Department of Ecology and Environmental Sciences
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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 Feb, 2002 | Pubmed ID: 11827951
Complete mitochondrial DNA sequence of the Japanese spiny lobster, Panulirus japonicus (Crustacea: Decapoda).
Gene Jul, 2002 | Pubmed ID: 12242015
Basal actinopterygian relationships: a mitogenomic perspective on the phylogeny of the "ancient fish".
Molecular phylogenetics and evolution Jan, 2003 | Pubmed ID: 12470943
Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences.
Molecular phylogenetics and evolution Jan, 2003 | Pubmed ID: 12470944
Mitochondrial genomics of ostariophysan fishes: perspectives on phylogeny and biogeography.
Journal of molecular evolution Apr, 2003 | Pubmed ID: 12664166
Basal euteleostean relationships: a mitogenomic perspective on the phylogenetic reality of the "Protacanthopterygii".
Molecular phylogenetics and evolution Jun, 2003 | Pubmed ID: 12742752
Complete mitochondrial DNA sequence of the swimming crab, Portunus trituberculatus (Crustacea: Decapoda: Brachyura).
Gene Jun, 2003 | Pubmed ID: 12853147
Evolution of the deep-sea gulper eel mitochondrial genomes: large-scale gene rearrangements originated within the eels.
Molecular biology and evolution Nov, 2003 | Pubmed ID: 12949142
How meaningful are Bayesian support values?
Molecular biology and evolution Jan, 2004 | Pubmed ID: 14595090
Complete mitochondrial DNA sequence of Tigriopus japonicus (Crustacea: Copepoda).
Marine biotechnology (New York, N.Y.) Sep, 2002 | Pubmed ID: 14961252
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 Apr, 2004 | Pubmed ID: 15019630
Organization of the mitochondrial genome of Antarctic krill Euphausia superba (Crustacea: Malacostraca).
Marine biotechnology (New York, N.Y.) May-Jun, 2004 | Pubmed ID: 15136912
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 and COI genes.
Gene May, 2004 | Pubmed ID: 15145056
Mitogenomic evidence for the monophyly of elopomorph fishes (Teleostei) and the evolutionary origin of the leptocephalus larva.
Molecular phylogenetics and evolution Jul, 2004 | Pubmed ID: 15186813
Gene rearrangements and evolution of tRNA pseudogenes in the mitochondrial genome of the parrotfish (Teleostei: Perciformes: Scaridae).
Journal of molecular evolution Sep, 2004 | Pubmed ID: 15553084
Molecular phylogeny and evolution of the freshwater eels genus Anguilla based on the whole mitochondrial genome sequences.
Molecular phylogenetics and evolution Jan, 2005 | Pubmed ID: 15579387
The mitochondrial genome of Indonesian coelacanth Latimeria menadoensis (Sarcopterygii: Coelacanthiformes) and divergence time estimation between the two coelacanths.
Gene Apr, 2005 | Pubmed ID: 15777665
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.) Sep-Oct, 2004 | Pubmed ID: 15791487
Evolution of the mitochondrial genome in cephalochordata as inferred from complete nucleotide sequences from two epigonichthys species.
Journal of molecular evolution Apr, 2005 | Pubmed ID: 15883887
Molecular systematics of the gonorynchiform fishes (Teleostei) based on whole mitogenome sequences: implications for higher-level relationships within the Otocephala.
Molecular phylogenetics and evolution Oct, 2005 | Pubmed ID: 15890536
Round and pointed-head grenadier fishes (Actinopterygii: Gadiformes) represent a single sister group: evidence from the complete mitochondrial genome sequences.
Molecular phylogenetics and evolution Jul, 2006 | Pubmed ID: 16603389
The mitochondrial genome of spotted green pufferfish Tetraodon nigroviridis (Teleostei: Tetraodontiformes) and divergence time estimation among model organisms in fishes.
Genes & genetic systems Feb, 2006 | Pubmed ID: 16607039
Phylogenetic relationships among anchovies, sardines, herrings and their relatives (Clupeiformes), inferred from whole mitogenome sequences.
Molecular phylogenetics and evolution Jun, 2007 | Pubmed ID: 17123838
Independent evolution of the specialized pharyngeal jaw apparatus in cichlid and labrid fishes.
BMC evolutionary biology Jan, 2007 | Pubmed ID: 17263894
Phylogenetic position of tetraodontiform fishes within the higher teleosts: Bayesian inferences based on 44 whole mitochondrial genome sequences.
Molecular phylogenetics and evolution Oct, 2007 | Pubmed ID: 17490896
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 Sep, 2007 | Pubmed ID: 17554749
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 Jan, 2008 | Pubmed ID: 17709262
Monophyly, phylogenetic position and inter-familial relationships of the Alepocephaliformes (Teleostei) based on whole mitogenome sequences.
Molecular phylogenetics and evolution Jun, 2008 | Pubmed ID: 18262798
Heterotypy in the N-terminal region of growth/differentiation factor 5 (GDF5) mature protein during teleost evolution.
