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List of works by Mutsumi Nishida

A molecular timescale for the evolution of the African freshwater fish family Kneriidae (Teleostei: Gonorynchiformes)

scientific article published on 14 December 2011

A new perspective on phylogeny and evolution of tetraodontiform fishes (Pisces: Acanthopterygii) based on whole mitochondrial genome sequences: basal ecological diversification?

scientific article

Adaptive evolution of fish hatching enzyme: one amino acid substitution results in differential salt dependency of the enzyme ⬇️

scientific article published on January 24, 2013

Ayu (Plecoglossus altivelis) in a contact zone between amphidromous and landlocked forms: genetic analyses of populations in the Yodo River system

scientific article

Basal actinopterygian relationships: a mitogenomic perspective on the phylogeny of the "ancient fish".

scientific article published in January 2003

Basal euteleostean relationships: a mitogenomic perspective on the phylogenetic reality of the “Protacanthopterygii” ⬇️

scientific article published on June 1, 2003

Body plan convergence in the evolution of skates and rays (Chondrichthyes: Batoidea).

scientific article published on 22 December 2011

Comparable ages for the independent origins of electrogenesis in African and South American weakly electric fishes

scientific article published on 14 May 2012

Complete mitochondrial DNA sequence of Tigriopus japonicus (Crustacea: Copepoda).

scientific article published in September 2002

Complete mitochondrial DNA sequence of the Japanese spiny lobster, Panulirus japonicus (Crustacea: Decapoda).

scientific article published in July 2002

Complete mitochondrial DNA sequence of the Lake Biwa wild strain of common carp (Cyprinus carpio L.): further evidence for an ancient origin

scientific article published in 2006

Complete mitochondrial DNA sequence of the swimming crab, Portunus trituberculatus (Crustacea: Decapoda: Brachyura).

scientific article published in June 2003

Conservation of the egg envelope digestion mechanism of hatching enzyme in euteleostean fishes ⬇️

scientific article published on November 11, 2010

Cryptic species of the gobioid paedomorphic genus Schindleria from Palau, Western Pacific Ocean ⬇️

scientific article published on 24 August 2010

Deep-ocean origin of the freshwater eels

scientific article

Deep-sea mystery solved: astonishing larval transformations and extreme sexual dimorphism unite three fish families

scientific article

Different hatching strategies in embryos of two species, pacific herring Clupea pallasii and Japanese anchovy Engraulis japonicus, that belong to the same order Clupeiformes, and their environmental adaptation

scientific article

Divergence time of the two regional medaka populations in Japan as a new time scale for comparative genomics of vertebrates

scientific article (publication date: 23 December 2009)

Diversification and adaptive evolution of putative sweet taste receptors in threespine stickleback

scientific article published on 31 March 2007

Ecosystem size predicts the probability of speciation in migratory freshwater fish

scientific article published on 13 March 2020

Electric charge divergence in proteins: insights into the evolution of their three-dimensional properties

scientific article published on 2 July 2008

Evolution and origin of vomeronasal-type odorant receptor gene repertoire in fishes

scientific article published on 3 October 2006

Evolution of multiple phosphodiesterase isoforms in stickleback involved in cAMP signal transduction pathway

scientific article

Evolution of the deep-sea gulper eel mitochondrial genomes: large-scale gene rearrangements originated within the eels.

scientific article

Evolution of the mitochondrial genome in cephalochordata as inferred from complete nucleotide sequences from two epigonichthys species

scientific article published on 01 April 2005

Evolution of trace amine associated receptor (TAAR) gene family in vertebrates: lineage-specific expansions and degradations of a second class of vertebrate chemosensory receptors expressed in the olfactory epithelium

scientific article published on 18 July 2007

Evolution of vomeronasal-type odorant receptor genes in the zebrafish genome

scientific article published on 14 October 2005

Evolutionary history of Otophysi (Teleostei), a major clade of the modern freshwater fishes: Pangaean origin and Mesozoic radiation

scientific article (publication date: 22 June 2011)

