The Experts below are selected from a list of 324 Experts worldwide ranked by ideXlab platform
Danwei Huang - One of the best experts on this subject based on the ideXlab platform.
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Transcriptome-based target-enrichment baits for stony corals (Cnidaria: Anthozoa: Scleractinia).
Molecular ecology resources, 2020Co-Authors: Randolph Z. B. Quek, Sudhanshi Sanjeev Jain, Mei Lin Neo, Greg W. Rouse, Danwei HuangAbstract:Despite the ecological and economic significance of stony corals (Scleractinia), a robust understanding of their phylogeny remains elusive due to patchy taxonomic and genetic sampling, as well as the limited availability of informative markers. To increase the number of genetic loci available for phylogenomic analyses in Scleractinia, we designed 15,919 DNA enrichment baits targeting 605 orthogroups (mean 565 ± SD 366 bp) over 1,139 exon regions. A further 236 and 62 barcoding baits were designed for COI and histone H3 genes respectively for quality and contamination checks. Hybrid capture using these baits was performed on 18 coral species spanning the presently understood Scleractinian phylogeny, with two corallimorpharians as outgroup. On average, 74% of all loci targeted were successfully captured for each species. Barcoding baits were matched unambiguously to their respective samples and revealed low levels of cross-contamination in accordance with expectation. We put the data through a series of stringent filtering steps to ensure only Scleractinian and phylogenetically informative loci were retained, and the final probe set comprised 13,479 baits, targeting 452 loci (mean 531 ± SD 307 bp) across 865 exon regions. Maximum likelihood, Bayesian and species tree analyses recovered maximally supported, topologically congruent trees consistent with previous phylogenomic reconstructions. The phylogenomic method presented here allows for consistent capture of orthologous loci among divergent coral taxa, facilitating the pooling of data from different studies and increasing the phylogenetic sampling of Scleractinians in the future.
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Effects of missing data and data type on phylotranscriptomic analysis of stony corals (Cnidaria: Anthozoa: Scleractinia).
Molecular phylogenetics and evolution, 2019Co-Authors: Zheng Bin Randolph Quek, Danwei HuangAbstract:Across the tree of life, phylogenetic analysis is increasingly being performed using transcriptome data. As a result of heterogeneous gene expression within individual organisms and unequal sequencing depth between samples, coverage of homologous loci in such datasets is typically inhomogeneous. Consequently, missing data are a common feature of phylotranscriptomic inference, but their impact on phylogenetic analysis remains poorly characterised empirically. Considering the complexity of the evolutionary history of stony corals (Cnidaria: Anthozoa: Scleractinia), transcriptome data hold great promise for resolving their phylogeny, particularly if there is a good understanding of missing data and data type (either amino acid or DNA) effects. Here, we reconstructed a broad phylogenetic tree of 39 Scleractinian species with 3 corallimorpharians as outgroups, including 15 transcriptomes that were newly sequenced and assembled in this study. Between 63 and 505 loci were used to analyse the Scleractinian phylogeny, and we quantified differences in tree topology, tree shape, bootstrap support and effects of conflicting gene trees among datasets of varying completeness for both amino acid and DNA sequences. Even with almost 70% missing data, tree topologies appear to be mostly unaffected, although there are higher incongruence levels in the less complete datasets. Furthermore, DNA trees outperform amino acid trees in bootstrap support and robustness against incongruent loci. Overall, our findings indicate that high levels of missing data can still produce expected tree topologies, but identifying and omitting incongruent loci can lead to more consistent branch length estimates.
