Papers - FUKAMI Hironobu
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Goniopora spp. collected at Akajima Island
Hironobu Fukami, Yuko Kitano
( 23 ) 4 - 7 2012.4
Language：Japanese Publishing type：Research paper (other academic)
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Symbiodinium Clade C Dominates Zooxanthellate Corals (Scleractinia) in the Temperate Region of Japan Reviewed
Y.-T. Lien, H. Fukami, Y. Yamashita
Zoological Science 29 173 - 180 2012.3
Language：English Publishing type：Research paper (scientific journal)
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Evidence of Genetic and Reproductive Isolation between Two Morphs of Subtropical-Dominant Coral Acropora solitaryensis in the Non-Reef Region of Japan Reviewed
Go Suzuki, Hironobu Fukami
Zoological Science 29 134 - 140 2012.2
Language：English Publishing type：Research paper (scientific journal)
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Preface : Introduction of Dr. Siro Kawaguti (1908-2004)
YAMASHIRO Hideyuki, FUKAMI Hironobu
Galaxea, Journal of Coral Reef Studies 14 ( 0 ) 3 - 4 2012
Language：Japanese Publishing type：Research paper (scientific journal) Publisher：The Japanese Coral Reef Society
DOI： 10.3755/galaxea.14.3
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Volcanic ashfall preserved in the skeleton of Acropora
YAMASHIRO Hideyuki, FUKAMI Hironobu
Galaxea, Journal of Coral Reef Studies 14 ( 1 ) 3 - 4 2012
Language：Japanese Publishing type：Research paper (scientific journal) Publisher：The Japanese Coral Reef Society
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日本における造礁性イシサンゴ類の同定の現状とその分類学的問題点（共著） Reviewed
深見裕伸, 立川浩之, 鈴木 豪, 永田俊輔, 杉原 薫
日本サンゴ礁学会誌 12 1 - 15 2011.5
Language：Japanese Publishing type：Research paper (scientific journal)
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Huang D., Licuanan W., Baird A., Fukami H.
BMC Evolutionary Biology 11 ( 1 ) 2011.2
Language：Japanese Publishing type：Research paper (scientific journal) Publisher：BMC Evolutionary Biology
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. © 2011 Huang et al; licensee BioMed Central Ltd.
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Seasonal changes in fish assemblages in an area of hermatypic corals in Yokonami, Tosa Bay, Japan.
Hirata Tomonori, Oguri Sosuke, Hirata Shiori, Fukami Hironobu, Nakamura Yohei, Yamaoka Kosaku
Jpn. J. Ichthyol. 58 ( 1 ) 49 - 64 2011
Language：Japanese Publishing type：Research paper (scientific journal) Publisher：The Ichthyological Society of Japan
A monthly underwater visual census was conducted in the coral-dominated habitat of Yokonami, Tosa Bay, Japan, from June 2006 to January 2009. A total of 12,586 individuals belonging to 168 species in 43 families were recorded during the study period. The number of species and individuals increased from June-August (summer), the highest numbers occurring in September-December (autumn), thereafter decreasing from January (winter) to the lowest point in May (spring). Labridae was the most dominant family in terms of species numbers (28 species), followed by Chaetodontidae (21 species) and Pomacentridae (18 species). In terms of individual numbers, Chaetodontidae was the most abundant (56.3% of total individual numbers), followed by Labridae (15%) and Pomacentridae (12.5%). The most dominant species were Chaetodon speculum (33.4%), Pomacentrus coelestis (11.1%), and C. lunulatus (8.2%). The fish assemblage was divided into 4 groups: (1) temperate fishes (1877 individuals in 26 species), (2) (sub-)tropical fishes (10,648 individuals in 136 species), (3) temperate-tropical fishes (28 individuals in 2 species), (4) unknown fishes (33 individuals in 4 species). Species and individual numbers of temperate fishes were high in summer and low in winter, whereas those of tropical fishes were high in summer and autumn and low in spring, suggesting that typhoons in summer and autumn, and low water temperatures in winter might affect fish recruitment and community density. Moreover, at least 44 tropical species were observed throughout the year during the study period.
