The significance of submerged fossil coral reefs as important archives of abrupt global sea level rise and climate change has been confirmed by investigations in the Caribbean [Fairbanks, 1989] and the Indo‐ Pacific (see Montaggioni [2005] for a summary) and by recent Integrated Ocean Drilling Program (IODP) activities in Tahiti [Camoin et al., 2007]. Similar submerged (40–130 meters) reef structures are preserved along the margin of the Great Barrier Reef (GBR), but they have not yet been systematically studied. The submerged reefs have the potential to provide critical new information about the nature of past global sea level and climate variability and about the response of the GBR to these past and perhaps future environmental changes [Beaman et al., 2008]. Equally important for GBR Marine Park managers is information about the role of the reefs as habitats and substrates for modern biological communities.

Humans have long sought to restore species but little attention has been directed at how best to do so for rich assemblages of foundation species that support ecosystems, like rainforests and coral reefs that are increasingly threatened by environmental change.We developed a two-part triage process for selecting optimized sets of species for restoration. We demonstrated this process using phenotypic traits and ecological characteristics for reef building corals found along the east coast of Australia. Without clear linkages between phenotypic traits and ecosystem functions, the first part of the triage hedges against function loss by ensuring an even spread of life history traits. The second part hedges against future species losses by weighting species based on characteristics that are known to increase their ecological persistence to current environmental pressures—abundance, species range and thermal bleaching tolerance— as well as their amenability to restoration methods.We identified sets of ecologically persistent and restorable species most likely to protect against functional loss by examining marginal returns in occupancy of phenotypic trait space per restored species.We also compared sets of species with those from the southern-most accretional reef as well as a coral restoration program to demonstrate how trait space occupancy is likely to protect against local loss of ecosystem function.Synthesis and applications. A quantitative approach to selecting sets of foundational species for restoration can inform decisions about ecosystem protection to guide and optimize future restoration efforts. The approach addresses the need to insure against unpredictable losses of ecosystem functions by investing in a wide range of phenotypes. Furthermore, the flexibility of the approach enables the functional goals of restoration to vary depending on environmental context, stakeholder values, and the spatial and temporal scales at which meaningful impacts can be achieved.

The ecology of habitats along the Great Barrier Reef (GBR) shelf-break has rarely been investigated. Thus, there is little understanding of how associated fishes interact with deeper environments. We examined relationships between deep-reef fish communities and benthic habitat structure. We sampled 48 sites over a large depth gradient (54–260 m) in the central GBR using Baited Remote Underwater Video Stations and multibeam sonar. Fish community composition differed both among multiple shelf-break reefs and habitats within reefs. Epibenthic cover decreased with depth. Deep epibenthic cover included sponges, corals, and macro-algae, with macro-algae present to 194 m. Structural complexity decreased with depth, with more calcified reef, boulders, and bedrock in shallower depths. Deeper sites were flatter and more homogeneous with softer substratum. Habitats were variable within depth strata and were reflected in different fish assemblages among sites and among locations. Overall, fish trophic groups changed with depth and included generalist and benthic carnivores, piscivores, and planktivores while herbivores were rare below 50 m. While depth influenced where trophic groups occurred, site orientation and habitat morphology determined the composition of trophic groups within depths. Future conservation strategies will need to consider the vulnerability of taxa with narrow distributions and habitat requirements in unique shelf-break environments.