Molecular Phylogeny and Taxonomy of the Coral Genus Cyphastrea (Cnidaria, Scleractinia, Merulinidae) in Japan, With the First Records of Two Species.

The scleractinian coral genus Cyphastrea is widely distributed in the Indo-Pacific region and is common from the subtropical to the warm-temperate regions in Japan. Three new species in this genus have recently been reported from south-eastern Australia or the Red Sea. However, taxonomic and species diversity have been little studied so far in Japan. In this study, we analyzed 112 specimens of Cyphastrea collected from the subtropical to the warm-temperate regions in Japan to clarify the species diversity in the country. This analysis was based on skeletal morphological and molecular analyses using three genetic markers of the nuclear 28S rDNA, histone H3 gene, and the mitochondrial noncoding intergenic region between COI and tRNAmet. The molecular phylogenetic trees showed that our specimens are separated mainly into four clades. Considering the morphological data with the molecular phylogenetic relationships, we confirmed a total of nine species, including two species, C. magna and C. salae, recorded for the first time in Japan. Although eight out of nine species were genetically included within Cyphastrea, one species, C. agassizi, was genetically distant from all other species and was closely related to the genus Leptastrea, suggesting the return of this species to the genus to which it was originally ascribed. Two newly recorded species were reciprocally monophyletic, while the other six species (excluding C. agassizi) clustered in two clades without forming species-specific lineages, including three polyphyletic species. Thus, the species boundary between species in Cyphastrea remains unclear in most species using these three sequenced loci.

Morpho-Molecular Evidence for Polymorphism in the Mushroom Coral Cycloseris hexagonalis (Scleractinia: Fungiidae), with a New Phylogenetic Position and the Establishment of a New Genus for the Species.

Mushroom corals are reef corals of the family Fungiidae, which live in the tropical and subtropical Indo-Pacific region. Recently, most species of this family have been revised taxonomically based on morphological and molecular analyses. However, the phylogenetic position of Cycloseris hexagonalis ( Milne Edwards and Haime, 1848 ) has not been analyzed and remains unclear. This species is believed to show allometric growth by changing its corallum shape from hexagonal in juveniles to irregularly circular with an undulated corallum margin in mature individuals. However, these morphological changes have not been monitored and their genetic basis has not been confirmed. In the present study morphological and molecular phylogenetic analyses were performed to evaluate the identity of the morpho-types in C. hexagonalis and to clarify the phylogenetic and taxonomic position of the species. In the morphological analysis, we used 20 specimens of C. hexagonalis collected from around Iriomote Island, Okinawa, Japan, and identified four morphotypes. Moreover, the molecular phylogenetic analyses using mitochondrial COI and nuclear ITS markers showed that all morpho-types of C. hexagonalis together form an independent clade, indicating that they are all conspecific. Molecular phylogenetic comparison between this species and other fungiids revealed that the clade of C. hexagonalis is clearly distant from the Cycloseris clade as well as from clades representing other genera in the Fungiidae. Considering these data, we establish a monotypic new genus, Sinuorota, to accommodate C. hexagonalis.

The reef-building coral Acropora conditionally hybridize under sperm limitation.

Multi-specific synchronous spawning risks both sperm limitation, which reduces fertilization success, and hybridization with other species. If available sperm of conspecifics are limited, hybridization with heterospecific sperm could be an alternative. Some species of the reef-building coral Acropora produce hybrid offspring in vitro, and therefore hybridization between such species does sometimes occur in nature. Here, we report that the interbreeding species Acropora florida and A. intermedia preferentially bred with conspecifics at optimal gamete concentrations (10(6) cells ml(-1)), but when sperm concentration was low (10(4) cells ml(-1)), A florida eggs displayed an increased incidence of fertilization by sperm of A intermedia However, A intermedia eggs never crossed with heterospecific sperm, regardless of gamete concentrations. It appears that A florida eggs conditionally hybridize with heterospecific sperm; in nature, this would allow A florida to cross with later-spawning species such as A intermedia These results indicate that hybridization between some Acropora species could occur in nature according to the number of available sperm, and the choice of heterospecific sperm for fertilization could be one of the fertilization strategies in the sperm-limited condition.

Molecular cytogenetic analysis of the scleractinian coral Acropora solitaryensis Veron & Wallace 1984.