Evolutionary history of anglerfishes (Teleostei: Lophiiformes): a mitogenomic perspective

scientific article

Evolutionary origin of the Scombridae (tunas and mackerels): members of a paleogene adaptive radiation with 14 other pelagic fish families

scientific article (publication date: 2013)

Evolutionary patterns and selective pressures of odorant/pheromone receptor gene families in teleost fishes

scientific article

Evolutionary process of iwame, a markless form of the red-spotted masu salmon Oncorhynchus masou ishikawae, in the Ôno River, Kyushu

Explosive speciation of Takifugu: another use of fugu as a model system for evolutionary biology

scientific article

Extensive lineage-specific gene duplication and evolution of the spiggin multi-gene family in stickleback.

scientific article

Freshwater fishes of the Minami River system in Reinan Region, Fukui Prefecture ⬇️

scientific article published in 2001

Gene rearrangements and evolution of tRNA pseudogenes in the mitochondrial genome of the parrotfish (Teleostei: Perciformes: Scaridae).

scientific article published in September 2004

Genetic relationships and origin of two geographic groups of the freshwater threespine stickleback, 'hariyo'.

scientific article published in February 2003

Geographical variation of mitochondrial DNA among non-indigenous populations of a freshwater goby, Tridentiger brevispinis ⬇️

scientific article published in 2005

Hatching enzyme of the ovoviviparous black rockfish Sebastes schlegelii- environmental adaptation of the hatching enzyme and evolutionary aspects of formation of the pseudogene

scientific article published on 22 April 2008

Heterotypy in the N-terminal region of growth/differentiation factor 5 (GDF5) mature protein during teleost evolution

scientific article

Hidden Diversity in a Reef-Dwelling Sea Slug, Pteraeolidia ianthina (Nudibranchia, Aeolidina), in the Northwestern Pacific ⬇️

scientific article published on June 1, 2012

Interploidy gene flow involving the sexual-asexual cycle facilitates the diversification of gynogenetic triploid Carassius fish

scientific article published in 2021

Interrelationships of Atherinomorpha (medakas, flyingfishes, killifishes, silversides, and their relatives): The first evidence based on whole mitogenome sequences

scientific article published on 19 August 2008

Interrelationships of the 11 gasterosteiform families (sticklebacks, pipefishes, and their relatives): a new perspective based on whole mitogenome sequences from 75 higher teleosts.

scientific article

Intraspecific mitochondrial DNA phylogeny of a Japanese brackish water goby, Luciogobius guttatus ⬇️

scientific article published in 2004

Intraspecific variation in the mitochondrial genome among local populations of Medaka Oryzias latipes

scientific article published on 26 February 2010

Intron-loss evolution of hatching enzyme genes in Teleostei

scientific article

Isolation and characterization of 13 microsatellite loci in the nine-spined stickleback (Pungitius pungitius) and cross-species amplification in 5 stickleback species (family Gasterosteidae)

Karyotypes and nuclear DNA contents of two Pseudolabrus species from the southern coasts of Japan ⬇️

scientific article published in 2002

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

scientific article

Low genetic differentiation between two geographically separated populations of demersal gadiform fishes in the Southern Hemisphere ⬇️

scientific article published on January 1, 2011

LuxA gene of light organ symbionts of the bioluminescent fish Acropoma japonicum (Acropomatidae) and Siphamia versicolor (Apogonidae) forms a lineage closely related to that of Photobacterium leiognathi ssp. mandapamensis

scientific article published in July 2006

Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences.

scientific article published on January 2003

MitoFish and MitoAnnotator: a mitochondrial genome database of fish with an accurate and automatic annotation pipeline.

