The coral genus Acropora is reviewed from Indonesia for the first time, following detailed collections made at 131 sites and additional material collected from approximately 40 sites throughout the archipelago during the period 1993–6. Eighty‐three species are recorded, four of these (Acropora halmaherae, A. awi, A. plumosa and A. simplex) new to science, six first described in 1994 and six in 1997. Records are compared with specimen‐based records from localities worldwide. The species of Acrokora occurring in Indonesian waters include five recorded only from the Indian Ocean and Indonesia, seven recorded only from the Pacific Ocean, South China Sea and Indonesia, and a further 10 species apparently endemic to Indonesia, as well as widespread Indo‐Pacific species. Two species (A. jacquelineae Wallace, 1994 and A. batunai Wallace, 1996) are recorded only from north central Indonesia and Papua New Guinea, and two species (A. russelli Wallace, 1994 and A. turaki Wallace, 1994) only from north central Indonesia and north western Australia. The findings contribute to a new view of the corals of the Indo‐Pacific ‘centre of diversity’ as a composite fauna with origins in a number of events in space and time.

Accepted Versionof a paper published in the journal Marine Biology.

No abstract

Species boundaries remain unresolved in many scleractinian corals. In this study, we examine evolutionary boundaries of species in the Acropora humilis species group.Five morphologically discrete units are recognized using principal components and hierarchical cluster analyses of quantitative and qualitative characters respectively.Maximum parsimony and likelihood analyses of partial 28S rDNA sequences suggest that these morphological units diverged to form two evolutionarily distinct lineages, with A. humilis and A. gemmifera in one lineage and A. digitifera and two morphological types of A. monticulosa in the other. Low levels of sequence divergence but distinct morphologies of A. humilis and A. gemmifera within the former lineage suggest recent divergence or ongoing hybridization between these species. Substantially higher levels of divergence within and between A. digitifera and A. monticulosa suggest a more ancient divergence between these species, with sequence types being shared through occasional introgression without disrupting morphological boundaries. These results suggest that morphology has evolved more rapidly than the 28S rDNA marker, and demonstrate the utility of using morphological and molecular characters as complementary tools for interpreting species boundaries in corals.

Coral reefs are diverse, ecologically important and globally threatened ecosystems. Numerous studies have reported on the threats to coral reefs, which include both local perturbations, 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 midshore (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.