We performed a molecular cytogenetic investigation of the scleractinian coral Acropora solitaryensis, which is dominant in the temperate region of Japan (30-35°N). Molecular cytogenetic analysis, using fluorescence in situ hybridization (FISH), was carried out for karyotyping and gene mapping. We propose the karyotype of this coral (2n = 30) based on C-banding and FISH analyses. FISH mapping of the rRNA gene was carried out with a probe generated by PCR amplification using rRNA gene primers. Furthermore, the telomeres and centromeres of all chromosomes were visualized using FISH. By comparative genomic hybridization using DNA from sperm and unfertilized eggs of this coral, we offer evidence suggesting the existence of sex chromosomes in this species. Collectively, these data advance our understanding of coral genetics.

Paragoniastreavariabilis Kishi, Nomura & Fukami, sp. nov. (Cnidaria, Anthozoa, Scleractinia), a new coral species previously considered as a variant of Paragoniastreadeformis, from Japan and northern Taiwan.

A new zooxanthellate scleractinian coral, Paragoniastreavariabilis Kishi, Nomura & Fukami, sp. nov. (Scleractinia, Merulinidae), is described from non-coral reef regions of Japan and northern Taiwan. This new species was previously recognized as a morphological variant of Paragoniastreadeformis (Veron, 1990) and can be morphologically distinguished from that species by lacking groove-and-tube structures on corallite wall joints, and by having larger calices, numerous septa, and up to three corallites in one valley. The new species also formed an independent clade from its congeners, P.australensis (Milne Edwards & Haime, 1857), P.deformis and P.russelli (Wells, 1954), in the molecular phylogeny based on the mitochondrial intergenic region and nuclear ribosomal internal transcribed spacers.

Novel organization of the mitochondrial genome in the deep-sea coral, Madrepora oculata (Hexacorallia, Scleractinia, Oculinidae) and its taxonomic implications.

Madrepora is one of the most ecologically important genera of reef-building scleractinians in the deep sea, occurring from tropical to high-latitude regions. Despite this, the taxonomic affinities and relationships within the genus Madrepora remain unclear. To clarify these issues, we sequenced the mitochondrial (mt) genome of the most widespread Madrepora species, M. oculata, and compared this with data for other scleractinians. The architecture of the M. oculata mt genome was very similar to that of other scleractinians, except for a novel gene rearrangement affecting only cox2 and cox3. This pattern of gene organization was common to four geographically distinct M. oculata individuals as well as the congeneric species M. minutiseptum, but was not shared by other genera that are closely related on the basis of cox1 sequence analysis nor other oculinids, suggesting that it might be unique to Madrepora.

Evidence of genetic and reproductive isolation between two morphs of subtropical-dominant coral Acropora solitaryensis in the non-reef region of Japan.

We reveal the existence of a cryptic species of Acropora solitaryensis ( Veron and Wallace, 1984 ), a dominant species in high-latitude coral communities. Although some morphs, such as arborescent table (AR), solid plate (PL), and intermediate (IM) forms, had been known in this species, it was unclear whether these are reproductively isolated from one another. Here, potential reproductive exchange between two representative morphs, AR and PL, were examined using genetic and reproductive methods. Molecular phylogenetic analyses using both mitochondrial and nuclear molecular markers (mitochondrial control region and mini-collagen intron, respectively) indicated that AR is clearly distinct from PL, suggesting that gene flow between the morphs is absent. In cross-fertilization experiments, gametic compatibility between AR and PL was extremely low, suggesting prezygotic isolation of these morphs. These results strongly suggest that AR and IM forms are variations of A. solitaryensis, whereas PL form may be an undescribed species. In addition, AR was closely related genetically to A. pruinosa, which is a high-latitude species with arborescent form, and AR and A. pruinosa were able to hybridize, although with lower fertilities than observed in intra-specific crosses. The two species are thus likely to have speciated not in tropical regions, but in non-reef regions due to habitat segregation.

Symbiodinium clade C dominates zooxanthellate corals (Scleractinia) in the temperate region of Japan.

