Coral reefs are diverse, ecologically important and globally threatened ecosystems. Numerous studies have reported on the threats to coral reefs, which include both local perturba- tions, such as pollution and overfishing, and widespread phenomena, such as bleaching. Here, we report on the history of the Jakarta Bay−Thousand Islands reef system from 1985 to 2011. Over this period, we recorded significant shifts in coral generic composition and an overall decline in coral cover with widely different trajectories between in-, mid- and offshore zones. In 1985, coral cover exhibited a clear on-to-offshore gradient with low coral cover inshore (10%), moderate cover mid- shore (49%) and high cover offshore (74%). The low coral cover inshore contrasts strongly with reports of high coral cover for inshore reefs in 1929. Inshore, coral cover declined from 10% in 1985 to <5% in 1995. The greatest change in coral cover and composition, however, occurred in offshore reefs, where mean cover declined from 74 to <20% between 1985 and 1995. Acropora species were particularly affected and declined from 36 to just 5% cover offshore. Recovery of coral cover occurred offshore between 1995 and 2005. From 2005 to 2011, however, a less severe loss in coral cover was observed. With the exception of inshore reefs, which appear to be on an ongoing trajectory of decline that started before the 1985 surveys, the reefs of the Jakarta Bay−Thousand Islands system have shown a propensity to recover

We develop species-level biogeographic hypotheses for Acropora, the largest extant coral genus and the dominant scleractinian coral of Indo-Pacific reefs, based on morphometric and phylogenetic analyses of the Acropora selago group. Fourteen morphometric characters differentiated species from this group with an accuracy of 95%. When the Tukey test was administered, 11 of these characters displayed nonoverlapping subsets. The most resolved phylogenetic tree resulted from an analysis based on both morphometric and qualitative characters. Cladistic-biogeographic analysis using this tree and areas derived from species-distribution patterns showed that species with the greatest degree of endemism within the A. selago group possess the most derived character states, while the most primitive species (A. yongei) is the most widespread. Within the range of the group, four areas are recognised: (1) the Red Sea, (2) western to central Indian Ocean, (3) eastern Indian Ocean and (4) western to central Pacific Ocean. Species ranges overlap in a stepwise fashion from west to east. Areas adjacent to one another are biogeographically more closely related than non-adjacent areas. Whilst we offer a scenario for the history of distribution patterns of the A. selago group, we propose that biogeographical hypotheses based on Acropora be tested using a number of different species-groups. Similar distributional ranges for other Acropora species-groups, as well as separate distributional ranges for further groups, suggest that Acropora will provide an appropriate taxon to examine the biogeography of the tropical marine realm.