Extending over 2,000 km along the coast of Queensland, Australia and comprising some 2,900 individual coral reefs, the Great Barrier Reef [GBR] is the largest coral reef ecosystem to have existed in recent times. The northern most point of the GBR extends beyond Australian waters towards Papua New Guinea, whilst its southern most point terminates just north of Fraser Island off the south coast of Queensland. The width of the GBR varies along its length, extending from the low water mark on the Queensland coast past the edge of the continental shelf, and encompasses an entire area of approximately 344,400 square kilometres (133,000 sq mi), approximately the same size as Italy or Japan.

Corals provide essential habitat structure and energy in coral reef systems, facilitating the existence of numerous reef associated species. Indo-Pacific coral reefs are home to over 600 species of hard corals (also called stony corals or scleractinian corals), and 4000-5000 species of reef fishes (Veron 2000, Lieske and Myers 2001). There are strong mutual dependencies between the reef-building corals and reef-inhabiting fishes, with many fish species depending on corals for food and habitat, while corals depend on the grazing by certain fishes for reproductive success. Even the spread of coral diseases may be mitigated by fishes. This article summarises what is known about these intricate mutual relationships.

Corals and many other reef invertebrates such as giants clams, gorgonians, sponges and hydroids live in a symbiotic relationship with dinoflagellates, also referred to as "zooxanthellae", that provide them with an important part of their daily energy requirement through photosynthesis. The genotype of dinoflagellates (Symbiodinium) plays an important role in determining the environmental tolerance range of their host. The genus Symbiodinium consists of nine broad genetic groups or clades that are genetically highly distinct (clades A-I).

This study investigated the influence of Great Barrier Reef Marine Park Zoning on fish abundance of the Great Barrier Reef. The fish populations of pairs of shoals, one in a Green zone (closed to fishing) and the other in a Blue (open to all fishing) were compared using Baited Remote Underwater Video Stations (BRUVS).

These BRUVS revealed a diverse fauna of fish, sharks, rays and sea snakes, including species prized by fishers, taken as bycatch, or not vulnerable to hook and line fishing.

This article outlines the use of two R packages, geoMap and geo, developed to analyse data and generate outputs for the e-atlas and ningaloo-atlas. geoMap generates a variety of plots that can be used for exploratory analysis, presentations and publication-quality maps. geo is an extensive set of spatial modelling techniques that produces fitted surfaces that can be added to publication graphics, or added to the e-atlas as layers, or used as KMLs.