Masaki Miya

Department of Ecology and Environmental Sciences, Natural History Museum and Institute, Chiba

Affiliated withNatural History Museum and Institute, Chiba

Research Area

Environment

Biography

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JoVE Journal Publications

Article Total : 1	Year
Publication title	2016

Other Publications

Article	Year
V-SINEs: a new superfamily of vertebrate SINEs that are widespread in vertebrate genomes and retain a strongly conserved segment within each repetitive unit. Genome research\| PubMed ID: 11827951	2002
Complete mitochondrial DNA sequence of the Japanese spiny lobster, Panulirus japonicus (Crustacea: Decapoda). Gene\| PubMed ID: 12242015	2002
Basal actinopterygian relationships: a mitogenomic perspective on the phylogeny of the "ancient fish". Molecular phylogenetics and evolution\| PubMed ID: 12470943	2003
Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences. Molecular phylogenetics and evolution\| PubMed ID: 12470944	2003
Mitochondrial genomics of ostariophysan fishes: perspectives on phylogeny and biogeography. Journal of molecular evolution\| PubMed ID: 12664166	2003
Basal euteleostean relationships: a mitogenomic perspective on the phylogenetic reality of the "Protacanthopterygii". Molecular phylogenetics and evolution\| PubMed ID: 12742752	2003
Complete mitochondrial DNA sequence of the swimming crab, Portunus trituberculatus (Crustacea: Decapoda: Brachyura). Gene\| PubMed ID: 12853147	2003
Evolution of the deep-sea gulper eel mitochondrial genomes: large-scale gene rearrangements originated within the eels. Molecular biology and evolution\| PubMed ID: 12949142	2003
How meaningful are Bayesian support values? Molecular biology and evolution\| PubMed ID: 14595090	2004
Complete mitochondrial DNA sequence of Tigriopus japonicus (Crustacea: Copepoda). Marine biotechnology (New York, N.Y.)\| PubMed ID: 14961252	2002
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. Molecular phylogenetics and evolution\| PubMed ID: 15019630	2004
Organization of the mitochondrial genome of Antarctic krill Euphausia superba (Crustacea: Malacostraca). Marine biotechnology (New York, N.Y.)\| PubMed ID: 15136912	2004
Large-scale gene rearrangements in the mitochondrial genomes of two calanoid copepods Eucalanus bungii and Neocalanus cristatus (Crustacea), with notes on new versatile primers for the srRNA... Gene\| PubMed ID: 15145056	2004
Mitogenomic evidence for the monophyly of elopomorph fishes (Teleostei) and the evolutionary origin of the leptocephalus larva. Molecular phylogenetics and evolution\| PubMed ID: 15186813	2004
Gene rearrangements and evolution of tRNA pseudogenes in the mitochondrial genome of the parrotfish (Teleostei: Perciformes: Scaridae). Journal of molecular evolution\| PubMed ID: 15553084	2004
Molecular phylogeny and evolution of the freshwater eels genus Anguilla based on the whole mitochondrial genome sequences. Molecular phylogenetics and evolution\| PubMed ID: 15579387	2005
The mitochondrial genome of Indonesian coelacanth Latimeria menadoensis (Sarcopterygii: Coelacanthiformes) and divergence time estimation between the two coelacanths. Gene\| PubMed ID: 15777665	2005
PCR-based approach for sequencing mitochondrial genomes of decapod crustaceans, with a practical example from kuruma prawn (Marsupenaeus japonicus). Marine biotechnology (New York, N.Y.)\| PubMed ID: 15791487	2004
Evolution of the mitochondrial genome in cephalochordata as inferred from complete nucleotide sequences from two epigonichthys species. Journal of molecular evolution\| PubMed ID: 15883887	2005
Molecular systematics of the gonorynchiform fishes (Teleostei) based on whole mitogenome sequences: implications for higher-level relationships within the Otocephala. Molecular phylogenetics and evolution\| PubMed ID: 15890536	2005
Round and pointed-head grenadier fishes (Actinopterygii: Gadiformes) represent a single sister group: evidence from the complete mitochondrial genome sequences. Molecular phylogenetics and evolution\| PubMed ID: 16603389	2006
The mitochondrial genome of spotted green pufferfish Tetraodon nigroviridis (Teleostei: Tetraodontiformes) and divergence time estimation among model organisms in fishes. Genes & genetic systems\| PubMed ID: 16607039	2006
Phylogenetic relationships among anchovies, sardines, herrings and their relatives (Clupeiformes), inferred from whole mitogenome sequences. Molecular phylogenetics and evolution\| PubMed ID: 17123838	2007
Independent evolution of the specialized pharyngeal jaw apparatus in cichlid and labrid fishes. BMC evolutionary biology\| PubMed ID: 17263894	2007
