A total of 20 survey sites were chosen using a combination of high resolution aerial photographs and local knowledge, to ensure that all significant reef systems in the central Keppel Island group were represented. Aerial photos were geo-rectified in Google EarthTM and reef area estimated by tracing the outline of the reef which was clearly visible in the photos. The sites chosen were located on the fringing reefs surrounding Bald Rocks, Barren Island and Child Island, Clam Bay, Egg Rock, Halftide Rocks, Halfway Island, Humpy Island, Leeke's Beach, Man and Wife Rocks, Miall Island, Middle Island, Monkey Point, Shelving Point, North Keppel Island, Outer Rocks, Parker's Bommie (Big Peninsula), Passage Rocks, Pelican Island, Pumpkin Island and Wreck Bay. Surveys were conducted between April 2008 and December 2009.Coral species and their abundance (ranked % abundance) were assessed during a random swim over ~60 minutes at each of the 20 sites. Species lists were limited to scleractinian corals. Most coral species could be adequately identified in the field with the exception of those in the Poritidae (massive growth form) and Fungiidae genera, which were counted as one species if these were present. Digital still photographs of the features of each species were taken to verify identity. Each species was ranked in terms of abundance and compared to the total live hard coral cover using a scale of 0-5 (0 = none present; 1 = 1-10%; 2 = 11-30%; 3 = 31-50%; 4 = 51-75%).The cover of benthic communities was assessed at each site (except for Leeke's Beach and Clam Bay) along two haphazard 50 m transects on the reef flat (0-2.0 m at chart datum, 2.4-4.8 m at mean sea level) and reef slope (6.0-12.0 m at chart datum, 8.4-14.4 m at mean sea level). Transects were photographed every 2 m at a height of 1 m above the substratum using a digital still camera (4 Mp) fitted with a 16 mm wide angle lens. To enable calculation of the average gradient between the reef flats and slopes, geo-referenced images were obtained for each transect using a towed GPS set to record a track at 5 second intervals, which was later matched to the images using the software RoboGeoTM. Digital still images were analysed using 20 random points per image with the program CPCeTM v3.1. Cover was assessed as the percentage of the total biotic and abiotic benthos averaged across the replicate transects on reef flats and slopes. Benthic cover was classified into the proportion of macro-algae, abiotic, coralline algae, turf algae, hard live coral and soft coral.To assess the variation in light levels across sites, predominantly due to variation in turbidity, the light attenuation coefficient (Kd) was derived from photosynthetically active radiation (PAR) loggers (Odyssey, Dataflow Systems, NZ) deployed at each site (except Leeke's Beach) at a depth of 5-7 m. Light was recorded every 10 minutes for periods of 1-12 weeks. Sea temperature was recorded at half-hourly intervals using Odyssey temperature loggers (Dataflow Systems Pty Ltd, NZ) deployed at each site (except Leeke's Beach) on the reef slope (5-7 m at LAT). Habitat profiles were estimated by measuring the gradient (slope) between the start of reef flat and slope transects for each site from the geo-rectified images using Google EarthTM. The depth at the reef flat was subtracted from the depth at the reef slope and then divided by the distance between the points.To assess the influence of current flow on the species assemblage at each site, current strengths were catagorized based on local knowledge as: 1 = strong tidal combined with longshore currents; 2 = medium current (mainly tidal) but some longshore current influence; 3 = mostly diurnal tidal currents which are protected from strong longshore currents and ocean swell.To assess the influence of 3-D habitat complexity (rugosity) on the coral species assemblages at the 20 sites, each site was subjectively categorized as: 1 = high rugosity as a result of bommies and rocks creating high 3-D habitat structure and a range of habitat types; 2 = average rugosity with reef flats and slopes exhibiting range of coral growth morphologies and scattered bommies; and 3 = low rugosity (reef flats and slopes with extensive mono-specific stands dominated mainly by Acropora spp.).
