[Adapted from: Randall et al. 2014 Ecology 95(7) 1981-1994]    

To assess the prevalence of coral diseases at each location, a survey area (1-10 km^2 depending on the region’s geographic features) of hard-bottom habitat was visually defined using Google Earth. The survey area was divided into 100 by 100 meter cells (using Google Earth Path 1.4.4). Within each location, twenty-five 100 by 100 meter cells were randomly selected as sites. These sites were defined as the primary sampling units. A single 10 by 10 meterquadrat was haphazardly placed within each site, for field-data collection. To maintain consistency across locations and to minimize potential effects of coral-assemblage differences, three criteria had to be met for a site to be surveyed: (1) the depth averaged between 5 and 10 meters, (2) the substrate was hard bottom, and (3) corals were present. If any one of these criteria was not met at a given site, it was rejected and the next randomly generated site was selected. In total, twenty-five, 10 by 10 meter quadrats were sampled at each location, for a total of 50 quadrats across two frequent-anomaly locations and 50 quadrats across two reference locations, for a total survey area of 10,000 m^2. 

All four locations were surveyed between 2 July and 1 September 2012. At each site, divers surveyed each 100 m^2 quadrat by systematically laying ten contiguous 1 x 10 m belt transects onto the reef substrate. Each coral colony with a disease sign was identified in situ and the species and disease signs were recorded. Four disease signs were identified: (1) white sign was defined as a bright, white band or patch of recent mortality adjacent to healthy-appearing tissue (i.e., the tissue bordered a well-defined edge of exposed skeleton not yet colonized by algae or other biofouling organisms) (sensu Bythell et al. 2004) , (2) dark spot was defined as tissue with purple, brown or black lesions, forming spots of irregular shapes (sensu Goreau et al. 1998), (3) black band was defined as a black band over the coral tissue exposing white skeleton with different stages of biofouling (sensu Richardson 2004), and (4) yellow sign was defined as a yellow discoloration of tissue forming a band or blotches (sensu Santavy et al. 1999). White signs and black bands were associated with recent tissue loss; yellow signs and dark spots were usually, but not always, associated with recent tissue loss. Notably, very few yellow bands were observed that followed the classical description (Reeves 1994). Instead, most coral colonies presented a patchy, non-uniform yellowing of the tissue; therefore the condition was termed ‘yellow sign.’ Additionally, any area of recently exposed white skeleton, which was not clearly caused by predation or a competitive interaction, was recorded as a white sign, including white plagues, white bands and white pox. The white-sign diseases were not differentiated because of similar- or identical-appearing signs, unknown etiologies for several diseases, and the possibility that the diseases were caused by the same pathogens (Bythell et al. 2004, Ainsworth et al. 2007). Coral colonies were occasionally recorded with two or more signs of disease, when those signs appeared to be spatially independent.

Disease mapping:

Four 100 m^2 quadrats per location were mapped in their entirety, for a total of eight 100 m^2 quadrats per temperature-stress level. Approximately 50 digital images were captured from each video-transect file using Free Video to JPG Converter v. 5.0.58 build 324. The digital images were stitched together using Adobe Photoshop CS5 v. 12.0, and ten 1–m by 10–m image mosaics were created for each 10 m by 10 m site. Each photo-mosaic was printed and, with the aid of the digital images and videos, the following data were measured and recorded for every coral colony within each site: (1) species, (2) spatial coordinates, (3) maximum diameter, (4) perpendicular diameter, (5) an estimate of percent partial mortality (0, <5, 25, 50, 75, or >95 %), and (6) ‘health’ status. Corals were identified as either healthy, or as having white signs, dark spots, black bands, yellow signs, or unknown signs of disease (as described above). Bleached or pale colonies also were recorded, and when multiple disease signs were present on an individual colony, both signs were recorded. Data from each site that was mapped are found in individual excel files in the folder called Disease mapping site data files.