Research Topics
| M MiyaSummaryAffiliation: Natural History Museum and Institute Country: Japan Publications
| Collaborators
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Detail Information
Publications
Transfer RNA gene arrangement and codon usage in vertebrate mitochondrial genomes: a new insight into gene order conservationTakashi P Satoh
Collection Center, National Museum of Nature and Science, 3 23 1 Hyakunincho, Shinjuku ku, Tokyo 169 0073, Japan
BMC Genomics 11:479. 2010..It remains unclear, however, whether such long-term persistence is a consequence of some constraints on the gene order...- Evolutionary history of Otophysi (Teleostei), a major clade of the modern freshwater fishes: Pangaean origin and Mesozoic radiationMasanori Nakatani
Atmosphere and Ocean Research Institute, The University of Tokyo, 5 1 5Kashiwanoha, Kashiwa shi, Chiba 277 8564, Japan
BMC Evol Biol 11:177. 2011..To gain insight into the history of otophysan diversification, we constructed a timetree based on whole mitogenome sequences across 110 species representing 55 of the 64 families... - Intron-loss evolution of hatching enzyme genes in TeleosteiMari Kawaguchi
Atmosphere and Ocean Research Institute, The University of Tokyo, 5 1 5 Kashiwanoha, Kashiwa, Chiba 277 8564, Japan
BMC Evol Biol 10:260. 2010..Here, we report on extensive studies of the exon-intron structures of teleostean hatching enzyme genes for insight into how and why introns were lost during evolution... - Mitogenomic evaluation of the historical biogeography of cichlids toward reliable dating of teleostean divergencesYoichiro Azuma
Division of Material Science and Biological Science, Graduate School of Science, Nagoya University, Furo cho, Chikusa ku, Nagoya 464 8602, Japan
BMC Evol Biol 8:215. 2008..We explored an alternative source of time constraints in teleostean phylogeny by evaluating a biogeographic hypothesis concerning freshwater fishes from the family Cichlidae (Perciformes: Labroidei)... - Independent evolution of the specialized pharyngeal jaw apparatus in cichlid and labrid fishesKohji Mabuchi
Ocean Research Institute, The University of Tokyo, 1 15 1 Minamidai, Nakano Ku, Tokyo 164 8639, Japan
BMC Evol Biol 7:10. 2007..We examined those based on 78 whole mitochondrial genome sequences (including 12 newly determined sequences) through partitioned Bayesian analyses with concatenated sequences (13,933 bp)... - Biogeography and evolution of the Carassius auratus-complex in East AsiaMikumi Takada
Laboratory of Fisheries Biology and Coral Reef Studies, Faculty of Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903 0213, Japan
BMC Evol Biol 10:7. 2010..As the first step in clarifying the evolutionary entity of the world's Carassius fishes, we attempted to clarify the phylogeny of C. auratus populations distributed in East Asia... - A new perspective on phylogeny and evolution of tetraodontiform fishes (Pisces: Acanthopterygii) based on whole mitochondrial genome sequences: basal ecological diversification?Yusuke Yamanoue
Ocean Research Institute, University of Tokyo, 1 15 1 Minamidai, Nakano Ku, Tokyo 164 8639, Japan
BMC Evol Biol 8:212. 2008.... 
Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequencesMasaki Miya
Department of Zoology, Natural History Museum and Institute, Chiba, 955 2 Aoba cho, Chuo Ku, Chiba 260 8682, Japan
Mol Phylogenet Evol 26:121-38. 2003..It should be noted that many unexpected, but highly supported relationships were found within the Percomorpha, being highly promising for the next investigative step towards resolution of this remarkably diversified group of teleosts...- Evolutionary history of anglerfishes (Teleostei: Lophiiformes): a mitogenomic perspectiveMasaki Miya
Natural History Museum and Institute, Chiba, 955 2 Aoba cho, Chuo Ku, Chiba 260 8682, Japan
BMC Evol Biol 10:58. 2010..Sequences of 77 higher teleosts including the 39 lophiiform sequences were unambiguously aligned and subjected to phylogenetic analysis and divergence time estimation... - Mitogenomic exploration of higher teleostean phylogenies: a case study for moderate-scale evolutionary genomics with 38 newly determined complete mitochondrial DNA sequencesM Miya
Natural History Museum and Institute, Chiba, Japan
Mol Biol Evol 18:1993-2009. 2001.... - Use of mitogenomic information in teleostean molecular phylogenetics: a tree-based exploration under the maximum-parsimony optimality criterionM Miya