DOI： 10.11369/jji.58.49
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和歌山産ヒラタオオトゲキクメイシに見られる生時の形態多型は種内変異か種間変異か？（共著） Reviewed
座安佑奈, 野村恵一, 鈴木豪, 白山義久, 深見裕伸
日本サンゴ礁学会誌 11 25 - 31 2010.8
Language：Japanese Publishing type：Research paper (scientific journal)
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和歌山産タカクキクメイシMontastraea valenciennesi（Milne Edwards and Haime, 1848）の隠蔽種の存在（共著） Reviewed
深見裕伸, 野村恵一
日本サンゴ礁学会誌 11 25 - 31 2010.8
Language：Japanese Publishing type：Research paper (scientific journal)
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FUKAMI Hironobu, TACHIKAWA Hiroyuki, SUZUKI Go, NAGATA Shunsuke, SUGIHARA Kaoru
Journal of the Japanese Coral Reef Society 12 17 - 31 2010
Language：Japanese Publishing type：Research paper (scientific journal) Publisher：The Japanese Coral Reef Society
Morphological classification of zooxanthellate (hermatypic) corals (hereafter corals) in the Screlactinia is currently based on skeletal features of the corallite and colony forms. These corals, however, have few taxonomically significant morphological characteristics because such characters show polymorphism, intraspecific variation, and phenotypic plasticity in response to environmental factors. Quantitative description of taxonomic features that comprise differences between morphologically similar genera and/or species is challenging. Recently in Japan, picture books and identification guides of the corals that focus mainly on their living features have become popular. These publications promote awareness of the corals, but they have decreased attention to the skeletal features of corals. A number of these publications do not adhere to the International Code of Zoological Nomenclature, especially with regard to scientific names, thereby reducing the current stability of coral taxonomy. This complicates the effort to obtain a consensus on the taxonomic identification of coral species, which is important for comparing results of studies, past and present. Application of molecular phylogenetic analyses to corals has provided useful information for understanding the relationships among closely related families and/or genera as well as neighboring species in the same genus. These analyses should be used to revise the traditional taxonomic scheme, which is based only on morphological characteristics. Compounding the difficulty, past studies may also have used misidentified coral species. To establish greater taxonomic consistency among coral species, the morphological characteristics used for traditional taxonomy should be quantitatively compared among closely related species. Identification of new morphological characteristics of the external or internal skeletal structures of colony and/or corallite that are consistent with available phylogenetic evidence is also necessary. Because of the possibility of misidentification, efforts should be taken to retain samples of soft tissues of these species as well as skeletal specimens of their corallite and/or colonies.
DOI： 10.3755/jcrs.12.17
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Fukami H., Chen C., Budd A., Collins A., Wallace C., Chuang Y., Chen C., Dai C., Iwao K., Sheppard C., Knowlton N.
PLoS ONE 3 ( 9 ) 2008.9
Language：Japanese Publishing type：Research paper (scientific journal) Publisher：PLoS ONE
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 (β-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.
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Re-evaluation of the systematics of the endemic corals of Brazil by molecular data
Nunes F., Fukami H., Vollmer S., Norris R., Knowlton N.
Coral Reefs 27 ( 2 ) 423 - 432 2008.6
Language：Japanese Publishing type：Research paper (scientific journal) Publisher：Coral Reefs
Recent genetic work on various coral genera has shown that morphological convergence between Atlantic and Pacific corals obscures evolutionary relationships and inferred levels of endemicity between the regions. Based on DNA sequences from nuclear and mitochondrial loci that provide higher resolution than those previously presented, this study shows that relationships within parts of the Atlantic coral fauna are also in need of substantial revision. The data presented here indicate that (1) the endemic Brazilian genus Mussismilia is a monophyletic clade, (2) Mussismilia is more closely related to the Caribbean Faviidae than Mussidae, the family in which it is currently placed, (3) the Brazilian endemic coral Favia leptophylla is much more closely related to Mussismilia than other species of Favia and has most likely been incorrectly placed in the genus Favia and (4) the other endemic Favia species found in Brazil, Favia gravida, is genetically distinct from Favia fragum, a Caribbean congener with which it is frequently synonymized. The nuclear data also suggest the possible presence of a cryptic species within Mussismilia, but additional sampling and morphological information is required to confirm this finding. © 2008 Springer-Verlag.
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Suzuki G., Hayashibara T., Shirayama Y., Fukami H.