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Species
2018Co-Authors: Danwei Huang, Emma E. Goldberg, Loke Ming Chou, Kaustuv RoyAbstract:List of all Scleractinian corals showing reef species, geographic states according to Hughes et al. (2013) and Veron et al. (2009, 2011) (0 = widespread, 1 = endemic to CT, 2 = outside of CT), as well as GenBank and morphological data sources used to reconstruct the phylogeny of Scleractinia (doi:10.1098/rstb.2014.0010) and Acroporidae
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RSTBtree
2018Co-Authors: Danwei Huang, Emma E. Goldberg, Loke Ming Chou, Kaustuv RoyAbstract:1000 posterior trees of Scleractinia based on random resolutions of the supertree (doi:10.1098/rstb.2014.0010); used for GeoSSE analyses
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Cyphastrea salae, a new species of hard coral from Lord Howe Island, Australia (Scleractinia, Merulinidae)
ZooKeys, 2017Co-Authors: Andrew H. Baird, Mia O. Hoogenboom, Danwei HuangAbstract:A new zooxanthellate reef-dwelling Scleractinian coral species, Cyphastrea salaesp. n. (Scleractinia, Merulinidae), is described from Lord Howe Island Australia. The new species can be distinguished morphologically from the only other congeneric species on Lord Howe Island, C. microphthalma, by the number of primary septa (12 vs. 10) and the much taller corallites (mean ± SE: 1.0 ± 0.07 mm v 0.4 ± 0.04 mm). The relationship of C. salae to four of the other eleven currently accepted species in the genus was explored through analyses of nuclear (28S rDNA) and mitochondrial (noncoding intergenic region) gene sequences. Cyphastrea salaesp. n. forms a strongly supported clade that is distinct from a clade containing three species found commonly in Australia, C. chalcidicum, C. serailia, and C. microphthalma. One specimen was also found in the Solitary Islands, another high latitude location in south-eastern Australia. The discovery of a new species in the genus Cyphastrea on high latitude reefs in south-eastern Australia suggests that other new species might be found among more diverse genera represented here and that the Scleractinian fauna of these isolated locations is more distinct than previously recognised.
Stephen D Cairns - One of the best experts on this subject based on the ideXlab platform.
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Scleractinian corals recorded in the Argentinean Antarctic expeditions between 2012 and 2014, with comments on Flabellum (Flabellum) areum Cairns, 1982
Polar Research, 2016Co-Authors: Laura Schejter, Claudia Bremec, Stephen D CairnsAbstract:In this contribution, we provide a list of the Scleractinian corals recorded during the Argentinean Antarctic expeditions on board the oceanographic vessel Puerto Deseado (Argentina) in the austral summers in 2012, 2013 and 2014. The identified taxa consist of six solitary species ( Flabellum impensum, F. flexuosum, F. areum, Caryophyllia antarctica, Paraconotrochus antarcticus and Javania antarctica ), recorded from 19 sampling sites located off the Antarctic Peninsula and South Shetland and South Orkney islands. We also update the information of F. areum, previously known only from south-west Atlantic waters, extending its distribution range to Antarctic waters and its upper bathymetric range to 218 m. Keywords: cold-water corals; Antarctica; range extension; bathymetric range extension; Scleractinia. (Published. 4 July 2016) To access the supplementary material for this article, please see the supplementary files in the column to the right (under Article Tools). Citation: Polar Research 2016, 35 , 29762, http://dx.doi.org/10.3402/polar.v35.29762
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Deltocyathiidae, an early‐diverging family of Robust corals (Anthozoa, Scleractinia)
Zoologica Scripta, 2012Co-Authors: Marcelo V. Kitahara, Stephen D Cairns, Jarosław Stolarski, David J. MillerAbstract:Over the last decade, molecular phylogenetics has called into question some fundamental aspects of coral systematics. Within the Scleractinia, most families composed exclusively by zooxanthellate species are polyphyletic on the basis of molecular data, and the second most speciose coral family, the Caryophylliidae (most members of which are azooxanthellate), is an unnatural grouping. As part of the process of resolving taxonomic affinities of 'caryophylliids', here a new 'Robust' Scleractinian family (Deltocyathiidae fam. n.) is proposed on the basis of combined molecular (CO1 and 28S rDNA) and morphological data, accommodating the early-diverging clade of traditional caryophylliids (represented today by the genus Deltocyathus). Whereas this family captures the full morphological diversity of the genus Deltocyathus, one species, Deltocyathus magnificus, is an outlier in terms of molecular data, and groups with the 'Complex' coral family Turbinoliidae. Ultrastructural data, however, place D. magnificus within Deltocyathiidae fam. nov. Unfortunately, limited ultrastructural data are as yet available for turbinoliids, but D. magnificus may represent the first documented case of morphological convergence at the microstructural level among Scleractinian corals.