Department of Zoology, Natural History Museum and Institute, Chiba, 955 2 Aoba cho, Chuo Ku, Chiba, 260 8682, Japan
Mol Phylogenet Evol 17:437-55. 2000.... - Molecular phylogeny and evolution of the deep-sea fish genus SternoptyxM Miya
Department of Zoology, Natural History Museum and Institute, Chiba, Japan
Mol Phylogenet Evol 10:11-22. 1998..There has been no discernible speciation event in the southern population, though the northern population has subsequently speciated into three contemporary species with largely allopatric/microallopatric distributions... - Mitogenomic evidence for the monophyly of elopomorph fishes (Teleostei) and the evolutionary origin of the leptocephalus larvaJun G Inoue
Ocean Research Institute, University of Tokyo, 1 15 1 Minamidai, Nakano Ku, Tokyo 164 8639, Japan
Mol Phylogenet Evol 32:274-86. 2004.... - Molecular systematics of the gonorynchiform fishes (Teleostei) based on whole mitogenome sequences: implications for higher-level relationships within the OtocephalaSébastien Lavoué
Department of Marine Bioscience, Ocean Research Institute, The University of Tokyo, Nakano Ku, Japan
Mol Phylogenet Evol 37:165-77. 2005..This result challenges the value of reductive or absent characters as synapomorphies in this group... - Interrelationships of the 11 gasterosteiform families (sticklebacks, pipefishes, and their relatives): a new perspective based on whole mitogenome sequences from 75 higher teleostsRyouka Kawahara
Ocean Research Institute, University of Tokyo, 1 15 1 Minamidai, Nakano Ku, Tokyo 164 8639, Japan
Mol Phylogenet Evol 46:224-36. 2008..Our study demonstrates a new perspective of gasterosteiform phylogeny, which will provide fundamental information for future studies of phylogeny, systematics, and evolution... - Evolution of the deep-sea gulper eel mitochondrial genomes: large-scale gene rearrangements originated within the eelsJun G Inoue
Ocean Research Institute, University of Tokyo, Tokyo, Japan
Mol Biol Evol 20:1917-24. 2003.... - Basal euteleostean relationships: a mitogenomic perspective on the phylogenetic reality of the "Protacanthopterygii"Naoya B Ishiguro
Ocean Research Institute, University of Tokyo, 1 15 1 Minamidai, Nakano Ku, Tokyo 164 8639, Japan
Mol Phylogenet Evol 27:476-88. 2003.... 
Phylogenetic utility of two existing and four novel nuclear gene loci in reconstructing Tree of Life of ray-finned fishes: the order Cypriniformes (Ostariophysi) as a case studyWei Jen Chen
Department of Biology, Saint Louis University, 3507 Laclede Avenue, St Louis, MO 63103 2010, USA
Gene 423:125-34. 2008..Phylogenetic performance of each gene, as well as their implications in the investigation of the evolution of cypriniform fishes were assessed and discussed...- Mitochondrial genomics of ostariophysan fishes: perspectives on phylogeny and biogeographyKenji Saitoh
Tohoku National Fisheries Research Institute, Shinhama, Shiogama 985 0001, Japan
J Mol Evol 56:464-72. 2003..This helps to explain the present geographic distribution of characiphysans... - Basal actinopterygian relationships: a mitogenomic perspective on the phylogeny of the "ancient fish"Jun G Inoue
Ocean Research Institute, University of Tokyo, 1 15 1 Minamidai, Nakano Ku, Tokyo 164 8639, Japan
Mol Phylogenet Evol 26:110-20. 2003..Although the tree topology differed from any of the previously proposed hypotheses based on morphology, it exhibited congruence with a recently proposed novel hypothesis based on nuclear markers... - Complete mitochondrial DNA sequence of the Japanese spiny lobster, Panulirus japonicus (Crustacea: Decapoda)Mitsugu Yamauchi
Ocean Research Institute, University of Tokyo, 1 15 1 Minamidai, Nakano Ku, Tokyo 164 8639, Japan
Gene 295:89-96. 2002.... - Phylogenetic position of tetraodontiform fishes within the higher teleosts: Bayesian inferences based on 44 whole mitochondrial genome sequencesYusuke Yamanoue
Ocean Research Institute, University of Tokyo, 1 15 1 Minamidai, Nakano Ku, Tokyo 164 8639, Japan
Mol Phylogenet Evol 45:89-101. 2007..Within the Tetraodontiformes, however, monophylies of the three superfamilies were not recovered and further taxonomic sampling and subsequent efforts should clarify these relationships... - How meaningful are Bayesian support values?Mark P Simmons
Department of Biology, Colorado State University, Fort Collins, USA