Marine Ecology Progress Series 355 149 - 159 2008.2
Language：Japanese Publishing type：Research paper (scientific journal) Publisher：Marine Ecology Progress Series
One of the most abundant genera of scleractinian corals, Acropora, shows considerable zonation along reef slopes. The zones are thought to be established by both selective larval settlement and post-settlement selection. The latter has been credited as more important, possibly due to the obvious relationship between colony shapes and habitat-specific environmental stress. However, there is no evidence that the former has less influence on the creation of the zones. To test the hypothesis that larvae settle selectively on species-specific suitable habitat, we identified recruits using mitochondrial and nuclear molecular markers. A 2-step molecular sorting process successfully identified the 7 most dominant species in the area. Comparing the species composition of 3 different depths, the distribution of the settlement of the 3 dominant species A. digitifera, A. hyacinthus and A. tenuis was significantly related to adult zonation, suggesting that Acropora larvae selectively settle on the suitable habitat. This is the first in situ evidence showing selective settlement of coral larvae, and from it we can conclude that the initial stage of the life cycle plays an important role in establishing habitat segregation at the species level in Acropora. © Inter-Research 2008.
DOI： 10.3354/meps07253
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Kishida T., Kubota S., Shirayama Y., Fukami H.
Biology Letters 3 ( 4 ) 428 - 430 2007.8
Language：Japanese Publishing type：Research paper (scientific journal) Publisher：Biology Letters
An olfactory receptor (OR) multigene family is responsible for the well-developed sense of smell possessed by terrestrial tetrapods. Mammalian OR genes had diverged greatly in the terrestrial environment after the fish-tetrapod split, indicating their importance to land habitation. In this study, we analysed OR genes of marine tetrapods (minke whale Balaenoptera acutorostrata, dwarf sperm whale Kogia sima, Dall's porpoise Phocoenoides dalli, Steller's sea lion Eumetopias jubatus and loggerhead sea turtle Caretta caretta) and revealed that the pseudogene proportions of OR gene repertoires in whales were significantly higher than those in their terrestrial relative cattle and also in sea lion and sea turtle. On the other hand, the pseudogene proportion of OR sequences in sea lion was not significantly higher compared with that in their terrestrial relative (dog). It indicates that secondary perfectly adapted marine vertebrates (cetaceans) have lost large amount of their OR genes, whereas secondary-semi-adapted marine vertebrates (sea lions and sea turtles) still have maintained their OR genes, reflecting the importance of terrestrial environment for these animals. © 2007 The Royal Society.
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Wallace C., Chen C., Fukami H., Muir P.
Coral Reefs 26 ( 2 ) 231 - 239 2007.6
Language：Japanese Publishing type：Research paper (scientific journal) Publisher：Coral Reefs
Many attempts have been made to recognise divisions within Acropora, the most diverse reef building coral genus on modern reefs, but only subgenera Acropora and Isopora are currently recognised. In this paper, morphological and genetic analyses, and study of reproductive mode and anatomy, demonstrate that an endemic Indonesian species A. (Acropora) togianensis, Wallace, 1997, belongs to Isopora. Despite the presence of a clear central axial corallite (indicating sub-genus Acropora), this species has supplementary axial corallites, broods planula larvae rather than broadcast-spawning for external fertilisation and develops stalked ova: all characters in common with the type species of subgenus Isopora A. (Isopora) palifera and the other species for which such data are available, A. (I.) cuneata and A. (I.) brueggemanni. Phylogenies are based on the protein-coding genes, mitochondrial cytochrome b (cytb) and nuclear histone 2a and 2b (h2ab) also group A. togianensis with these Isoporans. High bootstrapping and Bayesian support in the major lineages of the family Acroporidae demonstrate significant differences between Isopora (including A. togianensis) and Acropora. As the type species of both subgenera, A. (Acropora) muricata (Linneaus 1758) and A. (Isopora) palifera (Lamarck, 1816) are used in these analyses, elevation of Isopora Studer, 1878 to genus is formally proposed. © 2007 Springer-Verlag.
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Fukami H., Chen C., Chiou C., Knowlton N.