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The ancient evolutionary origins of Scleractinia revealed by azooxanthellate corals.
BMC evolutionary biology, 2011Co-Authors: Jarosław Stolarski, Stephen D Cairns, Marcelo V. Kitahara, David J. Miller, Maciej Mazur, Anders MeibomAbstract:Scleractinian corals are currently a focus of major interest because of their ecological importance and the uncertain fate of coral reefs in the face of increasing anthropogenic pressure. Despite this, remarkably little is known about the evolutionary origins of corals. The Scleractinia suddenly appear in the fossil record about 240 Ma, but the range of morphological variation seen in these Middle Triassic fossils is comparable to that of modern Scleractinians, implying much earlier origins that have so far remained elusive. A significant weakness in reconstruction(s) of early coral evolution is that deep-sea corals have been poorly represented in molecular phylogenetic analyses. By adding new data from a large and representative range of deep-water species to existing molecular datasets and applying a relaxed molecular clock, we show that two exclusively deep-sea families, the Gardineriidae and Micrabaciidae, diverged prior to the Complexa/Robusta coral split around 425 Ma, thereby pushing the evolutionary origin of Scleractinian corals deep into the Paleozoic. The early divergence and distinctive morphologies of the extant gardineriid and micrabaciid corals suggest a link with Ordovician "Scleractiniamorph" fossils that were previously assumed to represent extinct anthozoan skeletonized lineages. Therefore, Scleractinian corals most likely evolved from Paleozoic soft-bodied ancestors. Modern shallow-water Scleractinia, which are dependent on symbionts, appear to have had several independent origins from solitary, non-symbiotic precursors. The Scleractinia have survived periods of massive climate change in the past, suggesting that as a lineage they may be less vulnerable to future changes than often assumed.
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A Comprehensive Phylogenetic Analysis of the Scleractinia (Cnidaria, Anthozoa) Based on Mitochondrial CO1 Sequence Data
PloS one, 2010Co-Authors: Marcelo V. Kitahara, Stephen D Cairns, Jarosław Stolarski, David Blair, David J. MillerAbstract:Background: Classical morphological taxonomy places the approximately 1400 recognized species of Scleractinia (hard corals) into 27 families, but many aspects of coral evolution remain unclear despite the application of molecular phylogenetic methods. In part, this may be a consequence of such studies focusing on the reef-building (shallow water and zooxanthellate) Scleractinia, and largely ignoring the large number of deep-sea species. To better understand broad patterns of coral evolution, we generated molecular data for a broad and representative range of deep sea Scleractinians collected off New Caledonia and Australia during the last decade, and conducted the most comprehensive molecular phylogenetic analysis to date of the order Scleractinia. Methodology: Partial (595 bp) sequences of the mitochondrial cytochrome oxidase subunit 1 (CO1) gene were determined for 65 deep-sea (azooxanthellate) Scleractinians and 11 shallow-water species. These new data were aligned with 158 published sequences, generating a 234 taxon dataset representing 25 of the 27 currently recognized Scleractinian families. Principal Findings/Conclusions: There was a striking discrepancy between the taxonomic validity of coral families consisting predominantly of deep-sea or shallow-water species. Most families composed predominantly of deep-sea azooxanthellate species were monophyletic in both maximum likelihood and Bayesian analyses but, by contrast (and consistent with previous studies), most families composed predominantly of shallow-water zooxanthellate taxa were polyphyletic, although Acroporidae, Poritidae, Pocilloporidae, and Fungiidae were exceptions to this general pattern. One factor contributing to this inconsistency may be the greater environmental stability of deep-sea environments, effectively removing taxonomic “noise” contributed by phenotypic plasticity. Our phylogenetic analyses imply that the most basal extant Scleractinians are azooxanthellate solitary corals from deep-water, their divergence predating that of the robust and complex corals. Deep-sea corals are likely to be critical to understanding anthozoan evolution and the origins of the Scleractinia.