Phylogenetic position of tetraodontiform fishes within the higher teleosts: Bayesian inferences based on 44 whole mitochondrial genome sequences. Molecular phylogenetics and evolution\| PubMed ID: 17490896	2007
Phylogenetic relationships of Danio within the order Cypriniformes: a framework for comparative and evolutionary studies of a model species. Journal of experimental zoology. Part B, Molecular and developmental evolution\| PubMed ID: 17554749	2007
Interrelationships of the 11 gasterosteiform families (sticklebacks, pipefishes, and their relatives): a new perspective based on whole mitogenome sequences from 75 higher teleosts. Molecular phylogenetics and evolution\| PubMed ID: 17709262	2008
Monophyly, phylogenetic position and inter-familial relationships of the Alepocephaliformes (Teleostei) based on whole mitogenome sequences. Molecular phylogenetics and evolution\| PubMed ID: 18262798	2008
Heterotypy in the N-terminal region of growth/differentiation factor 5 (GDF5) mature protein during teleost evolution. Molecular biology and evolution\| PubMed ID: 18296700	2008
A new perspective on phylogeny and evolution of tetraodontiform fishes (Pisces: Acanthopterygii) based on whole mitochondrial genome sequences: basal ecological diversification? BMC evolutionary biology\| PubMed ID: 18638411	2008
Mitogenomic evaluation of the historical biogeography of cichlids toward reliable dating of teleostean divergences. BMC evolutionary biology\| PubMed ID: 18651942	2008
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. Gene\| PubMed ID: 18703121	2008
Interrelationships of Atherinomorpha (medakas, flyingfishes, killifishes, silversides, and their relatives): The first evidence based on whole mitogenome sequences. Molecular phylogenetics and evolution\| PubMed ID: 18771739	2008
Unique patterns of pelvic fin evolution: a case study of balistoid fishes (Pisces: Tetraodontiformes) based on whole mitochondrial genome sequences. Molecular phylogenetics and evolution\| PubMed ID: 19010428	2009
Stickleback phylogenies resolved: evidence from mitochondrial genomes and 11 nuclear genes. Molecular phylogenetics and evolution\| PubMed ID: 19027080	2009
Explosive speciation of Takifugu: another use of fugu as a model system for evolutionary biology. Molecular biology and evolution\| PubMed ID: 19074759	2009
Reconstructing the phylogenetic relationships of the earth's most diverse clade of freshwater fishes--order Cypriniformes (Actinopterygii: Ostariophysi): a case study using multiple nuclear ... Molecular phylogenetics and evolution\| PubMed ID: 19141325	2009
Deep-sea mystery solved: astonishing larval transformations and extreme sexual dimorphism unite three fish families. Biology letters\| PubMed ID: 19158027	2009
The historical biogeography of the freshwater knifefishes using mitogenomic approaches: a mesozoic origin of the Asian notopterids (Actinopterygii: Osteoglossomorpha). Molecular phylogenetics and evolution\| PubMed ID: 19444960	2009
Phylogenetic relationships of catostomid fishes (Actinopterygii: Cypriniformes) based on mitochondrial ND4/ND5 gene sequences. Molecular phylogenetics and evolution\| PubMed ID: 19527790	2010
Mitogenomic evaluation of the unique facial nerve pattern as a phylogenetic marker within the percifom fishes (Teleostei: Percomorpha). Molecular phylogenetics and evolution\| PubMed ID: 19540351	2009
Divergence time of the two regional medaka populations in Japan as a new time scale for comparative genomics of vertebrates. Biology letters\| PubMed ID: 19586967	2009
Mitochondrial phylogenomics of anchovies (family Engraulidae) and recurrent origins of pronounced miniaturization in the order Clupeiformes. Molecular phylogenetics and evolution\| PubMed ID: 19944773	2010
Deep-ocean origin of the freshwater eels. Biology letters\| PubMed ID: 20053660	2010
Biogeography and evolution of the Carassius auratus-complex in East Asia. BMC evolutionary biology\| PubMed ID: 20064277	2010
Evolutionary history of anglerfishes (Teleostei: Lophiiformes): a mitogenomic perspective. BMC evolutionary biology\| PubMed ID: 20178642	2010
Intraspecific variation in the mitochondrial genome among local populations of Medaka Oryzias latipes. Gene\| PubMed ID: 20193748	2010
Evolutionary origin and phylogeny of the modern holocephalans (Chondrichthyes: Chimaeriformes): a mitogenomic perspective. Molecular biology and evolution\| PubMed ID: 20551041	2010
Systematics of the subfamily Danioninae (Teleostei: Cypriniformes: Cyprinidae). Molecular phylogenetics and evolution\| PubMed ID: 20553898	2010
Transfer RNA gene arrangement and codon usage in vertebrate mitochondrial genomes: a new insight into gene order conservation. BMC genomics\| PubMed ID: 20723209	2010
