Background Coral bleaching events vary in severity, however, to date, the hierarchy of susceptibility to bleaching among coral taxa has been consistent over a broad geographic range and among bleaching episodes. Here we examine the extent of spatial and temporal variation in thermal tolerance among scleractinian coral taxa and between locations during the 2010 thermally induced, large-scale bleaching event in South East Asia. Methodology/Principal Findings Surveys to estimate the bleaching and mortality indices of coral genera were carried out at three locations with contrasting thermal and bleaching histories. Despite the magnitude of thermal stress being similar among locations in 2010, there was a remarkable contrast in the patterns of bleaching susceptibility. Comparisons of bleaching susceptibility within coral taxa and among locations revealed no significant differences between locations with similar thermal histories, but significant differences between locations with contrasting thermal histories (Friedman = 34.97; p<0.001). Bleaching was much less severe at locations that bleached during 1998, that had greater historical temperature variability and lower rates of warming. Remarkably, Acropora and Pocillopora , taxa that are typically highly susceptible, although among the most susceptible in Pulau Weh (Sumatra, Indonesia) where respectively, 94% and 87% of colonies died, were among the least susceptible in Singapore, where only 5% and 12% of colonies died. Conclusions/Significance The pattern of susceptibility among coral genera documented here is unprecedented. A parsimonious explanation for these results is that coral populations that bleached during the last major warming event in 1998 have adapted and/or acclimatised to thermal stress. These data also lend support to the hypothesis that corals in regions subject to more variable temperature regimes are more resistant to thermal stress than those in less variable environments.

The evolution rates of mtDNA in early metazoans hold important implications for DNA barcoding. Here, we present a comprehensive analysis of intra- and interspecific COI variabilities in Porifera and Cnidaria (separately as Anthozoa, Hydrozoa, and Scyphozoa) using a data set of 619 sequences from 224 species. We found variation within and between species to be much lower in Porifera and Anthozoa compared to Medusozoa (Hydrozoa and Scyphozoa), which has divergences similar to typical metazoans. Given that recent evidence has shown that fungi also exhibit limited COI divergence, slow-evolving mtDNA is likely to be plesiomorphic for the Metazoa. Higher rates of evolution could have originated independently in Medusozoa and Bilateria or been acquired in the Cnidaria + Bilateria clade and lost in the Anthozoa. Low identification success and substantial overlap between intra- and interspecific COI distances render the Anthozoa unsuitable for DNA barcoding. Caution is also advised for Porifera and Hydrozoa because of relatively low identification success rates as even threshold divergence that maximizes the "barcoding gap" does not improve identification success.

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While many studies of coral bleaching report on broad, regional scale responses, fewer examine variation in susceptibility among coral taxa and changes in community structure, before, during and after bleaching on individual reefs. Here we report in detail on the response to bleaching by a coral community on a highly disturbed reef site south of mainland Singapore before, during and after a major thermal anomaly in 2010. To estimate the capacity for resistance to thermal stress, we report on: a) overall bleaching severity during and after the event, b) differences in bleaching susceptibility among taxa during the event, and c) changes in coral community structure one year before and after bleaching. Approximately two thirds of colonies bleached, however, post-bleaching recovery was quite rapid and, importantly, coral taxa that are usually highly susceptible were relatively unaffected. Although total coral cover declined, there was no significant change in coral taxonomic community structure before and after bleaching. Several factors may have contributed to the overall high resistance of corals at this site including Symbiodinium affiliation, turbidity and heterotrophy. Our results suggest that, despite experiencing chronic anthropogenic disturbances, turbid shallow reef communities may be remarkably resilient to acute thermal stress.

Coral cover on reefs is declining globally due to coastal development, overfishing and climate change. Reefs isolated from direct human influence can recover from natural acute disturbances, but little is known about long term recovery of reefs experiencing chronic human disturbances. Here we investigate responses to acute bleaching disturbances on turbid reefs off Singapore, at two depths over a period of 27 years. Coral cover declined and there were marked changes in coral and benthic community structure during the first decade of monitoring at both depths. At shallower reef crest sites (3–4 m), benthic community structure recovered towards pre-disturbance states within a decade. In contrast, there was a net decline in coral cover and continuing shifts in community structure at deeper reef slope sites (6–7 m). There was no evidence of phase shifts to macroalgal dominance but coral habitats at deeper sites were replaced by unstable substrata such as fine sediments and rubble. The persistence of coral dominance at chronically disturbed shallow sites is likely due to an abundance of coral taxa which are tolerant to environmental stress. In addition, high turbidity may interact antagonistically with other disturbances to reduce the impact of thermal stress and limit macroalgal growth rates.

Environment-dependent variation in the morphological, physiological, or behavioural expression of a genotype is termed phenotypic plasticity. To test for small-scale morphological plasticity in the Indo-Pacific massive corals Favia speciosa (Dana, 1846) and Diploastrea heliopora (Lamark, 1816), fragments (clone-mates) from 12 colonies of each species were reciprocally transplanted among 6 new habitats located within 2 environmental gradients: a depth cline and a nearshore-to-offshore gradient in sedimentation rates and total suspended solids (TSS). After 7 mo, all fragments were collected, cleared of tissue, and 10 morphometric characters extracted from randomly chosen corallites. Reaction norms, analysis of variance, and canonical discriminant analysis describe environmentinduced changes in corallite architecture. These changes are more pronounced in the depth cline than along the sediment gradient. Similarity of response is suggested by exploratory factor analysis where, for both species, size attributes dominate the first factor, antisymmetry the second, and corallite exsertion the third. Highly significant genotype × environment interactions for F. speciosa indicate that, for this species, genotypes vary in the level of plasticity expressed. Light and TSS emerge as the primary correlates influencing morphological change, although other parameters might act additively, synergystically or antagonistically with them. In shallow waters, increased corallite exsertion may enhance light capture or, alternatively, protect the central (oral disc) area of each polyp from harmful UV radiation. Morphological variability, combined with environment-induced changes in pigmentation, could impede accurate identification of these taxa.

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The South China Sea in the Central Indo-Pacific is a large marine region that spans an area of more than 3 million km2 bounded by the coastlines of ten Asian nation states and contains numerous small islands. Although it abuts the western border of the Coral Triangle, the designated centre of maximum marine biodiversity, the South China Sea has received much less scientific and conservation attention. In particular, a consolidated estimate of the region's scleractinian reef coral diversity has yet to emerge. To address this issue, we assemble a comprehensive species distribution data set that comprises 16 reef areas spread across the entire South China Sea. Despite containing less than 17 % of the reef area as compared to the Coral Triangle, this region hosts 571 known species of reef corals, a richness that is comparable to the Coral Triangle's based on a standardised nomenclatural scheme. Similarity profile analysis and non-metric multidimensional scaling demonstrate that most areas are compositionally distinct from one another and are structured according to latitude but not longitude. More broadly, this study underscores the remarkable and unexpected diversity of reef corals in the South China Sea.