List of works - Masaki Miya

A 'living fossil' eel (Anguilliformes: Protanguillidae, fam. nov.) from an undersea cave in Palau ⬇️

scientific article (publication date: 7 March 2012)

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

A phylogenomic framework for pelagiarian fishes (Acanthomorpha: Percomorpha) highlights mosaic radiation in the open ocean

scientific article published on 11 September 2019

An illustrated manual for environmental DNA research: Water sampling guidelines and experimental protocols

scientific article published on 10 August 2020

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

Biogeography and evolution of the Carassius auratus-complex in East Asia

scientific article

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 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

Correction: Environmental DNA as a 'Snapshot' of Fish Distribution: A Case Study of Japanese Jack Mackerel in Maizuru Bay, Sea of Japan

scientific article published on 4 April 2016

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

Demonstration of the potential of environmental DNA as a tool for the detection of avian species

scientific article published on 14 March 2018

Demonstration of the potential of environmental DNA as a tool for the detection of avian species

Detection of the Largest Deep-Sea-Endemic Teleost Fish at Depths of Over 2,000 m Through a Combination of eDNA Metabarcoding and Baited Camera Observations

scientific article published on 01 July 2022

Determining an effective sampling method for eDNA metabarcoding: a case study for fish biodiversity monitoring in a small, natural river

scientific article published on 15 November 2020

Development and evaluation of PCR primers for environmental DNA (eDNA) metabarcoding of Amphibia

scientific article

Development of a new set of PCR primers for eDNA metabarcoding decapod crustaceans

scientific article published on 24 April 2019

Discovery of a colossal slickhead (Alepocephaliformes: Alepocephalidae): an active-swimming top predator in the deep waters of Suruga Bay, Japan ⬇️

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)

Effects of sampling seasons and locations on fish environmental DNA metabarcoding in dam reservoirs

scientific article published on 06 May 2020

Environmental DNA analysis shows high potential as a tool for estimating intraspecific genetic diversity in a wild fish population

scientific article published on 15 April 2020

Environmental DNA as a 'Snapshot' of Fish Distribution: A Case Study of Japanese Jack Mackerel in Maizuru Bay, Sea of Japan

scientific article

Environmental DNA enables detection of terrestrial mammals from forest pond water

scientific article

Environmental DNA metabarcoding for biodiversity monitoring of a highly diverse tropical fish community in a coral reef lagoon: Estimation of species richness and detection of habitat segregation

scientific article published on 29 August 2020

Environmental DNA metabarcoding reveals local fish communities in a species-rich coastal sea.

scientific article

Evaluation of detection probabilities at the water-filtering and initial PCR steps in environmental DNA metabarcoding using a multispecies site occupancy model

scientific article published on 05 March 2019

Evolution of bidirectional sex change and gonochorism in fishes of the gobiid genera Trimma, Priolepis, and Trimmatom

scientific article published in March 2017

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

Evolutionary affinities of the unfathomable Parabrotulidae: Molecular data indicate placement of Parabrotula within the family Bythitidae, Ophidiiformes

scientific article

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 and phylogeny of the modern holocephalans (Chondrichthyes: Chimaeriformes): 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)

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

scientific article

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

scientific article published in September 2004

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

scientific article

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 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

Limits and phylogenetic relationships of East Asian fishes in the subfamily Oxygastrinae (Teleostei: Cypriniformes: Cyprinidae)

scientific article (publication date: 20 June 2013)

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

scientific article published on January 2003

MiFish metabarcoding: a high-throughput approach for simultaneous detection of multiple fish species from environmental DNA and other samples

MitoFish and MiFish Pipeline: A Mitochondrial Genome Database of Fish with an Analysis Pipeline for Environmental DNA Metabarcoding.

scientific article

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

scientific article

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 genomic investigation of flatfish monophyly

scientific article

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 evaluation of the unique facial nerve pattern as a phylogenetic marker within the percifom fishes (Teleostei: Percomorpha).