Endosymbiotic algae of the genus Symbiodinium have been divided into nine clades (A-I) following genetic classification; some clades are known to have physiological properties that enable the coral hosts to adapt to different environmental conditions. To understand the relationships of coral-alga symbioses, we focused on Symbiodinium diversity in zooxanthellate corals living under the severe environmental conditions of the temperate region (30°-35°N) of Japan. We investigated Symbiodinium clades in 346 colonies belonging to 58 coral species from six locations. We then selected three coral species-Acropora hyacinthus, Acropora japonica, and Cyphastrea chalcidicum-to investigate whether Symbiodinium clades changed during winter or summer over the course of year (May 2009-Apr 2010) in Tanabe Bay, Japan. Three Symbiodinium clades (C, D, and F) were detected in corals in the temperate region. Notably, 56 coral species contained Symbiodinium clade C. Oulastrea crispata predominantly contained clade D, but traces of clade C were also detected in all samples. The temperate-specific species Alveopora japonica contained clades C and F simultaneously. Seasonal change of symbiont clades did not occur in the three coral species during the investigation period where SSTs range on 12.5-29.2°C. However, we found Acropora (2 spp.) and Cyphastrea (1 sp.) contained different subcladal types of clade C. These results reveal that most coral species harbored Symbiodinium clade C stably throughout the year, suggesting that Symbiodinium clade C shows low-temperature tolerance, and that two hypothetical possibilities; genetic differences of subcladal types generating physiological differences or wide physiological flexibility in the clade C.

Xeniakonohana sp. nov. (Cnidaria, Octocorallia, Alcyonacea), a new soft coral species in the family Xeniidae from Miyazaki, Japan.

A new soft coral species, Xeniakonohana sp. nov. (Alcyonacea, Xeniidae), is described from Miyazaki in the warm-temperate region of Japan. This new species has conspicuous and unique spindle sclerites in addition to the simple ellipsoid platelet-shaped sclerites typically found in the genus Xenia. These unique spindles are a specific key morphological characteristic for this new species and for differentiating this species among congeneric species.

First evidence for backcrossing of F1 hybrids in Acropora corals under sperm competition.

Acropora is a species-rich genus of reef-building corals with highly diverse morphologies. Hybridization among intercrossing species potentially influences species diversity within Acropora. However, the mechanisms that allow hybridization/backcrossing remain unknown. Although we tested a limited number of species, we hypothesized that Acropora gametes in the Indo-Pacific may preferentially fertilize conspecific gametes despite their compatibility with heterospecific gametes, leading to infrequent hybridization between potentially intercrossing species. In this study, F1 hybrids of Acropora florida and A. intermedia showed specific fertilization trends. For example, sperm had the ability to backcross with the parental species even in the presence of sperm from the parental species. Also, eggs of the hybrids produced from A. florida eggs and A. intermedia sperm ("FLOint") exhibited self-fertilization. Since a low ratio of hybridization between A. florida and A. intermedia is predicted, the population size of hybrids should be small. Therefore, self-fertilization would facilitate reproduction of the hybrid in nature, while remaining sperm could outcompete parental species sperm to backcross with eggs. Although we succeeded in breeding two colonies of hybrids, it is reasonable to speculate that hybrids show a high tendency to choose the most efficient sexual reproduction tactics.

Cleaning up the 'Bigmessidae': molecular phylogeny of scleractinian corals from Faviidae, Merulinidae, Pectiniidae and Trachyphylliidae.

BACKGROUND: Molecular phylogenetic studies on scleractinian corals have shown that most taxa are not reflective of their evolutionary histories. Based principally on gross morphology, traditional taxonomy suffers from the lack of well-defined and homologous characters that can sufficiently describe scleractinian diversity. One of the most challenging clades recovered by recent analyses is 'Bigmessidae', an informal grouping that comprises four conventional coral families, Faviidae, Merulinidae, Pectiniidae and Trachyphylliidae, interspersed among one another with no apparent systematic pattern. There is an urgent need for taxonomic revisions in this clade, but it is vital to first establish phylogenetic relationships within the group. In this study, we reconstruct the evolutionary history of 'Bigmessidae' based on five DNA sequence markers gathered from 76 of the 132 currently recognized species collected from five reef regions in the central Indo-Pacific and the Atlantic. RESULTS: We present a robust molecular phylogeny of 'Bigmessidae' based on the combined five-gene data, achieving a higher degree of resolution compared to previous analyses. Two Pacific species presumed to be in 'Bigmessidae' are more closely related to outgroup clades, suggesting that other unsampled taxa have unforeseen affinities. As expected, nested within 'Bigmessidae' are four conventional families as listed above, and relationships among them generally corroborate previous molecular analyses. Our more resolved phylogeny supports a close association of Hydnophora (Merulinidae) with Favites + Montastraea (Faviidae), rather than with the rest of Merulinidae, i.e., Merulina and Scapophyllia. Montastraea annularis, the only Atlantic 'Bigmessidae' is sister to Cyphastrea, a grouping that can be reconciled by their septothecal walls, a microstructural feature of the skeleton determined by recent morphological work. Characters at the subcorallite scale appear to be appropriate synapomorphies for other subclades, which cannot be explained using macromorphology. Indeed, wide geographic sampling here has revealed more instances of possible cryptic taxa confused by evolutionary convergence of gross coral morphology. CONCLUSIONS: Numerous examples of cryptic taxa determined in this study support the assertion that diversity estimates of scleractinian corals are erroneous. Fortunately, the recovery of most 'Bigmessidae' genera with only minor degrees of paraphyly offers some hope for impending taxonomic amendments. Subclades are well defined and supported by subcorallite morphological features, providing a robust framework for further systematic work.

