A baited, remote, underwater video sampling technique (BRUVS) was developed to survey the patterns of diversity and abundance of fishes, sharks, rays and sea snakes in all shelf depths and ‘inter-reef’ habitats throughout the Great Barrier Reef Marine Park (GBRMP). The use of bait greatly enhanced the ability to distinguish fish assemblages, including those containing functional groups thought to be either unresponsive to bait, or shy of the carnivores present in the field of view (e.g. scarids and siganids). A field comparison showed the BRUVS recorded more, larger, mobile species (e.g. carangids, scombrids, carcharhinids) than demersal trawls and performed best in daylight hours. Although the BRUVS did not record many sedentary and cryptic families collected as trawl ‘bycatch fauna’ (e.g. apogonids, priacanthids, pleuronectiformes), they did discriminate the same site groups – and with less classification error than the trawls. BRUVS could be used on any seafloor topography and any zone of the GBRMP, but their effectiveness was restricted by high turbidity and low irradiance at the seabed. As a result, BRUVS sampling was included in the largest exploration yet undertaken of seafloor biodiversity on a tropical shelf. Replicate BRUVS were deployed at 366 sites throughout the length (‘along’) and breadth (‘across’) of the GBRMP, enabling a comprehensive examination of the spatial patterns in vertebrate richness, assemblage structure and species occurrences in terms of the major environmental covariates presumed to govern fish distributions. These analyses were conducted with gradient boosting models and multivariate classification and regression trees. These approaches are robust and flexible and allow visualisation of complex interactions. The latitudinal gradient in richness of the 347 species was relatively weak, but there were strong cross-shelf gradients, with a ‘hump shaped’ peak in richness about a position ~0.8 ‘across’ the shelf. This was shown not to be the result of a random, mid-domain effect in species ranges but rather a response to the topographic complexity, epibenthic marine plants, low currents and mixed carbonate/mud sediments found (on average) at this position. Hierarchical, multivariate regression tree analyses (MRT) constrained by 28 selected environmental covariates, showed ten assemblages characterised by Dufrêne-Legendre species indicators. There were strong faunal boundaries, or ecotones, about Bowen in the south and Cooktown to Cape Flattery in the north. A position about ~0.5-0.8 across the continental shelf, where carbonate content of the sediments rose to ~84%, separated inshore ‘lagoonal’ assemblages from offshore ‘reefal’ assemblages. On either side of this demarcation there were fish assemblages distinguished by their association with finer or coarse\ud
sediments, beds of seagrass (Halophila) and banks of marine algae (Halimeda and others). There were more lethrinids, labrids, serranids and scarids offshore, but there was not strong replacement or zonation of vertebrate families along environmental gradients – unlike the generalisations from low latitude shelves in the Atlantic. Instead, there were changes amongst species within genera that followed sedimentary facies and other gradients. In the central section such gradients varied simply with position across the shelf, for example, from Nemipterus hexodon and N. peronii inshore, to N. furcosus and N. nematopus on the mid-shelf, to N. balinensoides on the outer shelf. Ubiquitous families of the highly evolved tetraodontiformes had advanced dentition and anti-predator defenses that no doubt enabled them to take advantage of the abundant, but often poor quality, sources of food in the vast plains of muddy and carbonate sediments. Boosted regression trees (BRT) were used to predict species responses to the environmental covariates, to identify important gradients and understand surrogacy and competition amongst the spatial and environmental predictors in models. The position of sites across and along the shelf gave the most parsimonious and easily interpretable models of species richness and assemblage structure, but the underlying gradients in properties of the sediments, epibenthos and water column were not so linear in these two dimensions. There were clearly three sections of the GBRMP, separated by ecotones, which differed in their flushing regime, tidal energy, oceanic influences, epibenthic habitats and sedimentary facies. The species responses and assemblage structure are discussed in terms of these influences on benthic communities and productivity of the water column, the functional morphology of the inter-reef vertebrates and the prevailing paradigms for tropical shelf faunas. In this study I conclude that spatial position and depth on linear tropical shelves are fundamental surrogates to provide insight on the major environmental drivers acting together to shape spatial gradients in vertebrate distributions, as well as identifying boundaries for management interventions