Molecular biology and evolution May, 2008 | Pubmed ID: 18296700
A new perspective on phylogeny and evolution of tetraodontiform fishes (Pisces: Acanthopterygii) based on whole mitochondrial genome sequences: basal ecological diversification?
BMC evolutionary biology Jul, 2008 | Pubmed ID: 18638411
Mitogenomic evaluation of the historical biogeography of cichlids toward reliable dating of teleostean divergences.
BMC evolutionary biology Jul, 2008 | Pubmed ID: 18651942
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 Nov, 2008 | Pubmed ID: 18703121
Interrelationships of Atherinomorpha (medakas, flyingfishes, killifishes, silversides, and their relatives): The first evidence based on whole mitogenome sequences.
Molecular phylogenetics and evolution Nov, 2008 | Pubmed ID: 18771739
Unique patterns of pelvic fin evolution: a case study of balistoid fishes (Pisces: Tetraodontiformes) based on whole mitochondrial genome sequences.
Molecular phylogenetics and evolution Jan, 2009 | Pubmed ID: 19010428
Stickleback phylogenies resolved: evidence from mitochondrial genomes and 11 nuclear genes.
Molecular phylogenetics and evolution Feb, 2009 | Pubmed ID: 19027080
Explosive speciation of Takifugu: another use of fugu as a model system for evolutionary biology.
Molecular biology and evolution Mar, 2009 | Pubmed ID: 19074759
Reconstructing the phylogenetic relationships of the earth's most diverse clade of freshwater fishes--order Cypriniformes (Actinopterygii: Ostariophysi): a case study using multiple nuclear loci and the mitochondrial genome.
Molecular phylogenetics and evolution Jun, 2009 | Pubmed ID: 19141325
Deep-sea mystery solved: astonishing larval transformations and extreme sexual dimorphism unite three fish families.
Biology letters Apr, 2009 | Pubmed ID: 19158027
The historical biogeography of the freshwater knifefishes using mitogenomic approaches: a mesozoic origin of the Asian notopterids (Actinopterygii: Osteoglossomorpha).
Molecular phylogenetics and evolution Jun, 2009 | Pubmed ID: 19444960
Phylogenetic relationships of catostomid fishes (Actinopterygii: Cypriniformes) based on mitochondrial ND4/ND5 gene sequences.
Molecular phylogenetics and evolution Mar, 2010 | Pubmed ID: 19527790
Mitogenomic evaluation of the unique facial nerve pattern as a phylogenetic marker within the percifom fishes (Teleostei: Percomorpha).
Molecular phylogenetics and evolution Oct, 2009 | Pubmed ID: 19540351
Divergence time of the two regional medaka populations in Japan as a new time scale for comparative genomics of vertebrates.
Biology letters Dec, 2009 | Pubmed ID: 19586967
Mitochondrial phylogenomics of anchovies (family Engraulidae) and recurrent origins of pronounced miniaturization in the order Clupeiformes.
Molecular phylogenetics and evolution Jul, 2010 | Pubmed ID: 19944773
Deep-ocean origin of the freshwater eels.
Biology letters Jun, 2010 | Pubmed ID: 20053660
Biogeography and evolution of the Carassius auratus-complex in East Asia.
BMC evolutionary biology Jan, 2010 | Pubmed ID: 20064277
Evolutionary history of anglerfishes (Teleostei: Lophiiformes): a mitogenomic perspective.
BMC evolutionary biology Feb, 2010 | Pubmed ID: 20178642
Intraspecific variation in the mitochondrial genome among local populations of Medaka Oryzias latipes.
Gene Jun, 2010 | Pubmed ID: 20193748
Evolutionary origin and phylogeny of the modern holocephalans (Chondrichthyes: Chimaeriformes): a mitogenomic perspective.
Molecular biology and evolution Nov, 2010 | Pubmed ID: 20551041
Systematics of the subfamily Danioninae (Teleostei: Cypriniformes: Cyprinidae).
Molecular phylogenetics and evolution Oct, 2010 | Pubmed ID: 20553898
Transfer RNA gene arrangement and codon usage in vertebrate mitochondrial genomes: a new insight into gene order conservation.
BMC genomics Aug, 2010 | Pubmed ID: 20723209
Intron-loss evolution of hatching enzyme genes in Teleostei.
BMC evolutionary biology Aug, 2010 | Pubmed ID: 20796321
Remarkable morphological stasis in an extant vertebrate despite tens of millions of years of divergence.
Proceedings. Biological sciences Apr, 2011 | Pubmed ID: 20880884
Multiple invasions into freshwater by pufferfishes (teleostei: tetraodontidae): a mitogenomic perspective.
PloS one Feb, 2011 | Pubmed ID: 21364898
Phylogeny of the gudgeons (Teleostei: Cyprinidae: Gobioninae).
Molecular phylogenetics and evolution Oct, 2011 | Pubmed ID: 21672635
Evolutionary history of Otophysi (Teleostei), a major clade of the modern freshwater fishes: Pangaean origin and Mesozoic radiation.
BMC evolutionary biology Jun, 2011 | Pubmed ID: 21693066
A 'living fossil' eel (Anguilliformes: Protanguillidae, fam. nov.) from an undersea cave in Palau.