Journal of Molecular Evolution 64 ( 5 ) 591 - 600 2007.5
Language：Japanese Publishing type：Research paper (scientific journal) Publisher：Journal of Molecular Evolution
Analyses of mitochondrial sequences revealed the existence of a group I intron in the cytochrome oxidase subunit 1 (cox1) gene in 13 of 41 genera (20 out of 73 species) of corals conventionally assigned to the suborder Faviina. With one exception, phylogenies of the coral cox1 gene and its intron were concordant, suggesting at most two insertions and many subsequent losses. The coral introns were inferred to encode a putative homing endonuclease with a LAGLI-DADG motif as reported for the cox1 group I intron in the sea anemone Metridium senile. However, the coral and sea anemone cox1 group I introns differed in several aspects, such as the intron insertion site and sequence length. The coral cox1 introns most closely resemble the mitochondrial cox1 group I introns of a sponge species, which also has the same insertion site. The coral introns are also more similar to the introns of several fungal species than to that of the sea anemone (although the insertion site differs in the fungi). This suggests either a horizontal transfer between a sponge and a coral or independent transfers from a similar fungal donor (perhaps one with an identical insertion site that has not yet been discovered). The common occurrence of this intron in corals strengthens the evidence for an elevated abundance of group I introns in the mitochondria of anthozoans. © 2007 Springer Science+Business Media, LLC.
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Lien Y., Nakano Y., Plathong S., Fukami H., Wang J., Chen C.
Coral Reefs 26 ( 1 ) 35 - 44 2007.3
Language：Japanese Publishing type：Research paper (scientific journal) Publisher：Coral Reefs
Biogeographic investigations have suggested that coral-symbiont associations can adapt to higher temperatures by hosting a heat-tolerant Symbiodinium, phylotype D. It is hypothesized that phylotype D is absent in high latitudes due to its heat-tolerant characteristics. In this study, this hypothesis was tested by examining the symbiont diversity in a scleractinian coral, Oulastrea crispata, throughout its entire latitudinal distribution range in the West Pacific. Molecular phylotyping of the 5′-end of the nuclear large subunit of ribosomal DNA (lsu rDNA) indicated that phylotype D was the dominant Symbiodinium in O. crispata from the tropical reefs to the marginal non-reefal coral communities. Several colonies of tropical populations were associated with phylotype C, either alone or simultaneously with phylotype D. Analysis of the polymerase chain reaction products using single-strand conformation polymorphism (SSCP) detected relatively low densities of phylotype C in most of the O. crispata colonies surveyed. These results provide evidence for the occurrence of phylotype D in cold-water outlying coral communities. The dominant occurrence of phylotype C in some O. crispata colonies on tropical reefs and the relatively low densities of phylotype C identified by SSCP in subtropical and temperate populations show that the dominant symbiont type can vary in this coral species and that multiple symbionts can co-occur in the same host. © 2007 Springer-Verlag.
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和歌山県田辺湾沿岸海域で1931年から2005年までに記録された造礁性イシサンゴ類（刺胞動物門、花虫綱、六放サンゴ亜綱）の目録
久保田 信, 深見裕伸, 内田紘臣
瀬戸臨海実験所年報 18 32 - 36 2005.12
Language：Japanese Publishing type：Research paper (bulletin of university, research institution)
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Fukami H., Knowlton N.
Coral Reefs 24 ( 3 ) 410 - 417 2005.11
Language：Japanese Publishing type：Research paper (scientific journal) Publisher：Coral Reefs
Complete mitochondrial nucleotide sequences of two individuals each of Montastraea annularis, Montastraea faveolata, and Montastraea franksi were determined. Gene composition and order differed substantially from the sea anemone Metridium senile, but were identical to that of the phylogenetically distant coral genus Acropora. However, characteristics of the non-coding regions differed between the two scleractinian genera. Among members of the M. annularis complex, only 25 of 16,134 base pair positions were variable. Sixteen of these occurred in one colony of M. franksi, which (together with additional data) indicates the existence of multiple divergent mitochondrial lineages in this species. Overall, rates of evolution for these mitochondrial genomes were extremely slow (0.03-0.04% per million years based on the fossil record of the M. annularis complex). At higher taxonomic levels, patterns of genetic divergence and synonymous/nonsynonymous substitutions suggest non-neutral and unequal rates of evolution between the two lineages to which Montastraea and Acropora belong. © Springer-Verlag 2005.