Variations in interspecific competition, abundance, and alpha and beta diversities of corals were studied from 1962 to 2000 at different localities on the reef at Heron Island, Great Barrier Reef, Australia. Reductions in abundance and diversity were caused by direct damage by storms and elimination in competition. Recovery after such reductions was influenced by differences in the size of the species pools of recruits, and in contrasting competitive processes in different environments. In some places, the species pool of coral larval recruits is very low, so species richness (S) and diversity (D) never rise very high. At other sites, this species pool of recruits is larger, and S and D soon rise to high levels. After five different hurricanes destroyed corals at some sites during the 38year period, recovery times of S and D ranged from 3 to 25 years. One reason for the variety of recovery times is that the physical environment was sometimes so drastically changed during the hurricane that a long period was required to return it to a habitat suitable for corals. Once S and D have peaked during recolonization, they may either remain at a high level, or decline. In shallow water, with no deleterious changes in environmental conditions, S and D may not decline over time, because superior competitors cannot overtop inferior competitors without exposing themselves to deleterious aerial exposure at low tide. At other times and places, S and D did decline over time. One cause of this was a gradual deterioration of the physical environment, as corals grew upward into the intertidal region and died of exposure. S and D also fell because the wave action in hurricanes either killed colonies in whole or part, or changed the drainage patterns over the reef crest, leaving corals high and dry at low tide. At deeper sites, declines in S and D were sometimes caused by heavy wave action, or by interspecific competition, as some corals overgrew or overtopped their neighbors and eliminated them.

Sea cucumbers (Holothuroidea) are a morphologically diverse, ecologically important, and economically valued clade of echinoderms; however, the understanding of the overall systematics of the group remains controversial. Here, we present a phylogeny of extant Holothuroidea assessed with maximum parsimony, maximum likelihood, and Bayesian approaches using approximately 4.3kb of mt- (COI, 16S, 12S) and nDNA (H3, 18S, 28S) sequences from 82 holothuroid terminals representing 23 of the 27 widely-accepted family-ranked taxa. Currently five holothuroid taxa of ordinal rank are accepted. We find that three of the five orders are non-monophyletic, and we revise the taxonomy of the groups accordingly. Apodida is sister to the rest of Holothuroidea, here considered Actinopoda. Within Actinopoda, Elasipodida in part is sister to the remaining Actinopoda. This latter clade, comprising holothuroids with respiratory trees, is now called Pneumonophora. The traditional Aspidochirotida is paraphyletic, with representatives from three orders (Molpadida, Dendrochirotida, and Elasipodida in part) nested within. Therefore, we discontinue the use of Aspidochirotida and instead erect Holothuriida as the sister group to the remaining Pneumonophora, here termed Neoholothuriida. We found four well-supported major clades in Neoholothuriida: Dendrochirotida, Molpadida and two new clades, Synallactida and Persiculida. The mapping of traditionally-used morphological characters in holothuroid systematics onto the phylogeny revealed marked homoplasy in most characters demonstrating that further taxonomic revision of Holothuroidea is required. Two time-tree analyses, one based on calibrations for uncontroversial crown group dates for Eleutherozoa, Echinozoa and Holothuroidea and another using these calibrations plus four more from within Holothuroidea, showed major discrepancies, suggesting that fossils of Holothuroidea may need reassessment in terms of placing these forms with existing crown clades.

Vegetated coastal ecosystems provide goods and services to billions of people. In the aftermath of a series of recent natural disasters, including the Indian Ocean Tsunami, Hurricane Katrina and Cyclone Nargis, coastal vegetation has been widely promoted for the purpose of reducing the impact of large storm surges and tsunami. In this paper, we review the use of coastal vegetation as a "bioshield" against these extreme events. Our objective is to alter bioshield policy and reduce the long-term negative consequences for biodiversity and human capital. We begin with an overview of the scientific literature, in particular focusing on studies published since the Indian Ocean Tsunami in 2004 and discuss the science of wave attenuation by vegetation. We then explore case studies from the Indian subcontinent and evaluate the detrimental impacts bioshield plantations can have upon native ecosystems, drawing a distinction between coastal restoration and the introduction of exotic species in inappropriate locations. Finally, we place bioshield policies into a political context, and outline a new direction for coastal vegetation policy and research.

We investigated the functional morphology and ecology of biting among the squamipinnes, an assemblage of nine successful and distinctive reef fish families. We demonstrate that an intramandibular joint (IMJ) may have evolved at least three and possibly five times in this assemblage and discuss the impact of this recurring innovation in facilitating prey-capture by biting. Using character mapping on a supertree for the squamipinnes, we reveal up to seven gains or losses of intramandibular flexion, all associated with trophic transitions between free-living and attached prey utilization. IMJs are basal in six of the studied families whereas the origin of intramandibular flexion in the Chaetodontidae (butterflyfishes) coincides with a transition from ram-suction feeding to benthic coral feeding, with flexion magnitude reaching its peak (49 ± 2.7°) in the coral scraping subgenus Citharoedus. Although IMJs generally function to augment vertical gape expansion during biting behaviours to remove small invertebrates, algae or coral from the reef, the functional ecology of IMJs in the Pomacanthidae (angelfishes) stands in contrast. Pomacanthid IMJs exhibit over 35°of flexion, permitting gape closure when the jaws are fully protruded. We demonstrate the widespread IMJ occurrence among extant biters to result from a complex convergent evolutionary history, indicating that the IMJ is a major functional innovation that enhances biting strategies in several prominent reef fish groups.