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Monophyletic origin of Caryophyllia (Scleractinia, Caryophylliidae), with descriptions of six new species
Systematics and Biodiversity, 2010Co-Authors: Marcelo V. Kitahara, Stephen D Cairns, David J. MillerAbstract:The genus Caryophyllia Lamarck, 1816 is the most diverse genus within the azooxanthellate Scleractinia comprising 66 Recent species and a purported 195 nominal fossil species. Examination of part of the deep-sea Scleractinian collection made by the Paris Museum off New Caledonia and part of the material collected by CSIRO off Australian waters revealed the occurrence of 23 species of Caryophyllia, of which six are new to science. All new records, including the new species, are described, and synonyms, distribution, type locality, type material and illustration are provided for each species. An identification key to all Recent species of Caryophyllia is presented. In addition, the validity of the genus Caryophyllia was investigated by phylogenetic analyses of a dataset consisting of partial mitochondrial 16S rRNA sequences from 12 species assigned to this genus together with seven species representing some of the most morphologically similar caryophylliid genera, and 14 non-caryophyllid species representing 14 Scleractinian families. Irrespective of the method of analysis employed, all of the Caryophyllia species formed a well-supported clade together with Dasmosmilia lymani and Crispatotrochus rugosus. Although based on a subset of the Recent Caryophyllia species, these results are consistent with Caryophyllia being a valid genus, but call for a reexamination of Dasmosmilia and Crispatotrochus.
David J. Miller - One of the best experts on this subject based on the ideXlab platform.
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Comparative genomics reveals the distinct evolutionary trajectories of the robust and complex coral lineages
Genome Biology, 2018Co-Authors: Hua Ying, Sylvain Foret, Ira Cooke, Susanne Sprungala, Weiwen Wang, David C. Hayward, Yurong Tang, Gavin Huttley, Eldon E. Ball, David J. MillerAbstract:Background Despite the biological and economic significance of Scleractinian reef-building corals, the lack of large molecular datasets for a representative range of species limits understanding of many aspects of their biology. Within the Scleractinia, based on molecular evidence, it is generally recognised that there are two major clades, Complexa and Robusta, but the genomic bases of significant differences between them remain unclear. Results Draft genome assemblies and annotations were generated for three coral species: Galaxea fascicularis (Complexa), Fungia sp. , and Goniastrea aspera (Robusta). Whilst phylogenetic analyses strongly support a deep split between Complexa and Robusta, synteny analyses reveal a high level of gene order conservation between all corals, but not between corals and sea anemones or between sea anemones. HOX-related gene clusters are, however, well preserved across all of these combinations. Differences between species are apparent in the distribution and numbers of protein domains and an apparent correlation between number of HSP20 proteins and stress tolerance. Uniquely amongst animals, a complete histidine biosynthesis pathway is present in robust corals but not in complex corals or sea anemones. This pathway appears to be ancestral, and its retention in the robust coral lineage has important implications for coral nutrition and symbiosis. Conclusions The availability of three new coral genomes enabled recognition of a de novo histidine biosynthesis pathway in robust corals which is only the second identified biosynthetic difference between corals. These datasets provide a platform for understanding many aspects of coral biology, particularly the interactions of corals with their endosymbionts.
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Complete mitochondrial genome sequences of Atlantic representatives of the invasive Pacific coral species Tubastraea coccinea and T. tagusensis (Scleractinia, Dendrophylliidae): Implications for species identification
Gene, 2016Co-Authors: K. C. C. Capel, Zac H. Forsman, David J. Miller, Mei-fang Lin, Alvaro Esteves Migotto, Carla Zilberberg, Marcelo V. KitaharaAbstract:Members of the azooxanthellate coral genus Tubastraea are invasive species with particular concern because they have become established and are fierce competitors in the invaded areas in many parts of the world. Pacific Tubastraea species are spreading fast throughout the Atlantic Ocean, occupying over 95% of the available substrate in some areas and out-competing native endemic species. Approximately half of all known coral species are azooxanthellate but these are seriously under-represented compared to zooxanthellate corals in terms of the availability of mitochondrial (mt) genome data. In the present study, the complete mt DNA sequences of Atlantic individuals of the invasive Scleractinian species Tubastraea coccinea and Tubastraea tagusensis were determined and compared to the GenBank reference sequence available for a Pacific "T. coccinea" individual. At 19,094bp (compared to 19,070bp for the GenBank specimen), the mt genomes assembled for the Atlantic T. coccinea and T. tagusensis were among the longest sequence determined to date for "Complex" Scleractinians. Comparisons of genomes data showed that the "T. coccinea" sequence deposited on GenBank was more closely related to that from Dendrophyllia arbuscula than to the Atlantic Tubastraea spp., in terms of genome length and base pair similarities. This was confirmed by phylogenetic analysis, suggesting that the former was misidentified and might actually be a member from the genus Dendrophyllia. In addition, although in general the COX1 locus has a slow evolutionary rate in Scleractinia, it was the most variable region of the Tubastraea mt genome and can be used as markers for genus or species identification. Given the limited data available for azooxanthellate corals, the results presented here represent an important contribution to our understanding of phylogenetic relationships and the evolutionary history of the Scleractinia.
