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1.  A Phylogeny of the Family Poritidae (Cnidaria, Scleractinia) Based on Molecular and Morphological Analyses 
PLoS ONE  2014;9(5):e98406.
The family Poritidae formerly included 6 genera: Alveopora, Goniopora, Machadoporites, Porites, Poritipora, and Stylaraea. Morphologically, the genera can be differentiated based on the number of tentacles, the number of septa and their arrangement, the length of the polyp column, and the diameter of the corallites. However, the phylogenetic relationships within and between the genera are unknown or contentious. On the one hand, Alveopora has been transferred to the Acroporidae recently because it was shown to be more closely related to this family than to the Poritidae by previous molecular studies. On the other hand, Goniopora is morphologically similar to 2 recently described genera, Machadoporites and Poritipora, particularly with regard to the number of septa (approximately 24), but they have not yet been investigated at the molecular level. In this study, we analyzed 93 samples from all 5 poritid genera and Alveopora using 2 genetic markers (the barcoding region of the mitochondrial COI and the ITS region of the nuclear rDNA) to investigate their phylogenetic relationships and to revise their taxonomy. The reconstructed molecular trees confirmed that Alveopora is genetically distant from all poritid genera but closely related to the family Acroporidae, whereas the other genera are genetically closely related. The molecular trees also revealed that Machadoporites and Poritipora were indistinguishable from Goniopora. However, Goniopora stutchburyi was genetically isolated from the other congeneric species and formed a sister group to Goniopora together with Porites and Stylaraea, thus suggesting that 24 septa could be an ancestral feature in the Poritidae. Based on these data, we move G. stutchburyi into a new genus, Bernardpora gen. nov., whereas Machadoporites and Poritipora are merged with Goniopora.
PMCID: PMC4037213  PMID: 24871224
2.  DNA barcoding reveals the coral “laboratory-rat”, Stylophora pistillata encompasses multiple identities 
Scientific Reports  2013;3:1520.
Stylophora pistillata is a widely used coral “lab-rat” species with highly variable morphology and a broad biogeographic range (Red Sea to western central Pacific). Here we show, by analysing Cytochorme Oxidase I sequences, from 241 samples across this range, that this taxon in fact comprises four deeply divergent clades corresponding to the Pacific-Western Australia, Chagos-Madagascar-South Africa, Gulf of Aden-Zanzibar-Madagascar, and Red Sea-Persian/Arabian Gulf-Kenya. On the basis of the fossil record of Stylophora, these four clades diverged from one another 51.5-29.6 Mya, i.e., long before the closure of the Tethyan connection between the tropical Indo-West Pacific and Atlantic in the early Miocene (16–24 Mya) and should be recognised as four distinct species. These findings have implications for comparative ecological and/or physiological studies carried out using Stylophora pistillata as a model species, and highlight the fact that phenotypic plasticity, thought to be common in scleractinian corals, can mask significant genetic variation.
PMCID: PMC3605610  PMID: 23519209
3.  Molecular Evidence Shows Low Species Diversity of Coral-Associated Hydroids in Acropora Corals 
PLoS ONE  2012;7(11):e50130.
A novel symbiosis between scleractinians and hydroids (Zanclea spp.) was recently discovered using taxonomic approaches for hydroid species identification. In this study, we address the question whether this is a species-specific symbiosis or a cosmopolitan association between Zanclea and its coral hosts. Three molecular markers, including mitochondrial 16S and nuclear 28S ribosomal genes, and internal transcribed spacer (ITS), were utilized to examine the existence of Zanclea species from 14 Acropora species and 4 other Acroporidae genera including 142 coral samples collected from reefs in Kenting and the Penghu Islands, Taiwan, Togian Island, Indonesia, and Osprey Reef and Orpheus Island on the Great Barrier Reef, Australia. Molecular phylogenetic analyses of the 16S and 28S genes showed that Acropora-associated Zanclea was monophyletic, but the genus Zanclea was not. Analysis of the ITS, and 16S and 28S genes showed either identical or extremely low genetic diversity (with mean pairwise distances of 0.009 and 0.006 base substitutions per site for the 16S and 28S genes, respectively) among Zanclea spp. collected from diverse Acropora hosts in different geographic locations, suggesting that a cosmopolitan and probably genus-specific association occurs between Zanclea hydroids and their coral hosts.
PMCID: PMC3510231  PMID: 23209655
4.  Stylobates birtlesi sp. n., a new species of carcinoecium-forming sea anemone (Cnidaria, Actiniaria, Actiniidae) from eastern Australia 
ZooKeys  2011;1-13.