scientific article

Mitochondrial DNA phylogeny of Japanese freshwater goby, Odontobutis obscura, and an evidence for artificial transplantation to Kanto District ⬇️

scientific article published in 2003

Mitochondrial genome and a nuclear gene indicate a novel phylogenetic position of deep-sea tube-eye fish (Stylephoridae)

article

Mitochondrial genomes and phylogeny of the ocean sunfishes (Tetraodontiformes: Molidae) ⬇️

scholarly article by Yusuke Yamanoue et al published August 2004 in Ichthyological Research

Mitochondrial genomics of ostariophysan fishes: perspectives on phylogeny and biogeography

scientific article (publication date: April 2003)

Mitochondrial phylogenomics of anchovies (family Engraulidae) and recurrent origins of pronounced miniaturization in the order Clupeiformes

scientific article published on 26 November 2009

Mitogenomic circumscription of a novel percomorph fish clade mainly comprising "Syngnathoidei" (Teleostei).

scientific article

Mitogenomic evaluation of the historical biogeography of cichlids toward reliable dating of teleostean divergences

scientific article (publication date: 23 July 2008)

Mitogenomic evidence for an Indo-West Pacific origin of the Clupeoidei (Teleostei: Clupeiformes)

scientific article published in 2013

Mitogenomic evidence for the monophyly of elopomorph fishes (Teleostei) and the evolutionary origin of the leptocephalus larva

scientific article published in July 2004

Mitogenomic phylogeny of the Percichthyidae and Centrarchiformes (Percomorphaceae): comparison with recent nuclear gene-based studies and simultaneous analysis

scientific article

Mitogenomic sequences and evidence from unique gene rearrangements corroborate evolutionary relationships of myctophiformes (Neoteleostei).

scientific article

Molecular Systematics of the Deep-Sea Fish GenusGonostoma(Stomiiformes: Gonostomatidae): Two Paraphyletic Clades and Resurrection ofSigmops

scientific article published in May 2000

Molecular co-evolution of a protease and its substrate elucidated by analysis of the activity of predicted ancestral hatching enzyme.

scientific article

Molecular mechanisms of adaptation and evolution of odor perception in fishes with special reference to the evolutionary dynamics of chemosensory receptor gene families. ⬇️

scientific article published in 2007

Molecular phylogeny and evolution of the freshwater eels genus Anguilla based on the whole mitochondrial genome sequences

scientific article published on 01 January 2005

Molecular phylogeny and possible scenario of ponyfish (Perciformes:Leiognathidae) evolution

scientific article

Molecular phylogeny and stripe pattern evolution in the cardinalfish genus Apogon

scientific article

Molecular systematics of the gonorynchiform fishes (Teleostei) based on whole mitogenome sequences: implications for higher-level relationships within the Otocephala.

scientific article

Monophyly, phylogenetic position and inter-familial relationships of the Alepocephaliformes (Teleostei) based on whole mitogenome sequences

scientific article published on 14 December 2007

Multiple occurrences of spiggin genes in sticklebacks.

scientific article

New complete mitochondrial DNA sequence of the lancelet Branchiostoma lanceolatum (Cephalochordata) and the identity of this species' sequences

scientific article published on 01 June 2005

Organization of the mitochondrial genome of Antarctic krill Euphausia superba (Crustacea: Malacostraca).

scientific article

PCR-based approach for sequencing mitochondrial genomes of decapod crustaceans, with a practical example from kuruma prawn (Marsupenaeus japonicus).

scientific article published on 13 May 2004

Parallel Mitogenome Sequencing Alleviates Random Rooting Effect in Phylogeography

scientific article

Phylogenetic position of tetraodontiform fishes within the higher teleosts: Bayesian inferences based on 44 whole mitochondrial genome sequences

scientific article published on 27 March 2007

Phylogenetic relationships among anchovies, sardines, herrings and their relatives (Clupeiformes), inferred from whole mitogenome sequences

scientific article published on 7 October 2006

Phylogenetic relationships and natural hybridization in rabbitfishes (Teleostei: Siganidae) inferred from mitochondrial and nuclear DNA analyses

scientific article published on 8 May 2007

Phylogeny and biogeography of highly diverged freshwater fish species (Leuciscinae, Cyprinidae, Teleostei) inferred from mitochondrial genome analysis.

