Coral reef habitats have a unique three-dimensional (3D) structural complexity which is important in providing interstitial spaces and unique environmental niches, which have increased local species diversity. Structure-from-Motion (SfM) photogrammetry techniques were utilized to create Digital Elevation Models (DEMs) and ultra-high resolution orthomosaics (cm/pixel) of three sites with contrasting water flow conditions in the southern Gulf of California. This area is considered marginal for coral development, having physicochemical parameters above or beyond the normal limits. Using SfM photogrammetry, two metrics of habitat structural complexity were investigated: surface complexity and slope. The metrics were calculated from exported DEM rasters at a spatial resolution of 1 cm, and the resulting orthomosaics were assessed for benthic cover on the CoralNet platform. The low-flow site yielded the lowest surface complexity values, averaging 94% Pocillopora coral cover and 4% rock. The high-flow site had the highest structural complexity for both metrics and a more varied benthic cover with 68% Pocillopora, 15% rock, 10% coral fragments, and 5% sand. Results give insight into the behaviors of these structural complexity metrics when studied in monospecific coral communities in marginal areas to aid in future conservation and management plans especially in the context of the climate crisis.
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