Mapping benthic habitats on the south west of Puerto Rico as determined by side scan sonar

Knowledge of benthic habitat distributions is essential for understanding complex coral reef systems. Habitat maps can help quantify habitat disturbances, identify hotspots of habitat/species diversity, and determine the role habitat spatial distributions play in controlling species distributions, dynamics and ecology. The main objective of this study was to generate a detailed benthic habitat map in a coral reef environment over a 60-km2 area (shoreline to shelfedge) using a 300-KHz Side Scan Sonar (SSS) deployed from a small boat. Twenty-one habitat types were identified from 0.15-m resolution SSS imagery. Qualitative descriptions of all habitats (107 sites) and quantitative species and rugosity measurements from most (11) habitats (57 sites) were used to discriminate habitats on the basis of species composition, which was associated with topographic complexity. Habitats detected from SSS imagery are thus biologically distinct and ecologically relevant. Statistical discriminations also provided a basis for a hierarchical habitat classification scheme. Nineteen habitat maps were made by digitizing georeferenced SSS mosaics, based on visual interpretation of bottom features and a 4-m2 minimum mapping unit (MMU); maps were analyzed using a geographic information system. The maps were particularly useful in depicting the highly fragmented nature of the reef system on the outer shelf, charting new areas of reef coverage, and determining the amount and size and spatial distribution of habitats across the shelf. Coral and gorgonian habitats covered 28% of the shelf, vegetated habitats 13.2% and habitats of unconsolidated sediment, 58.8%. To examine the scale dependence of estimations of habitat abundance and distribution patterns, two sites (300 ha each) were mapped at resolutions of both 4 and 400 m2 MMU. At the fine scale, small coral patches were dominant and had more complex shapes, while coarse scale maps lost most information about small or rare habitats, and the estimation of habitat abundance varied significantly due to the existence of mixed habitat categories. Habitat diversity was not affected by scale. Reef fish community composition and structure were affected by reef patch size (100–102-m diameter), with diversity and abundance inversely related to patch size. Species abundance and size structure also varied with patch size.*; *This dissertation is multimedia (contains text and other applications not available in printed format). The accompanying CD requires the following system requirements: Adobe Acrobat; Microsoft Office.