M Miya

Summary

Affiliation: Natural History Museum and Institute
Country: Japan

Publications

  1. pmc Evolutionary origin of the Scombridae (tunas and mackerels): members of a paleogene adaptive radiation with 14 other pelagic fish families
    Masaki Miya
    Natural History Museum and Institute, Chiba, Chiba, Japan
    PLoS ONE 8:e73535. 2013
  2. pmc A 'living fossil' eel (Anguilliformes: Protanguillidae, fam. nov.) from an undersea cave in Palau
    G David Johnson
    Division of Fishes, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
    Proc Biol Sci 279:934-43. 2012
  3. pmc Mitogenomic sequences and evidence from unique gene rearrangements corroborate evolutionary relationships of myctophiformes (Neoteleostei)
    Jan Y Poulsen
    Natural History Collections, University Museum of Bergen, University of Bergen, Allegaten 41, P O Box 7800, Bergen N 5020, Norway
    BMC Evol Biol 13:111. 2013
  4. pmc Transfer RNA gene arrangement and codon usage in vertebrate mitochondrial genomes: a new insight into gene order conservation
    Takashi 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
  5. pmc Evolutionary history of Otophysi (Teleostei), a major clade of the modern freshwater fishes: Pangaean origin and Mesozoic radiation
    Masanori 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
  6. pmc Intron-loss evolution of hatching enzyme genes in Teleostei
    Mari 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
  7. pmc Mitogenomic evaluation of the historical biogeography of cichlids toward reliable dating of teleostean divergences
    Yoichiro 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
  8. pmc Independent evolution of the specialized pharyngeal jaw apparatus in cichlid and labrid fishes
    Kohji Mabuchi
    Ocean Research Institute, The University of Tokyo, 1 15 1 Minamidai, Nakano Ku, Tokyo 164 8639, Japan
    BMC Evol Biol 7:10. 2007
  9. pmc Biogeography and evolution of the Carassius auratus-complex in East Asia
    Mikumi 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
  10. pmc 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