scientific article

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 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 of the cyprinid tribe Labeonini (Teleostei: Cypriniformes)

scientific article published in November 2012

Molecular systematics of the anchovy genus Encrasicholina in the Northwest Pacific

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

Multilocus phylogenetic analysis of the first molecular data from the rare and monotypic Amarsipidae places the family within the Pelagia and highlights limitations of existing data sets in resolving pelagian interrelationships.

scientific article published on 8 March 2018

New PCR primers for metabarcoding environmental DNA from freshwater eels, genus Anguilla

scientific article published on 28 May 2019

Optimization of environmental DNA extraction and amplification methods for metabarcoding of deep-sea fish

scientific article published on 23 January 2021

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 position of the rainbow sardine Dussumieria (Dussumieriidae) and its bearing on the early evolution of the Clupeoidei

scientific article

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

scientific article published on 7 October 2006

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 crypti

scientific article

Phylogenetic relationships of Danio within the order Cypriniformes: a framework for comparative and evolutionary studies of a model species

scientific article

Phylogenetic relationships of catostomid fishes (Actinopterygii: Cypriniformes) based on mitochondrial ND4/ND5 gene sequences.

scientific article published on 13 June 2009

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.

scientific article

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

scientific article

Phylogeny and polyploidy: resolving the classification of cyprinine fishes (Teleostei: Cypriniformes).

scientific article published on 16 February 2015

Phylogeny of the Elopomorpha (Teleostei): evidence from six nuclear and mitochondrial markers

scientific article

Phylogeny of the gudgeons (Teleostei: Cyprinidae: Gobioninae).

scientific article

Pike and salmon as sister taxa: detailed intraclade resolution and divergence time estimation of Esociformes + Salmoniformes based on whole mitochondrial genome sequences.

scientific article

Preservation Obscures Pelagic Deep-Sea Fish Diversity: Doubling the Number of Sole-Bearing Opisthoproctids and Resurrection of the Genus Monacoa (Opisthoproctidae, Argentiniformes)

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

scientific article (publication date: 7 April 2011)

Resolving deep-sea pelagic saccopharyngiform eel mysteries: Identification of Neocyema and Monognathidae leptocephali and establishment of a new fish family "Neocyematidae" based on larvae, adults and mitogenomic gene orders

scientific article published in PLoS ONE

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

article

Sedimentary eDNA provides different information on timescale and fish species composition compared with aqueous eDNA

scientific article published on 21 February 2020

Species traits and ecosystem characteristics affect species detection by <scp>eDNA</scp> metabarcoding in lake fish communities

scientific article published in 2023

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

Systematics of the subfamily Danioninae (Teleostei: Cypriniformes: Cyprinidae).

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

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

scientific article

Use of a Filter Cartridge for Filtration of Water Samples and Extraction of Environmental DNA.

scientific article

The use of citizen science in fish eDNA metabarcoding for evaluating regional biodiversity in a coastal marine region: A pilot study

scientific article published on 23 May 2022

List of works by Masaki Miya

A 'living fossil' eel (Anguilliformes: Protanguillidae, fam. nov.) from an undersea cave in Palau ⬇️

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

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

A phylogenomic framework for pelagiarian fishes (Acanthomorpha: Percomorpha) highlights mosaic radiation in the open ocean

An illustrated manual for environmental DNA research: Water sampling guidelines and experimental protocols

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

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

Biogeography and evolution of the Carassius auratus-complex in East Asia

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

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

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

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

Correction: Environmental DNA as a 'Snapshot' of Fish Distribution: A Case Study of Japanese Jack Mackerel in Maizuru Bay, Sea of Japan

Deep-ocean origin of the freshwater eels

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

Demonstration of the potential of environmental DNA as a tool for the detection of avian species

Demonstration of the potential of environmental DNA as a tool for the detection of avian species