We describe a new species of carcinoecium-forming sea anemone, Stylobates birtlesi sp. n., from sites 590–964 m deep in the Coral Sea, off the coast of Queensland, Australia. An anemone of this genus settles on a gastropod shell inhabited by a hermit crab, then covers and extends the shell to produce a chitinous structure termed a carcinoecium. Stylobates birtlesi sp. n. is symbiotic with the hermit crab Sympagurus trispinosus (Balss, 1911). The nature of marginal sphincter muscle and nematocyst size and distribution distinguish Stylobates birtlesi sp. n. from other species in the genus. The four known species of Stylobates are allopatric, each inhabiting a separate ocean basin of the Indo-West Pacific. We also extend the known range of Stylobates loisetteae in the Indian Ocean off the coast of Western Australia.
PMCID: PMC3082962  PMID: 21594082
Anthozoa; Hexacorallia; deep sea; symbiosis; hermit crab
5.  Some Rare Indo-Pacific Coral Species Are Probable Hybrids 
PLoS ONE  2008;3(9):e3240.
Coral reefs worldwide face a variety of threats and many coral species are increasingly endangered. It is often assumed that rare coral species face higher risks of extinction because they have very small effective population sizes, a predicted consequence of which is decreased genetic diversity and adaptive potential.
Methodology/Principal Findings
Here we show that some Indo-Pacific members of the coral genus Acropora have very small global population sizes and are likely to be unidirectional hybrids. Whether this reflects hybrid origins or secondary hybridization following speciation is unclear.
The interspecific gene flow demonstrated here implies increased genetic diversity and adaptive potential in these coral species. Rare Acropora species may therefore be less vulnerable to extinction than has often been assumed because of their propensity for hybridization and introgression, which may increase their adaptive potential.
PMCID: PMC2531234  PMID: 18813338
6.  Mitochondrial and Nuclear Genes Suggest that Stony Corals Are Monophyletic but Most Families of Stony Corals Are Not (Order Scleractinia, Class Anthozoa, Phylum Cnidaria) 
PLoS ONE  2008;3(9):e3222.
Modern hard corals (Class Hexacorallia; Order Scleractinia) are widely studied because of their fundamental role in reef building and their superb fossil record extending back to the Triassic. Nevertheless, interpretations of their evolutionary relationships have been in flux for over a decade. Recent analyses undermine the legitimacy of traditional suborders, families and genera, and suggest that a non-skeletal sister clade (Order Corallimorpharia) might be imbedded within the stony corals. However, these studies either sampled a relatively limited array of taxa or assembled trees from heterogeneous data sets. Here we provide a more comprehensive analysis of Scleractinia (127 species, 75 genera, 17 families) and various outgroups, based on two mitochondrial genes (cytochrome oxidase I, cytochrome b), with analyses of nuclear genes (ß-tubulin, ribosomal DNA) of a subset of taxa to test unexpected relationships. Eleven of 16 families were found to be polyphyletic. Strikingly, over one third of all families as conventionally defined contain representatives from the highly divergent “robust” and “complex” clades. However, the recent suggestion that corallimorpharians are true corals that have lost their skeletons was not upheld. Relationships were supported not only by mitochondrial and nuclear genes, but also often by morphological characters which had been ignored or never noted previously. The concordance of molecular characters and more carefully examined morphological characters suggests a future of greater taxonomic stability, as well as the potential to trace the evolutionary history of this ecologically important group using fossils.
PMCID: PMC2528942  PMID: 18795098
7.  Diverse staghorn corals (Acropora) in high-latitude Eocene assemblages: implications for the evolution of modern diversity patterns of reef corals 
Acropora is the most diverse genus of reef-building corals in the world today. It occurs in all three major oceans; it is restricted to latitudes 31° N–31° S, where most coral reefs occur, and reaches greatest diversity in the central Indo-Pacific. As an exemplar genus, the long-term history of Acropora has implications for the evolution and origins of present day biodiversity patterns of reef corals and for predicting their response to future climate change. Diversification of Acropora was thought to have occurred in the central Indo-Pacific within the previous two million years. We examined Eocene fossils from southern England and northern France and found evidence that precursors of up to nine of 20 currently recognized Acropora species groups existed 49–34 Myr, at palaeolatitudes far higher than current limits, to 51° N. We propose that pre-existing diversity contributed to later rapid speciation in this important functional group of corals.
PMCID: PMC1560246  PMID: 16627283
Eocene; coral reefs; biogeography; climate change; molecular clock

Results 1-7 (7)