*2.2. Coral Community Composition and Coral Health Surveys*

To assess benthic cover and coral health, we deployed 15 m line intercept transects (LIT) [90] and 15 m × 2 m belt transects, respectively [28]. At each of the four sites, three transects were laid at both 5 m (reef flat) and 10 m (reef slope) depths, for a total of 24 transects across all sites. The first of three transects at each site and depth was chosen haphazardly, with the subsequent transects at least 5 m away from the start/end of other transects on the appropriate depth contour. For the LIT surveys, all benthos under the 15 m tape was categorized into a major benthic category (hard coral, soft coral, substrate/sand, macroalgae, turf algae, cyanobacteria, and crustose coralline algae [CCA]). LIT transects were conducted by two volunteers per survey trip who were at least ReefCheck certified. On the coral health belt transects performed by the first author, every coral colony within the 15 × 2 m transect area was identified to genus and assessed visually for coral disease and signs of potentially compromised coral health, such as overgrowth by macroalgae, turf and cyanobacteria overgrowth, encrusting invertebrates (sponges, tunicates, flatworm infestation), burrowing invertebrates (gastropods, bivalves, crustaceans, etc.), signs of predation (fish and *Drupella* spp. snails), signs of bleaching (partial or total loss of algal symbionts appearing white), signs of coral response (pigmentation, mucus), and physical damage (sedimentation, breakage) as per protocols developed by the Global Environment Facility and World Bank Coral Disease Working Group (Figure 2 and Figure S1; Table S3) [28]. High prevalence or increasing numbers of burrowing invertebrates or overgrowth of corals by turf algae and invertebrates could be indicative of reef degradation due to anthropogenic disturbances [91]. No *Acanthaster* spp. sea stars or feeding scars were observed during surveys. Any uncertain diagnoses were photographed for later consultation. The prevalence

of disease and compromised health was calculated as the number of corals affected by the disease/compromised health category divided by the total number of coral colonies in the transect [28]. The GPS coordinates at the start of each transect were recorded and used for the second survey in July 2017 (Table S4).

**Figure 2.** Examples of disease and compromised health recorded on surveys undertaken in Timor-Leste between 15–27 November 2015. Photos outlined in red represent close-ups of adjacent photos (**b1**,**c1**). (**a**) WS–White Syndrome band of distinct tissue loss on tabulate acroporids with white skeleton abutting live tissue with exposed skeleton gradually colonized by turf algae, (**a1**) exposed coral skeleton caused by coral tissue loss from WS, (**b**) bleached tissue displaying white, living tissue lacking symbionts, (**c**) flatworm infestation on a *Fungia* coral, (**d**) turf algae overgrowth on a massive *Porites* coral, and (**e**) cyanobacterial (purple) overgrowth on a reef affecting more than one genus (i.e., *Fungia* and branching montiporids). See Figure S1 for other compromised states and Table S3 for more information.