Detection of the Largest Deep-Sea-Endemic Teleost Fish at Depths of Over 2,000 m Through a Combination of eDNA Metabarcoding and Baited Camera Observations

Determining an effective sampling method for eDNA metabarcoding: a case study for fish biodiversity monitoring in a small, natural river

Development and evaluation of PCR primers for environmental DNA (eDNA) metabarcoding of Amphibia

Development of a new set of PCR primers for eDNA metabarcoding decapod crustaceans

Discovery of a colossal slickhead (Alepocephaliformes: Alepocephalidae): an active-swimming top predator in the deep waters of Suruga Bay, Japan ⬇️

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

Effects of sampling seasons and locations on fish environmental DNA metabarcoding in dam reservoirs

Environmental DNA analysis shows high potential as a tool for estimating intraspecific genetic diversity in a wild fish population

Environmental DNA as a 'Snapshot' of Fish Distribution: A Case Study of Japanese Jack Mackerel in Maizuru Bay, Sea of Japan

Environmental DNA enables detection of terrestrial mammals from forest pond water

Environmental DNA metabarcoding for biodiversity monitoring of a highly diverse tropical fish community in a coral reef lagoon: Estimation of species richness and detection of habitat segregation

Environmental DNA metabarcoding reveals local fish communities in a species-rich coastal sea.

Evaluation of detection probabilities at the water-filtering and initial PCR steps in environmental DNA metabarcoding using a multispecies site occupancy model

Evolution of bidirectional sex change and gonochorism in fishes of the gobiid genera Trimma, Priolepis, and Trimmatom

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

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

Evolutionary affinities of the unfathomable Parabrotulidae: Molecular data indicate placement of Parabrotula within the family Bythitidae, Ophidiiformes

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

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

Evolutionary origin and phylogeny of the modern holocephalans (Chondrichthyes: Chimaeriformes): a mitogenomic perspective

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

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

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

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

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

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

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

Intron-loss evolution of hatching enzyme genes in Teleostei

Limits and phylogenetic relationships of East Asian fishes in the subfamily Oxygastrinae (Teleostei: Cypriniformes: Cyprinidae)

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

MiFish metabarcoding: a high-throughput approach for simultaneous detection of multiple fish species from environmental DNA and other samples

MitoFish and MiFish Pipeline: A Mitochondrial Genome Database of Fish with an Analysis Pipeline for Environmental DNA Metabarcoding.

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

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

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

Mitochondrial genomic investigation of flatfish monophyly

Mitochondrial genomics of ostariophysan fishes: perspectives on phylogeny and biogeography

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

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

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

Mitogenomic evaluation of the unique facial nerve pattern as a phylogenetic marker within the percifom fishes (Teleostei: Percomorpha).

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

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

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

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

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

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

Molecular phylogeny of the cyprinid tribe Labeonini (Teleostei: Cypriniformes)

Molecular systematics of the anchovy genus Encrasicholina in the Northwest Pacific

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

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

Multilocus phylogenetic analysis of the first molecular data from the rare and monotypic Amarsipidae places the family within the Pelagia and highlights limitations of existing data sets in resolving pelagian interrelationships.

New PCR primers for metabarcoding environmental DNA from freshwater eels, genus Anguilla

Optimization of environmental DNA extraction and amplification methods for metabarcoding of deep-sea fish

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

Phylogenetic position of the rainbow sardine Dussumieria (Dussumieriidae) and its bearing on the early evolution of the Clupeoidei

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

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 crypti

Phylogenetic relationships of Danio within the order Cypriniformes: a framework for comparative and evolutionary studies of a model species

Phylogenetic relationships of catostomid fishes (Actinopterygii: Cypriniformes) based on mitochondrial ND4/ND5 gene sequences.

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.

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

The use of citizen science in fish eDNA metabarcoding for evaluating regional biodiversity in a coastal marine region: A pilot study