Collaborators

Detail Information

Publications37

  1. pmc Evolutionary origin of the Scombridae (tunas and mackerels): members of a paleogene adaptive radiation with 14 other pelagic fish families
    Masaki Miya
    Natural History Museum and Institute, Chiba, Chiba, Japan
    PLoS ONE 8:e73535. 2013
    ..We name this clade of open-ocean fishes containing Scombridae "Pelagia" in reference to the common habitat preference that links the 15 families. ..
  2. pmc A 'living fossil' eel (Anguilliformes: Protanguillidae, fam. nov.) from an undersea cave in Palau
    G David Johnson
    Division of Fishes, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
    Proc Biol Sci 279:934-43. 2012
    ..in the new family Protanguillidae...
  3. pmc Mitogenomic sequences and evidence from unique gene rearrangements corroborate evolutionary relationships of myctophiformes (Neoteleostei)
    Jan Y Poulsen
    Natural History Collections, University Museum of Bergen, University of Bergen, Allegaten 41, P O Box 7800, Bergen N 5020, Norway
    BMC Evol Biol 13:111. 2013
    ..This study attempts to resolve major myctophiform phylogenies from both mitogenomic sequences and corroborating evidence in the form of unique mitochondrial gene order rearrangements...
  4. pmc Transfer RNA gene arrangement and codon usage in vertebrate mitochondrial genomes: a new insight into gene order conservation
    Takashi 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...
  5. pmc Evolutionary history of Otophysi (Teleostei), a major clade of the modern freshwater fishes: Pangaean origin and Mesozoic radiation
    Masanori 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...
  6. pmc Intron-loss evolution of hatching enzyme genes in Teleostei
    Mari 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...
  7. pmc Mitogenomic evaluation of the historical biogeography of cichlids toward reliable dating of teleostean divergences
    Yoichiro 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)...
  8. pmc Independent evolution of the specialized pharyngeal jaw apparatus in cichlid and labrid fishes
    Kohji 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)...
  9. pmc Biogeography and evolution of the Carassius auratus-complex in East Asia
    Mikumi 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...
  10. pmc 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
    ....
  11. ncbi request reprint Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences
    Masaki 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...
  12. ncbi request reprint Mitogenomic exploration of higher teleostean phylogenies: a case study for moderate-scale evolutionary genomics with 38 newly determined complete mitochondrial DNA sequences
    M Miya
    Natural History Museum and Institute, Chiba, Japan
    Mol Biol Evol 18:1993-2009. 2001
    ....
  13. ncbi request reprint Use of mitogenomic information in teleostean molecular phylogenetics: a tree-based exploration under the maximum-parsimony optimality criterion
    M 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
    ....
  14. pmc Evolutionary history of anglerfishes (Teleostei: Lophiiformes): a mitogenomic perspective
    Masaki 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...
  15. ncbi request reprint Molecular phylogeny and evolution of the deep-sea fish genus Sternoptyx
    M 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...
  16. ncbi request reprint The mitochondrial genome of Indonesian coelacanth Latimeria menadoensis (Sarcopterygii: Coelacanthiformes) and divergence time estimation between the two coelacanths
    Jun G Inoue
    Ocean Research Institute, The University of Tokyo, 1 15 1 Minamidai, Nakano Ku, Tokyo 164 8639, Japan
    Gene 349:227-35. 2005
    ....
  17. ncbi request reprint Efficiently resolving the basal clades of a phylogenetic tree using Bayesian and parsimony approaches: a case study using mitogenomic data from 100 higher teleost fishes
    Mark P Simmons
    Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
    Mol Phylogenet Evol 31:351-62. 2004
    ....
  18. doi request reprint 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 study
    Wei 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...
  19. ncbi request reprint 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...
  20. ncbi request reprint Evolution of the deep-sea gulper eel mitochondrial genomes: large-scale gene rearrangements originated within the eels
    Jun G Inoue
    Ocean Research Institute, University of Tokyo, Tokyo, Japan
    Mol Biol Evol 20:1917-24. 2003
    ....
  21. ncbi request reprint 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
    ....
  22. ncbi request reprint Mitochondrial genomics of ostariophysan fishes: perspectives on phylogeny and biogeography
    Kenji 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...
  23. ncbi request reprint 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...
  24. ncbi request reprint 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
    ....
  25. ncbi request reprint Mitogenomic evidence for the monophyly of elopomorph fishes (Teleostei) and the evolutionary origin of the leptocephalus larva
    Jun 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
    ....
  26. ncbi request reprint Round and pointed-head grenadier fishes (Actinopterygii: Gadiformes) represent a single sister group: evidence from the complete mitochondrial genome sequences
    Takashi 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...
  27. ncbi request reprint Evolution of the mitochondrial genome in cephalochordata as inferred from complete nucleotide sequences from two epigonichthys species
    Masahiro 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
    ....
  28. ncbi request reprint Molecular systematics of the gonorynchiform fishes (Teleostei) based on whole mitogenome sequences: implications for higher-level relationships within the Otocephala
    Sébastien 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...
  29. ncbi request reprint The mitochondrial genome of spotted green pufferfish Tetraodon nigroviridis (Teleostei: Tetraodontiformes) and divergence time estimation among model organisms in fishes
    Yusuke 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...
  30. ncbi request reprint Phylogenetic relationships among anchovies, sardines, herrings and their relatives (Clupeiformes), inferred from whole mitogenome sequences
    Sébastien 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...
  31. ncbi request reprint 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
    ....
  32. ncbi request reprint Phylogenetic position of tetraodontiform fishes within the higher teleosts: Bayesian inferences based on 44 whole mitochondrial genome sequences
    Yusuke 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...
  33. ncbi request reprint Interrelationships of the 11 gasterosteiform families (sticklebacks, pipefishes, and their relatives): a new perspective based on whole mitogenome sequences from 75 higher teleosts
    Ryouka 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...
  34. ncbi request reprint Molecular phylogeny and evolution of the freshwater eels genus Anguilla based on the whole mitochondrial genome sequences
    Yuki 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...
  35. ncbi request reprint Phylogenetic relationships of Danio within the order Cypriniformes: a framework for comparative and evolutionary studies of a model species
    Richard 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...
  36. pmc V-SINEs: a new superfamily of vertebrate SINEs that are widespread in vertebrate genomes and retain a strongly conserved segment within each repetitive unit
    Ikuo 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...
  37. doi request reprint Monophyly, phylogenetic position and inter-familial relationships of the Alepocephaliformes (Teleostei) based on whole mitogenome sequences
    Sébastien 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...