*2.1. Site Selection and Substrate Survey*

Field surveys were conducted in the summers of 2018 and 2019 across 8 reef sites, which varied in their distance from shore (1.62 to 8.86 km) and depth (3.0 to 8.1 m), in the middle of Florida Keys National Marine Sanctuary (Figure 1). Depths were calculated during the mid-tide transition using a depth finder on a boat when it was positioned over the middle of the reef. Each reef area was surveyed using a permanent 50 m transect that ran parallel to the primary axis of the reef, and 4 30 m transects that were laid perpendicular to and crossing the permanent transect at distances of 10, 20, 30, and 40 m, creating a 50 × 30 m grid. The substrate cover of the study area was recorded using digital photographs of 50 × 50 cm portions of the substrate, starting with 2 pictures on each side of the permanent 50 m transect at 0 m, 2 pictures again at 10 m, at 20 m, at 30 m, at 40 m, and again at 50 m (i.e., a total of 12 images per reef = 96 images for all reefs). Percent substrate cover by the major substrates (hard corals, soft corals, sponges, fleshy algae, turf algae, calcareous algae, sand) was estimated using 25 randomly selected points per photograph, with the aid of Coral Point Count with the Excel extension [46]. Rugosity was measured 3 times on each of the 4 30 m perpendicular transects using a chain and tape method. A 2 m chain was placed along the side of the 30 m transect and the beginning and end chain measurements were recorded and subtracted from each other. If a reef was flat, the chain would extend a full 2 m on the transect tape, giving an overall measurement of low rugosity. If a reef was more complex, the chain would not extend the full 2 m. The rugosity measurements for each site (3 per 30 m transect × 4 per 30 m transects = 12 rugosity measurements) were then averaged to obtain an overall rugosity across the site.

**Figure 1.** Map to show the location of the eight study sites in the middle of Florida Keys, USA, surveyed during the summers of 2018 and 2019. These eight sites are located inside the Florida Keys National Marine Sanctuary.