Conventional taxonomy obscures deep divergence between Pacific and Atlantic corals.

Only 17% of 111 reef-building coral genera and none of the 18 coral families with reef-builders are considered endemic to the Atlantic, whereas the corresponding percentages for the Indo-west Pacific are 76% and 39%. These figures depend on the assumption that genera and families spanning the two provinces belong to the same lineages (that is, they are monophyletic). Here we show that this assumption is incorrect on the basis of analyses of mitochondrial and nuclear genes. Pervasive morphological convergence at the family level has obscured the evolutionary distinctiveness of Atlantic corals. Some Atlantic genera conventionally assigned to different families are more closely related to each other than they are to their respective Pacific 'congeners'. Nine of the 27 genera of reef-building Atlantic corals belong to this previously unrecognized lineage, which probably diverged over 34 million years ago. Although Pacific reefs have larger numbers of more narrowly distributed species, and therefore rank higher in biodiversity hotspot analyses, the deep evolutionary distinctiveness of many Atlantic corals should also be considered when setting conservation priorities.

An efficient coral survey method based on a large-scale 3-D structure model obtained by Speedy Sea Scanner and U-Net segmentation.

Over the last 3 decades, a large portion of coral cover has been lost around the globe. This significant decline necessitates a rapid assessment of coral reef health to enable more effective management. In this paper, we propose an efficient method for coral cover estimation and demonstrate its viability. A large-scale 3-D structure model, with resolutions in the x, y and z planes of 0.01 m, was successfully generated by means of a towed optical camera array system (Speedy Sea Scanner). The survey efficiency attained was 12,146 m2/h. In addition, we propose a segmentation method utilizing U-Net architecture and estimate coral coverage using a large-scale 2-D image. The U-Net-based segmentation method has shown higher accuracy than pixelwise CNN modeling. Moreover, the computational cost of a U-Net-based method is much lower than that of a pixelwise CNN-based one. We believe that an array of these survey tools can contribute to the rapid assessment of coral reefs.

High species diversity of the soft coral family Xeniidae (Octocorallia, Alcyonacea) in the temperate region of Japan revealed by morphological and molecular analyses.

The soft coral family Xeniidae, commonly found in tropical and subtropical regions, consists of 20 genera and 162 species. To date, few studies on this family have been conducted in Japan, especially at higher latitudes. Although molecular phylogenetic analyses have recently been used to distinguish soft coral species, it is difficult to identify species and genera in this family due to the limited taxonomic indices and high morphological variation. In this study, we found a large Xeniidae community off the coast of Oshima Island (31°31.35'N, 131°24.27'E) at Miyazaki, Kyushu Island, located in the temperate region of Japan. The species composition and molecular phylogenetic relationships were investigated to uncover the species diversity of Xeniidae in this community. A total of 182 xeniid specimens were collected and identified to the species level, after which the samples were molecularly analyzed using a mitochondrial marker (ND2) and a nuclear marker (ITS) to infer the phylogenetic relationships. A total of 14 xeniid species were identified, including five undescribed species from five genera (Anthelia, Heteroxenia, Sympodium, Xenia, and Yamazatum). Miyazaki was identified as having the highest xeniid species diversity in Japan. The molecular phylogenetic trees inferred from each marker recovered very similar topologies: four genera (Anthelia, Heteroxenia, Sympodium, and Yamazatum) were monophyletic, whereas one (Xenia) was polyphyletic. Thus, except for Xenia, the morphological characteristics used for traditional taxonomy well reflected the phylogeny of the Xeniidae at the genus level. On the other hand, our results show that further taxonomic revisions of Xenia are needed.

Maternal inheritance of F1 hybrid morphology and colony shape in the coral genus Acropora.