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mitochondrial genome rearrangements in the Scleractinia corallimorpharia complex implications for coral phylogeny
Genome Biology and Evolution, 2014Co-Authors: Marcelo V. Kitahara, David J. Miller, Mei-fang Lin, Haiwei Luo, Dianne M. Tracey, Jonathan B. Geller, Hironobu Fukami, Chaolun Allen ChenAbstract: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.
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Mitochondrial Genome Rearrangements in the Scleractinia/Corallimorpharia Complex: Implications for Coral Phylogeny
Genome biology and evolution, 2014Co-Authors: Mei-fang Lin, Marcelo V. Kitahara, David J. Miller, Haiwei Luo, Dianne M. Tracey, Jonathan B. Geller, Hironobu Fukami, Chaolun Allen ChenAbstract: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.
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the naked coral hypothesis revisited evidence for and against Scleractinian monophyly
PLOS ONE, 2014Co-Authors: Marcelo V. Kitahara, David J. Miller, Sylvain Foret, Gavin A Huttley, Chaolun Allen ChenAbstract:The relationship between Scleractinia and Corallimorpharia, Orders within Anthozoa distinguished by the presence of an aragonite skeleton in the former, is controversial. Although classically considered distinct groups, some phylogenetic analyses have placed the Corallimorpharia within a larger Scleractinia/Corallimorpharia clade, leading to the suggestion that the Corallimorpharia are “naked corals” that arose via skeleton loss during the Cretaceous from a Scleractinian ancestor. Scleractinian paraphyly is, however, contradicted by a number of recent phylogenetic studies based on mt nucleotide (nt) sequence data. Whereas the “naked coral” hypothesis was based on analysis of the sequences of proteins encoded by a relatively small number of mt genomes, here a much-expanded dataset was used to reinvestigate hexacorallian phylogeny. The initial observation was that, whereas analyses based on nt data support Scleractinian monophyly, those based on amino acid (aa) data support the “naked coral” hypothesis, irrespective of the method and with very strong support. To better understand the bases of these contrasting results, the effects of systematic errors were examined. Compared to other hexacorallians, the mt genomes of “Robust” corals have a higher (A+T) content, codon usage is far more constrained, and the proteins that they encode have a markedly higher phenylalanine content, leading us to suggest that mt DNA repair may be impaired in this lineage. Thus the “naked coral” topology could be caused by high levels of saturation in these mitochondrial sequences, long-branch effects or model violations. The equivocal results of these extensive analyses highlight the fundamental problems of basing coral phylogeny on mitochondrial sequence data.
Marcelo V. Kitahara - One of the best experts on this subject based on the ideXlab platform.