scientific article

Phylogeny, hybridization, and life history evolution of Rhinogobius gobies in Japan, inferred from multiple nuclear gene sequences

scientific article published on 27 April 2015

Polymorphism in Nucleotide Sequence of Mitochondrial Intergenic Region in Scleractinian Coral (Galaxea fascicularis)

scientific article published on 01 January 2005

Post-duplication charge evolution of phosphoglucose isomerases in teleost fishes through weak selection on many amino acid sites

scientific article

Proximate mechanisms causing morphological variation in a turban snail among different shores

scientific article published on November 2006

Rapid and effective isolation of candidate sequences for development of microsatellite markers in 30 fish species by using kit-based target capture and multiplexed parallel sequencing

Rapid genome reshaping by multiple-gene loss after whole-genome duplication in teleost fish suggested by mathematical modeling

scientific article

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

scientific article

Remarkable consistency of exon-intron structure of hatching enzyme genes and molecular phylogenetic relationships of teleostean fishes

article

Remarkable morphological stasis in an extant vertebrate despite tens of millions of years of divergence

scientific article (publication date: 7 April 2011)

Revision of the systematics of the cardinalfishes (Percomorpha: Apogonidae) based on molecular analyses and comparative reevaluation of morphological characters

scientific article (publication date: August 2014)

Round and pointed-head grenadier fishes (Actinopterygii: Gadiformes) represent a single sister group: evidence from the complete mitochondrial genome sequences

article

Screening the V2R-type putative odorant receptor gene repertoire in bitterling Tanakia lanceolata

scientific article

Species phylogeny and diversification process of Northeast Asian Pungitius revealed by AFLP and mtDNA markers

scientific article

Stickleback phylogenies resolved: evidence from mitochondrial genomes and 11 nuclear genes

scientific article published on 5 November 2008

Structure and variation of the mitochondrial genome of fishes

scientific article

Sub-functionalization of duplicated genes in the evolution of nine-spined stickleback hatching enzyme.

scientific article

Temporal pattern of loss/persistence of duplicate genes involved in signal transduction and metabolic pathways after teleost-specific genome duplication

scientific article

The historical biogeography of the freshwater knifefishes using mitogenomic approaches: a mesozoic origin of the Asian notopterids (Actinopterygii: Osteoglossomorpha).

scientific article

The mitochondrial genome of Indonesian coelacanth Latimeria menadoensis (Sarcopterygii: Coelacanthiformes) and divergence time estimation between the two coelacanths

scientific article

The mitochondrial genome of spotted green pufferfish Tetraodon nigroviridis (Teleostei: Tetraodontiformes) and divergence time estimation among model organisms in fishes

scientific article published in February 2006

The mitogenomic contributions to molecular phylogenetics and evolution of fishes: a 15-year retrospect

scholarly article by Masaki Miya & Mutsumi Nishida published 14 November 2014 in Ichthyological Research

The phylogenetic position of an undescribed paedomorphic clupeiform taxon: mitogenomic evidence

article

Transfer RNA gene arrangement and codon usage in vertebrate mitochondrial genomes: a new insight into gene order conservation

scientific article

Trophic evolution in African citharinoid fishes (Teleostei: Characiformes) and the origin of intraordinal pterygophagy

scientific article

Unexpected Ceiling of Genetic Differentiation in the Control Region of the Mitochondrial DNA between Different Subspecies of the Ayu Plecoglossus altivelis

scientific article (publication date: April 2005)

Unique patterns of pelvic fin evolution: a case study of balistoid fishes (Pisces: Tetraodontiformes) based on whole mitochondrial genome sequences

scientific article

Using dense locality sampling resolves the subtle genetic population structure of the dispersive fish species Plecoglossus altivelis

scientific article

Zooplankton diversity analysis through single-gene sequencing of a community sample

scientific article

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