Intron-loss evolution of hatching enzyme genes in Teleostei. BMC evolutionary biology\| PubMed ID: 20796321	2010
Remarkable morphological stasis in an extant vertebrate despite tens of millions of years of divergence. Proceedings. Biological sciences\| PubMed ID: 20880884	2011
Multiple invasions into freshwater by pufferfishes (teleostei: tetraodontidae): a mitogenomic perspective. PloS one\| PubMed ID: 21364898	2011
Phylogeny of the gudgeons (Teleostei: Cyprinidae: Gobioninae). Molecular phylogenetics and evolution\| PubMed ID: 21672635	2011
Evolutionary history of Otophysi (Teleostei), a major clade of the modern freshwater fishes: Pangaean origin and Mesozoic radiation. BMC evolutionary biology\| PubMed ID: 21693066	2011
A 'living fossil' eel (Anguilliformes: Protanguillidae, fam. nov.) from an undersea cave in Palau. Proceedings. Biological sciences\| PubMed ID: 21849321	2012
Body plan convergence in the evolution of skates and rays (Chondrichthyes: Batoidea). Molecular phylogenetics and evolution\| PubMed ID: 22209858	2012
Comparable ages for the independent origins of electrogenesis in African and South American weakly electric fishes. PloS one\| PubMed ID: 22606250	2012
Molecular phylogeny of the cyprinid tribe Labeonini (Teleostei: Cypriniformes). Molecular phylogenetics and evolution\| PubMed ID: 22728909	2012
Phylogeny and biogeography of highly diverged freshwater fish species (Leuciscinae, Cyprinidae, Teleostei) inferred from mitochondrial genome analysis. Gene\| PubMed ID: 23174367	2013
Mitogenomic evidence for an Indo-West Pacific origin of the Clupeoidei (Teleostei: Clupeiformes). PloS one\| PubMed ID: 23431379	2013
Mitogenomic sequences and evidence from unique gene rearrangements corroborate evolutionary relationships of myctophiformes (Neoteleostei). BMC evolutionary biology\| PubMed ID: 23731841	2013
Pike and salmon as sister taxa: detailed intraclade resolution and divergence time estimation of Esociformes + Salmoniformes based on whole mitochondrial genome sequences. Gene\| PubMed ID: 23954876	2013
MitoFish and MitoAnnotator: a mitochondrial genome database of fish with an accurate and automatic annotation pipeline. Molecular biology and evolution\| PubMed ID: 23955518	2013
Evolutionary origin of the Scombridae (tunas and mackerels): members of a paleogene adaptive radiation with 14 other pelagic fish families. PloS one\| PubMed ID: 24023883	2013
Phylogeny of the Elopomorpha (Teleostei): evidence from six nuclear and mitochondrial markers. Molecular phylogenetics and evolution\| PubMed ID: 24041936	2014
Mitogenomic circumscription of a novel percomorph fish clade mainly comprising "Syngnathoidei" (Teleostei). Gene\| PubMed ID: 24680775	2014
Mitogenomic phylogeny of the Percichthyidae and Centrarchiformes (Percomorphaceae): comparison with recent nuclear gene-based studies and simultaneous analysis. Gene\| PubMed ID: 25026502	2014
Mitochondrial genomic investigation of flatfish monophyly. Gene\| PubMed ID: 25172210	2014
Limits and phylogenetic relationships of East Asian fishes in the subfamily Oxygastrinae (Teleostei: Cypriniformes: Cyprinidae). Zootaxa\| PubMed ID: 25232592	2013
Phylogenetic relationships of Acheilognathidae (Cypriniformes: Cyprinoidea) as revealed from evidence of both nuclear and mitochondrial gene sequence variation: evidence for necessary taxono... Molecular phylogenetics and evolution\| PubMed ID: 25238947	2014
Phylogeny and polyploidy: resolving the classification of cyprinine fishes (Teleostei: Cypriniformes). Molecular phylogenetics and evolution\| PubMed ID: 25698355	2015
Composition of glycosaminoglycans in elasmobranchs including several deep-sea sharks: identification of chondroitin/dermatan sulfate from the dried fins of Isurus oxyrinchus and Prionace gla... PloS one\| PubMed ID: 25803296	2015
Environmental DNA as a 'Snapshot' of Fish Distribution: A Case Study of Japanese Jack Mackerel in Maizuru Bay, Sea of Japan. PloS one\| PubMed ID: 26933889	2016
Correction: Environmental DNA as a 'Snapshot' of Fish Distribution: A Case Study of Japanese Jack Mackerel in Maizuru Bay, Sea of Japan. PloS one\| PubMed ID: 27042824	2016
Preservation Obscures Pelagic Deep-Sea Fish Diversity: Doubling the Number of Sole-Bearing Opisthoproctids and Resurrection of the Genus Monacoa (Opisthoproctidae, Argentiniformes). PloS one\| PubMed ID: 27508419	2016
Structure and variation of the mitochondrial genome of fishes. BMC genomics\| PubMed ID: 27604148	2016
Wide distribution range of rhizobial symbionts associated with pantropical sea-dispersed legumes. Antonie van Leeuwenhoek\| PubMed ID: 27664091	2016