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Complete mitochondrial genome sequences of Atlantic representatives of the invasive Pacific coral species Tubastraea coccinea and T. tagusensis (Scleractinia, Dendrophylliidae): Implications for species identification
Gene, 2016Co-Authors: K. C. C. Capel, Zac H. Forsman, David J. Miller, Mei-fang Lin, Alvaro Esteves Migotto, Carla Zilberberg, Marcelo V. KitaharaAbstract:Members of the azooxanthellate coral genus Tubastraea are invasive species with particular concern because they have become established and are fierce competitors in the invaded areas in many parts of the world. Pacific Tubastraea species are spreading fast throughout the Atlantic Ocean, occupying over 95% of the available substrate in some areas and out-competing native endemic species. Approximately half of all known coral species are azooxanthellate but these are seriously under-represented compared to zooxanthellate corals in terms of the availability of mitochondrial (mt) genome data. In the present study, the complete mt DNA sequences of Atlantic individuals of the invasive Scleractinian species Tubastraea coccinea and Tubastraea tagusensis were determined and compared to the GenBank reference sequence available for a Pacific "T. coccinea" individual. At 19,094bp (compared to 19,070bp for the GenBank specimen), the mt genomes assembled for the Atlantic T. coccinea and T. tagusensis were among the longest sequence determined to date for "Complex" Scleractinians. Comparisons of genomes data showed that the "T. coccinea" sequence deposited on GenBank was more closely related to that from Dendrophyllia arbuscula than to the Atlantic Tubastraea spp., in terms of genome length and base pair similarities. This was confirmed by phylogenetic analysis, suggesting that the former was misidentified and might actually be a member from the genus Dendrophyllia. In addition, although in general the COX1 locus has a slow evolutionary rate in Scleractinia, it was the most variable region of the Tubastraea mt genome and can be used as markers for genus or species identification. Given the limited data available for azooxanthellate corals, the results presented here represent an important contribution to our understanding of phylogenetic relationships and the evolutionary history of the Scleractinia.
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Description of the mitochondrial genome of the tree coral Dendrophyllia arbuscula (Anthozoa, Scleractinia)
Mitochondrial DNA. Part A DNA mapping sequencing and analysis, 2015Co-Authors: Bruna Louise Pereira Luz, K. C. C. Capel, Sérgio N. Stampar, Marcelo V. KitaharaAbstract:Dendrophylliidae is one of the few monophyletic families within the Scleractinia that embraces zooxanthellate and azooxanthellate species represented by both solitary and colonial forms. Among the exclusively azooxanthellate genera, Dendrophyllia is reported worldwide from 1 to 1200 m deep. To date, although three complete mitochondrial (mt) genomes from representatives of the family are available, only that from Turbinaria peltata has been formally published. Here we describe the complete nucleotide sequence of the mt genome from Dendrophyllia arbuscula that is 19 069 bp in length and comprises two rDNAs, two tRNAs, and 13 protein-coding genes arranged in the canonical Scleractinian mt gene order. No genes overlap, resulting in the presence of 18 intergenic spacers and one of the longest Scleractinian mt genome sequenced to date.
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mitochondrial genome rearrangements in the Scleractinia corallimorpharia complex implications for coral phylogeny
Genome Biology and Evolution, 2014Co-Authors: Marcelo V. Kitahara, David J. Miller, Mei-fang Lin, Haiwei Luo, Dianne M. Tracey, Jonathan B. Geller, Hironobu Fukami, Chaolun Allen ChenAbstract: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.
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Mitochondrial Genome Rearrangements in the Scleractinia/Corallimorpharia Complex: Implications for Coral Phylogeny
Genome biology and evolution, 2014Co-Authors: Mei-fang Lin, Marcelo V. Kitahara, David J. Miller, Haiwei Luo, Dianne M. Tracey, Jonathan B. Geller, Hironobu Fukami, Chaolun Allen ChenAbstract: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.