BACKGROUND: The coral genus Acropora contains more than 150 species with very high morphological diversity. This high diversity may have been caused by repeated hybridization via mass spawning. However, we have little information whether hybrids are formed in these corals. Identifying morphological differences between hybrids and their parental species would provide an opportunity to find wild hybrids in the field and to understand how colony shapes of Acropora have become highly diversified throughout evolutionary history. In the two morphologically distinctive coral species Acropora florida and A. intermedia in the Indo-Pacific, their gametes show high rates of bi-directional intercrossing in vitro, and thus these two species are ideal species to investigate the morphological traits of the hybrids. METHODS: We examined morphological characters of F1 hybrids from A. florida to A. intermedia, which were produced from in vitro crossing experiments. To compare morphological differences, we grew juveniles and mature colonies of reciprocal F1 hybrids (FLOint: A. florida eggs × A. intermedia sperm, and INTflo: A. intermedia eggs × A. florida sperm) and of the parental species (purebreds of A. intermedia and A. florida). We analyzed skeletal morphology such as colony size, branch length, and branching number, and compared them with those of a putative F1 hybrid between A. florida and A. intermedia found in the field. We also confirmed the molecular phylogenetic position of F1 hybrids, parental species, and a putative F1 hybrid using the mitochondrial non-coding region. RESULTS: Our morphological analysis revealed that branching number of the F1 hybrids was intermediate relative to the parental species. Moreover, the FLOint hybrids were morphologically more closely related to the maternal species A. florida, and the INTflo hybrids were to A. intermedia. Molecular data showed that A. florida and A. intermedia were clearly divided into two clades, and that F1 hybrids grouped in the clade based on their maternal parent. A very similar pattern to the INTflo hybrids was obtained for the putative F1 hybrid in nature. DISCUSSION: Our results revealed that F1 hybrids between two Indo-Pacific species A. florida and A. intermedia had intermediate morphology relative to their parent species but reflected the maternal parent more. Similarity to maternal species in hybrids is opposite to the Caribbean Acropora species that had more paternal morphological characters in hybrids. These results further suggest that some genetic factor in eggs is likely to affect determination of colony shape in the Indo-Pacific. At present, we have considered colonies with intermediate morphs between different species to be intra-specific morphological variation, but they may be real F1 hybrids. Indeed, a putative F1 hybrid represented similar morphological and molecular features to the F1 hybrids, and thus it is plausible to be attributed as a "real" F1 hybrid in nature.

Loss and Gain of Group I Introns in the Mitochondrial Cox1 Gene of the Scleractinia (Cnidaria; Anthozoa).

Yaoyang Chuang, Marcelo Kitahara, Hironobu Fukami, Dianne Tracey, David J. Miller, and Chaolun Allen Chen (2017) Group I introns encoding a homing endonuclease gene (HEG) that is potentially capable of sponsoring mobility are present in the cytochrome oxidase subunit 1 (cox1) gene of some Hexacorallia, including a number of scleractinians assigned to the "robust" coral clade. In an e ort to infer the evolutionary history of this cox1 group I intron, DNA sequences were determined for 12 representative "basal" and "complex" corals and for 11 members of the Corallimorpharia, a sister order of the Scleractinia. Comparisons of insertion sites, secondary structures, and amino acid sequences of the HEG implied a common origin for cox1 introns of corallimorpharians, and basal and complex corals, but cox1 introns of robust corals were highly divergent, most likely reflecting independent acquisition. Phylogenetic analyses with a calibrated molecular clock suggested that cox1 introns of scleractinians and corallimorpharians have persisted at the same insertion site as that in the common ancestor 552 million years ago (mya). This ancestral intron was probably lost in complex corals around 213 to 190 mya at the junction between the Trassic and Jurassic. The coral cox1 gene remained intronless until new introns, probably from sponges or fungi, reinvaded different positions of the cox1 gene in robust corals around 135 mya in the Cretaceous, and then it subsequently began to lose them around 65.5 mya in some robust coral lineages coincident with the later Maastrichtian extinction at the Cretaceous-Tertiary boundary.

Geographic differences in species boundaries among members of the Montastraea annularis complex based on molecular and morphological markers.

