures PERMANOVA, pseudo-*F*(1,47) = 3.8234; *p* = 0.0005] and site and depth [pseudo-*F*(3,47) = 2.3313; *p* = 0.0150]. Rural-N had the lowest prevalence of disease and compromised health among all sites in both 2015 (22.4 ± 0.8%) and 2017 (23.2 ± 2.1%). However, Rural-N was the only site where the prevalence of compromised health and disease increased between survey years. Despite this, Rural-N was also characterized by the highest percentage of healthy corals (77.2 ± 1.1%) [three-way ANOVA <sup>χ</sup>2(3) = 30.7576, *<sup>p</sup>* < 0.0001}, significantly higher than all other sites (*p* < 0.05). This site also had the lowest prevalence of algal overgrowth on corals in 2015 (5.3 ± 1.2%) and the lowest amount of coral bleaching in both years (6.0 ± 0.9% in 2015, 0.8 ± 0.2% in 2017; Figure 5).