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the naked coral hypothesis revisited evidence for and against Scleractinian monophyly
PLOS ONE, 2014Co-Authors: Marcelo V. Kitahara, David J. Miller, Sylvain Foret, Gavin A Huttley, Chaolun Allen ChenAbstract:The relationship between Scleractinia and Corallimorpharia, Orders within Anthozoa distinguished by the presence of an aragonite skeleton in the former, is controversial. Although classically considered distinct groups, some phylogenetic analyses have placed the Corallimorpharia within a larger Scleractinia/Corallimorpharia clade, leading to the suggestion that the Corallimorpharia are “naked corals” that arose via skeleton loss during the Cretaceous from a Scleractinian ancestor. Scleractinian paraphyly is, however, contradicted by a number of recent phylogenetic studies based on mt nucleotide (nt) sequence data. Whereas the “naked coral” hypothesis was based on analysis of the sequences of proteins encoded by a relatively small number of mt genomes, here a much-expanded dataset was used to reinvestigate hexacorallian phylogeny. The initial observation was that, whereas analyses based on nt data support Scleractinian monophyly, those based on amino acid (aa) data support the “naked coral” hypothesis, irrespective of the method and with very strong support. To better understand the bases of these contrasting results, the effects of systematic errors were examined. Compared to other hexacorallians, the mt genomes of “Robust” corals have a higher (A+T) content, codon usage is far more constrained, and the proteins that they encode have a markedly higher phenylalanine content, leading us to suggest that mt DNA repair may be impaired in this lineage. Thus the “naked coral” topology could be caused by high levels of saturation in these mitochondrial sequences, long-branch effects or model violations. The equivocal results of these extensive analyses highlight the fundamental problems of basing coral phylogeny on mitochondrial sequence data.
Chaolun Allen Chen - One of the best experts on this subject based on the ideXlab platform.
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Correction: Resurrecting a subgenus to genus: molecular phylogeny of Euphyllia and Fimbriaphyllia (order Scleractinia; family Euphylliidae; clade V).
PeerJ, 2017Co-Authors: Katrina S. Luzon, Mei-fang Lin, Ma. Carmen A. Ablan Lagman, Wilfredo Roehl Y. Licuanan, Chaolun Allen ChenAbstract:Background. The corallum is crucial in building coral reefs and in diagnosing systematic relationships in the order Scleractinia. However, molecular phylogenetic analyses revealed a paraphyly in a majority of traditional families and genera among Scleractinia showing that other biological attributes of the coral, such as polyp morphology and reproductive traits, are underutilized. Among Scleractinian genera, the Euphyllia, with nine nominal species in the Indo-Pacific region, is one of the groups that await phylogenetic resolution. Multiple genetic markers were used to construct the phylogeny of six Euphyllia species, namely E. ancora, E. divisa, E. glabrescens, E. paraancora, E. par a divisa, and E. yaeyamaensis. The phylogeny guided the inferences on the contributions of the colony structure, polyp morphology, and life history traits to the systematics of the largest genus in Euphyllidae (clade V) and, by extension, to the rest of clade V. Results. Analyses of cytochrome oxidase 1 (cox 1), cytochrome b(cytb), and beta-tubulin genes of 36 colonies representing Euphyllia and a confamilial species, Galaxea fascicularis, reveal two distinct groups in the Euphyllia that originated from different ancestors. Euphyllia glabrescens formed a separate group. Euphyllia ancora, E. divisa, E. para ancora, E. paradivisa, and E. yaeyamaensis clustered together and diverged from the same ancestor as G. fascicularis. The 3'-end of the cox1 gene of Euphyllia was able to distinguish morphospecies. Discussion. Species of Euphyllia were traditionally classified into two subgenera, Euphyllia and Fimbriaphyllia, which represented a dichotomy on colony structure. The paraphyletic groups retained the original members of the subgenera providing a strong basis for recognizing Fimbriaphyllia as a genus. However, colony structure was found to be a convergent trait between Euphyllia and Fimbriaphyllia, while polyp shape and length, sexuality, and reproductive mode defined the dichotomy better. Species in a genus are distinguished by combining polyp morphology and colony form. The cluster of E. glabrescens of the Euphyllia group is a hermaphroditic brooder with long, tubular tentacles with knob-like tips, and a phaceloid colony structure. The Fimbriaphyllia group, with F. paraancora, F. paradivisa, F. ancora, F. divisa, and F. yaeyamaensis, are gonochoric broadcast spawners with short polyps, mixed types of tentacle shapes, and a phaceloid or flabello-meandroid skeleton. Soft-tissue morphology of G. fascicularis and Ctenella chagius were found to be consistent with the dichotomy. Conclusions. The paraphyly of the original members of the previous subgenera justify recognizing Fimbriaphyllia as a genus. The integrated approach demonstrates that combining polyp features, reproductive traits, and skeletal morphology is of high systematic value not just to Euphyllia and Fimbriaphyllia but also to clade V; thus, laying the groundwork for resolving the phylogeny of clade V.