Proceedings. Biological sciences Mar, 2012 | Pubmed ID: 21849321
Body plan convergence in the evolution of skates and rays (Chondrichthyes: Batoidea).
Molecular phylogenetics and evolution Apr, 2012 | Pubmed ID: 22209858
Comparable ages for the independent origins of electrogenesis in African and South American weakly electric fishes.
PloS one , 2012 | Pubmed ID: 22606250
Molecular phylogeny of the cyprinid tribe Labeonini (Teleostei: Cypriniformes).
Molecular phylogenetics and evolution Nov, 2012 | Pubmed ID: 22728909
Phylogeny and biogeography of highly diverged freshwater fish species (Leuciscinae, Cyprinidae, Teleostei) inferred from mitochondrial genome analysis.
Gene Feb, 2013 | Pubmed ID: 23174367
Mitogenomic evidence for an Indo-West Pacific origin of the Clupeoidei (Teleostei: Clupeiformes).
PloS one , 2013 | Pubmed ID: 23431379
Mitogenomic sequences and evidence from unique gene rearrangements corroborate evolutionary relationships of myctophiformes (Neoteleostei).
BMC evolutionary biology , 2013 | Pubmed ID: 23731841
Pike and salmon as sister taxa: detailed intraclade resolution and divergence time estimation of Esociformes + Salmoniformes based on whole mitochondrial genome sequences.
Gene Nov, 2013 | Pubmed ID: 23954876
MitoFish and MitoAnnotator: a mitochondrial genome database of fish with an accurate and automatic annotation pipeline.
Molecular biology and evolution Nov, 2013 | Pubmed ID: 23955518
Evolutionary origin of the Scombridae (tunas and mackerels): members of a paleogene adaptive radiation with 14 other pelagic fish families.
PloS one , 2013 | Pubmed ID: 24023883
Phylogeny of the Elopomorpha (Teleostei): evidence from six nuclear and mitochondrial markers.
Molecular phylogenetics and evolution Jan, 2014 | Pubmed ID: 24041936
Mitogenomic circumscription of a novel percomorph fish clade mainly comprising "Syngnathoidei" (Teleostei).
Gene Jun, 2014 | Pubmed ID: 24680775
Mitogenomic phylogeny of the Percichthyidae and Centrarchiformes (Percomorphaceae): comparison with recent nuclear gene-based studies and simultaneous analysis.
Gene Oct, 2014 | Pubmed ID: 25026502
Mitochondrial genomic investigation of flatfish monophyly.
Gene Nov, 2014 | Pubmed ID: 25172210
Limits and phylogenetic relationships of East Asian fishes in the subfamily Oxygastrinae (Teleostei: Cypriniformes: Cyprinidae).
Zootaxa , 2013 | Pubmed ID: 25232592
Phylogenetic relationships of Acheilognathidae (Cypriniformes: Cyprinoidea) as revealed from evidence of both nuclear and mitochondrial gene sequence variation: evidence for necessary taxonomic revision in the family and the identification of cryptic species.
Molecular phylogenetics and evolution Dec, 2014 | Pubmed ID: 25238947
Phylogeny and polyploidy: resolving the classification of cyprinine fishes (Teleostei: Cypriniformes).
Molecular phylogenetics and evolution Apr, 2015 | Pubmed ID: 25698355
Composition of glycosaminoglycans in elasmobranchs including several deep-sea sharks: identification of chondroitin/dermatan sulfate from the dried fins of Isurus oxyrinchus and Prionace glauca.
PloS one , 2015 | Pubmed ID: 25803296
Environmental DNA as a 'Snapshot' of Fish Distribution: A Case Study of Japanese Jack Mackerel in Maizuru Bay, Sea of Japan.
PloS one , 2016 | Pubmed ID: 26933889
Correction: Environmental DNA as a 'Snapshot' of Fish Distribution: A Case Study of Japanese Jack Mackerel in Maizuru Bay, Sea of Japan.
PloS one , 2016 | Pubmed ID: 27042824
Preservation Obscures Pelagic Deep-Sea Fish Diversity: Doubling the Number of Sole-Bearing Opisthoproctids and Resurrection of the Genus Monacoa (Opisthoproctidae, Argentiniformes).
PloS one , 2016 | Pubmed ID: 27508419
Structure and variation of the mitochondrial genome of fishes.
BMC genomics Sep, 2016 | Pubmed ID: 27604148
Wide distribution range of rhizobial symbionts associated with pantropical sea-dispersed legumes.
Antonie van Leeuwenhoek Dec, 2016 | Pubmed ID: 27664091
Masaki Miya1,
Toshifumi Minamoto2,
Hiroki Yamanaka3,
Shin-ichiro Oka4,
Keiichi Sato4,
Satoshi Yamamoto2,
Tetsuya Sado1,
Hideyuki Doi5
1Department of Ecology and Environmental Sciences, Natural History Museum and Institute, Chiba,
2Graduate School of Human Development and Environment, Kobe University,
3Faculty of Science and Technology, Ryukoku University,
4, Okinawa Churashima Research Center,
5Graduate School of Simulation Studies, University of Hyogo
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