The three members of the Montastraea annularis complex (M. annularis, M. franksi, and M. faveolata) are dominant reef builders in the western Atlantic whose species status has been controversial for over a decade. Although differences in colony morphology and reproductive characteristics exist, interspecific fertilizations are possible in the laboratory and genetic differentiation is slight. Here we compare the three taxa genetically and morphologically in Panama and the Bahamas, widely separated locations spanning most of their geographic ranges. In Panama, analyses of three AFLP loci, a noncoding region of the mitochondrial genome, and ITS sequences reveal that M. faveolata is strongly differentiated genetically. Discriminant function analysis also indicates no overlap with the other two species in the fine structure of the corallites that comprise the colony. Genetic analyses of larvae from interspecific crosses between M. faveolata and the other two taxa confirmed the hybrid status of the larvae, but no examples of the most probable F1 genotype were observed in the field. Although M. annularis and M. franksi were more similar, they also exhibited strong frequency differences at two AFLP loci and in the mitochondrial noncoding region, as well as distinct corallite structure. In the Bahamas, in contrast, the three taxa exhibited overlapping morphologies. Montastraeafranksi and M. annularis were indistinguishable genetically, and M. faveolata was distinct at fewer genetic loci. Once again, however, the most probable F1 genotype involving M. faveolata was not observed. Geographic differences between Panama and the Bahamas explain why past studies have come to different conclusions concerning the status of the three species. In general, the genetic and morphological data suggest a north to south hybridization gradient, with evidence for introgression strongest in the north. However, reproductive data show no such trend, with intrinsic barriers to gene flow comparable or stronger in the north.

Mechanisms of reproductive isolation among sympatric broadcast-spawning corals of the Montastraea annularis species complex.

Many coral species spawn simultaneously and have compatible gametes, leading to controversy over the nature of species boundaries and the frequency with which hybridization occurs. Three western Atlantic corals, Montastraea annularis, M. faveolata, and M. franksi, typify this controversy; they all spawn sympatrically on the same evenings after the fall full moons. Here we show, in both Panama and the Bahamas for multiple years, how a variety of mechanisms may act in concert to reproductively isolate all three species. Field studies indicate that M. franksi spawns two hours earlier than the other two species, and the eggs released during this earlier period disperse an average of 500 m by the time the other species spawn. Field measures of fertilization indicate that peak fertilization occurs when spawning synchrony is high and that corals that spawn at the tails of the spawning distributions have greatly reduced fertilization success. Laboratory studies indicate that there is a gametic incompatibility between M. faveolata and the other two species. There are regional differences in the gametic compatibility of M. franksi and M. annularis. In Panama, the two species are completely compatible, whereas in the Bahamas, M. franksi sperm can fertilize M. annularis eggs but the reciprocal cross often fails. Gamete age influences patterns of fertilization, such that very young eggs seem resistant to fertilization and old sperm lose viability after two hours. In sum, the combination of temporal differences in spawning, sperm aging, gamete dispersal and dilution, and gametic incompatibility act in various combinations among the three species, making it unlikely that hybrid fertilization would occur.

A phylogeny of the family Poritidae (Cnidaria, Scleractinia) based on molecular and morphological analyses.

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.

Mitochondrial genome rearrangements in the scleractinia/corallimorpharia complex: implications for coral phylogeny.

Corallimorpharia is a small Order of skeleton-less animals that is closely related to the reef-building corals (Scleractinia) and of fundamental interest in the context of understanding the potential impacts of climate change in the future on coral reefs. The relationship between the nominal Orders Corallimorpharia and Scleractinia is controversial-the former is either the closest outgroup to the Scleractinia or alternatively is derived from corals via skeleton loss. This latter scenario, the "naked coral" hypothesis, is strongly supported by analyses based on mitochondrial (mt) protein sequences, whereas the former is equally strongly supported by analyses of mt nucleotide sequences. The "naked coral" hypothesis seeks to link skeleton loss in the putative ancestor of corallimorpharians with a period of elevated oceanic CO2 during the Cretaceous, leading to the idea that these skeleton-less animals may be harbingers for the fate of coral reefs under global climate change. In an attempt to better understand their evolutionary relationships, we examined mt genome organization in a representative range (12 species, representing 3 of the 4 extant families) of corallimorpharians and compared these patterns with other Hexacorallia. The most surprising finding was that mt genome organization in Corallimorphus profundus, a deep-water species that is the most scleractinian-like of all corallimorpharians on the basis of morphology, was much more similar to the common scleractinian pattern than to those of other corallimorpharians. This finding is consistent with the idea that C. profundus represents a key position in the coral <-> corallimorpharian transition.