Coral reefs, the most diverse of marine ecosystems, currently experience unprecedented levels of degradation. Diseases are now recognized as a major cause of mortality in reef-forming corals and are complicit in phase shifts of reef ecosystems to algal-dominated states worldwide. Even so, factors contributing to disease occurrence, spread, and impact remain poorly understood. Ecosystem resilience has been linked to the conservation of functional diversity, whereas overfishing reduces functional diversity through cascading, top-down effects. Hence, we tested the hypothesis that reefs with trophically diverse reef fish communities have less coral disease than overfished reefs. We surveyed reefs across the central Philippines, including well-managed marine protected areas (MPAs), and found that disease prevalence was significantly negatively correlated with fish taxonomic diversity. Further, MPAs had significantly higher fish diversity and less disease than unprotected areas. We subsequently investigated potential links between coral disease and the trophic components of fish diversity, finding that only the density of coral-feeding chaetodontid butterflyfishes, seldom targeted by fishers, was positively associated with disease prevalence. These previously uncharacterized results are supported by a second large-scale dataset from the Great Barrier Reef. We hypothesize that members of the charismatic reef-fish family Chaetodontidae are major vectors of coral disease by virtue of their trophic specialization on hard corals and their ecological release in overfished areas, particularly outside MPAs.

Sexuality and reproductive mode are two fundamental life-history traits that exhibit largely unexplained macroevolutionary patterns among the major groups of multicellular organisms. For example, the cnidarian class Anthozoa (corals and anemones) is mainly comprised of gonochoric (separate sex) brooders or spawners, while one order, Scleractinia (skeleton-forming corals), appears to be mostly hermaphroditic spawners. Here, using the most complete phylogeny of scleractinians, we reconstruct how evolutionary transitions between sexual systems (gonochorism versus hermaphrodism) and reproductive modes (brooding versus spawning) have generated large-scale taxonomic patterns in these characters. Hermaphrodites have independently evolved in three large, distantly related lineages consisting of mostly reef-building species. Reproductive mode in corals has evolved at twice the rate of sexuality, while the evolution of sexuality has been heavily biased: gonochorism is over 100 times more likely to be lost than gained, and can only be acquired by brooders. This circuitous evolutionary pathway accounts for the prevalence of hermaphroditic spawners among reef-forming scleractinians, despite their ancient gonochoric heritage.

The supertree algorithm matrix representation with parsimony was used to combine existing hypotheses of coral relationships and provide the most comprehensive species-level estimate of scleractinian phylogeny, comprised of 353 species (27% of extant species), 141 genera (63%) and 23 families (92%) from all seven suborders. The resulting supertree offers a guide for future studies in coral systematics by highlighting regions of concordance and conflict in existing source phylogenies. It should also prove useful in formal comparative studies of character evolution. Phylogenetic effort within Scleractinia has been taxonomically uneven, with a third of studies focussing on the Acroporidae or its most diverse genera. Sampling has also been geographically non-uniform, as tropical, reef-forming taxa have been considered twice as often as non-reef species. The supertree indicated that source trees concur on numerous aspects of coral relationships, such as the division between robust versus complex corals and the distant relationship between families in Archaeocoeniina. The supertree also supported the existence of a large, taxonomically diverse and monophyletic group of corals with many Atlantic representatives having exsert corallites. Another large, unanticipated clade consisted entirely of solitary deep-water species from three families. Important areas of ambiguity include the relationship of Astrocoeniidae to Pocilloporidae and the relative positions of several, mostly deep-water genera of Caryophylliidae. Conservative grafting of species at the base of congeneric groups with uncontroversial monophyletic status resulted in a more comprehensive, though less resolved tree of 1016 taxa.

A B S T R A C TMulti-locus phylogenetic studies of echinoderms based on Sanger and RNA-seq technologies and the fossil record have provided evidence for the Asterozoa-Echinozoa hypothesis. This hypothesis posits a sister relationship between asterozoan classes (Asteroidea and Ophiuroidea) and a similar relationship between echinozoan classes (Echinoidea and Holothuroidea). Despite this consensus around Asterozoa-Echinozoa, phylogenetic relationships within the class Asteroidea (sea stars or starfish) have been controversial for over a century. Open questions include relationships within asteroids and the status of the enigmatic taxon Xyloplax. Xyloplax is thought by some to represent a newly discovered sixth class of echinoderms -and by others to be an asteroid. To address these questions, we applied a novel workflow to a large RNA-seq dataset that encompassed a broad taxonomic and genomic sample. This study included 15 species sampled from all extant orders and 13 families, plus four ophiuroid species as an outgroup. To expand the taxonomic coverage, the study also incorporated five previously published transcriptomes and one previously published expressed sequence tags (EST) dataset. We developed and applied methods that used a range of alignment parameters with increasing permissiveness in terms of gap characters present within an alignment. This procedure facilitated the selection of phylogenomic data subsets from large amounts of transcriptome data. The results included 19 nested data subsets that ranged from 37 to 4,281 loci. Tree searches on all data subsets reconstructed Xyloplax as a velatid asteroid rather than a new class. This result implies that asteroid morphology remains labile well beyond the establishment of the body plan of the group. In the phylogenetic tree with the highest average asteroid nodal support several monophyletic groups were recovered. In this tree, Forcipulatida and Velatida are monophyletic and form a clade that includes Brisingida as sister to Forcipulatida. Xyloplax is consistently recovered as sister to Pteraster. Paxillosida and Spinulosida are each monophyletic, with Notomyotida as sister to the Paxillosida. Valvatida is recovered as paraphyletic. The results from other data subsets are largely consistent with these results. Our results support the hypothesis that the earliest divergence event among extant asteroids separated Velatida and Forcipulatacea from Valvatacea and Spinulosida.