Mol Biol Evol 21:188-99. 2004..We advocate the continued use of the relatively conservative bootstrap and jackknife approaches to estimating branch support rather than the more extreme overestimates provided by the Markov Chain Monte Carlo-based Bayesian methods... - Gene rearrangements and evolution of tRNA pseudogenes in the mitochondrial genome of the parrotfish (Teleostei: Perciformes: Scaridae)Kohji Mabuchi
Ocean Research Institute, University of Tokyo, 1 15 1 Minamidai, Nakano Ku, Tokyo 164 8639, Japan
J Mol Evol 59:287-97. 2004.... - The mitochondrial genome of Indonesian coelacanth Latimeria menadoensis (Sarcopterygii: Coelacanthiformes) and divergence time estimation between the two coelacanthsJun G Inoue
Ocean Research Institute, The University of Tokyo, 1 15 1 Minamidai, Nakano Ku, Tokyo 164 8639, Japan
Gene 349:227-35. 2005.... - Evolution of the mitochondrial genome in cephalochordata as inferred from complete nucleotide sequences from two epigonichthys speciesMasahiro Nohara
Yokohama R and D Center, HITEC Co, Ltd, 3-55-1 Hagoromo-cho, Naka-ku, Yokohama, Kanagawa, 231-0047, Japan
J Mol Evol 60:526-37. 2005.... - Efficiently resolving the basal clades of a phylogenetic tree using Bayesian and parsimony approaches: a case study using mitogenomic data from 100 higher teleost fishesMark P Simmons
Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
Mol Phylogenet Evol 31:351-62. 2004.... - Round and pointed-head grenadier fishes (Actinopterygii: Gadiformes) represent a single sister group: evidence from the complete mitochondrial genome sequencesTakashi P Satoh
Ocean Research Institute, The University of Tokyo, 1-15-1 Minamidai, Nakano-ku, Tokyo 164-8639, Japan
Mol Phylogenet Evol 40:129-38. 2006..The overall topology of the present tree differed from any of the previously proposed, morphology-based phylogenetic hypotheses... - The mitochondrial genome of spotted green pufferfish Tetraodon nigroviridis (Teleostei: Tetraodontiformes) and divergence time estimation among model organisms in fishesYusuke Yamanoue
Ocean Research Institute, University of Tokyo, Japan
Genes Genet Syst 81:29-39. 2006..torafugu, 183 MYA vs. three-spined stickleback, 191 MYA vs. medaka, and 324 MYA vs. zebrafish, all of which were about twice as old as the divergence times estimated by their earliest occurrences in fossil records... - Phylogenetic relationships among anchovies, sardines, herrings and their relatives (Clupeiformes), inferred from whole mitogenome sequencesSébastien Lavoué
Department of Marine Bioscience, Ocean Research Institute, The University of Tokyo, 1 15 1 Minamidai, Tokyo, Japan
Mol Phylogenet Evol 43:1096-105. 2007..Instead, our mitogenomic data provide strong support for new clades within the Clupeidae, some of which are composed of members of more than one of the previously accepted subfamilies... - Monophyly, phylogenetic position and inter-familial relationships of the Alepocephaliformes (Teleostei) based on whole mitogenome sequencesSébastien Lavoué
Department of Marine Bioscience, Ocean Research Institute, The University of Tokyo, 1 15 1 Minamidai, Tokyo 164 8639, Japan
Mol Phylogenet Evol 47:1111-21. 2008..Inferred relationships among alepocephaliform taxa were not congruent with any of the previously published phylogenetic hypotheses based on morphological characters... - Molecular phylogeny and evolution of the freshwater eels genus Anguilla based on the whole mitochondrial genome sequencesYuki Minegishi
Ocean Research Institute, The University of Tokyo, 1 15 1 Minamidai, Nakano Ku, Tokyo 164 8639, Japan
Mol Phylogenet Evol 34:134-46. 2005..The results of the present study suggest that the hypotheses for the dispersal route and divergence time of the genus Anguilla should be reconsidered... - V-SINEs: a new superfamily of vertebrate SINEs that are widespread in vertebrate genomes and retain a strongly conserved segment within each repetitive unitIkuo Ogiwara
Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
Genome Res 12:316-24. 2002..It seems plausible that V-SINEs may have some function(s) that have been maintained by the coevolution of SINEs and LINEs during the evolution of vertebrates... - Phylogenetic relationships of Danio within the order Cypriniformes: a framework for comparative and evolutionary studies of a model speciesRichard L Mayden
Department of Biology, 3507 Laclede Avenue, Saint Louis University, St Louis, Missouri 63103, USA
J Exp Zool B Mol Dev Evol 308:642-54. 2007..Danio rerio is sister to D. kyathit among the species of Danio evaluated in this analysis. Microrasbora and Rasbora are non-monophyletic assemblages; however, Boraras is monophyletic...