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mitochondrial genome rearrangements in the Scleractinia corallimorpharia complex implications for coral phylogeny
Genome Biology and Evolution, 2014Co-Authors: Marcelo V. Kitahara, David J. Miller, Mei-fang Lin, Haiwei Luo, Dianne M. Tracey, Jonathan B. Geller, Hironobu Fukami, Chaolun Allen ChenAbstract: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.
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Mitochondrial Genome Rearrangements in the Scleractinia/Corallimorpharia Complex: Implications for Coral Phylogeny
Genome biology and evolution, 2014Co-Authors: Mei-fang Lin, Marcelo V. Kitahara, David J. Miller, Haiwei Luo, Dianne M. Tracey, Jonathan B. Geller, Hironobu Fukami, Chaolun Allen ChenAbstract: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.
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the naked coral hypothesis revisited evidence for and against Scleractinian monophyly
PLOS ONE, 2014Co-Authors: Marcelo V. Kitahara, David J. Miller, Sylvain Foret, Gavin A Huttley, Chaolun Allen ChenAbstract:The relationship between Scleractinia and Corallimorpharia, Orders within Anthozoa distinguished by the presence of an aragonite skeleton in the former, is controversial. Although classically considered distinct groups, some phylogenetic analyses have placed the Corallimorpharia within a larger Scleractinia/Corallimorpharia clade, leading to the suggestion that the Corallimorpharia are “naked corals” that arose via skeleton loss during the Cretaceous from a Scleractinian ancestor. Scleractinian paraphyly is, however, contradicted by a number of recent phylogenetic studies based on mt nucleotide (nt) sequence data. Whereas the “naked coral” hypothesis was based on analysis of the sequences of proteins encoded by a relatively small number of mt genomes, here a much-expanded dataset was used to reinvestigate hexacorallian phylogeny. The initial observation was that, whereas analyses based on nt data support Scleractinian monophyly, those based on amino acid (aa) data support the “naked coral” hypothesis, irrespective of the method and with very strong support. To better understand the bases of these contrasting results, the effects of systematic errors were examined. Compared to other hexacorallians, the mt genomes of “Robust” corals have a higher (A+T) content, codon usage is far more constrained, and the proteins that they encode have a markedly higher phenylalanine content, leading us to suggest that mt DNA repair may be impaired in this lineage. Thus the “naked coral” topology could be caused by high levels of saturation in these mitochondrial sequences, long-branch effects or model violations. The equivocal results of these extensive analyses highlight the fundamental problems of basing coral phylogeny on mitochondrial sequence data.
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Unique Mitogenomic Features in the Scleractinian Family Pocilloporidae (Scleractinia: Astrocoeniina)
Marine Biotechnology, 2008Co-Authors: Chienhsun Chen, Chih-yung Chiou, Chaolun Allen ChenAbstract:The complete DNA sequences of three mitochondrial (mt) genomes were obtained from the Scleractinian corals, Stylophora pistillata , Pocillopora damicornis , and Madracis mirabilis , and were compared to the published mt genomes to elucidate phylogenetically unique features of the family Pocilloporidae. The entire mt genomes of pocilloporid corals ranged from 16,951 to 17,425 bp with the A+T contents of their sense strands ranging from 68.4% to 70.2%. The gene order of protein-coding genes was identical to those of other Scleractinian corals. The novel atp8 gene, first described in confamilial Seriatopora corals, was also confirmed using reverse transcription-polymerase chain reaction (RT-PCR), Northern blot, and sequence analyses in other genera of the Pocilloporidae. The intergenic spacer between atp6 and nad4 , containing distinct repeated elements, conserved sequence blocks and domains, and functional structures, possesses typical characteristics of a putative control region for the four coral genera. A duplicated trnW , detected in the region close to the cox1 gene and which shares the highly conserved primary and secondary structures of its original counterpart, was discovered in both Seriatopora and Stylophora . These molecular characteristics are unique and provide the phylogenetic information for future evaluation of the status of the family Pocilloporidae in the evolutionary history of Scleractinian corals.
