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Ecology and Evolution
Japan
2026

D-Index & Metrics

Ecology and Evolution

D-Index
84
Citations
22524
World Ranking
684
National Ranking
2

Research.com Recognitions

  • 2026 - Research.com Ecology and Evolution in Japan Leader Award

Overview

Masaki Miya is affiliated with the American Museum of Natural History in the United States. Their research spans primarily Environmental Science and Biochemistry, Genetics and Molecular Biology, with a focus on subfields such as Ecology, Molecular Biology, Nature and Landscape Conservation, Global and Planetary Change, and Ecology, Evolution, Behavior and Systematics.

The main topics in their work include Environmental DNA in Biodiversity Studies, Identification and Quantification in Food, Microbial Community Ecology and Physiology, Genomics and Phylogenetic Studies, Fish Biology, Ecology, and Behavior, Ichthyology and Marine Biology, and Isotope Analysis in Ecology.

Several frequent co-authors have contributed to their research, including:

  • Tetsuya Sado
  • Toshifumi Minamoto
  • Masayuki Ushio
  • Shin-ichiro Oka
  • Hiroki Yamanaka

Masaki Miya has published extensively in venues such as:

  • bioRxiv (Cold Spring Harbor Laboratory)
  • Environmental DNA
  • Metabarcoding and Metagenomics
  • MethodsX
  • Limnology

Significant recent papers include:

  • MiFish metabarcoding: a high-throughput approach for simultaneous detection of multiple fish species from environmental DNA and other samples, 2020, Fisheries Science
  • Environmental DNA Metabarcoding: A Novel Method for Biodiversity Monitoring of Marine Fish Communities, 2021, Annual Review of Marine Science
  • An illustrated manual for environmental DNA research: Water sampling guidelines and experimental protocols, 2020, Environmental DNA
  • Sedimentary eDNA provides different information on timescale and fish species composition compared with aqueous eDNA, 2020, Environmental DNA
  • MitoFish, MitoAnnotator, and MiFish Pipeline: Updates in 10 Years, 2023, Molecular Biology and Evolution

Best Publications

  • MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species.

    M. Miya;Y. Sato;T. Fukunaga;T. Sado

  • Phylogenetic classification of bony fishes.

    Ricardo Betancur-R;Ricardo Betancur-R;Edward O. Wiley;Edward O. Wiley;Gloria Arratia;Arturo Acero

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

    Masaki Miya;Hirohiko Takeshima;Hiromitsu Endo;Naoya B Ishiguro

  • MitoFish and MitoAnnotator: A Mitochondrial Genome Database of Fish with an Accurate and Automatic Annotation Pipeline

    Wataru Iwasaki;Tsukasa Fukunaga;Ryota Isagozawa;Koichiro Yamada

  • Mitogenomic Exploration of Higher Teleostean Phylogenies: A Case Study for Moderate-Scale Evolutionary Genomics with 38 Newly Determined Complete Mitochondrial DNA Sequences

    Masaki A. Miya;Akira Kawaguchi;Mutsumi Nishida

  • How Meaningful Are Bayesian Support Values

    Mark P. Simmons;Kurt M. Pickett;Masaki Miya

  • Mitogenomic evolution and interrelationships of the Cypriniformes (Actinopterygii: Ostariophysi): the first evidence toward resolution of higher-level relationships of the world's largest freshwater fish clade based on 59 whole mitogenome sequences.

    K. Saitoh;T. Sado;R. L. Mayden;N. Hanzawa

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

    Satoshi Yamamoto;Reiji Masuda;Yukuto Sato;Tetsuya Sado

  • Use of Mitogenomic Information in Teleostean Molecular Phylogenetics: A Tree-Based Exploration under the Maximum-Parsimony Optimality Criterion

    Masaki Miya;Mutsumi Nishida

  • Organization of the Mitochondrial Genome of a Deep-Sea Fish, Gonostoma gracile (Teleostei: Stomiiformes): First Example of Transfer RNA Gene Rearrangements in Bony Fishes.

    Masaki Miya;Mutsumi Nishida

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

    Jun G Inoue;Masaki Miya;Katsumi Tsukamoto;Mutsumi Nishida

  • Phylogeny and polyploidy: Resolving the classification of cyprinine fishes (Teleostei: Cypriniformes)

    Lei Yang;Tetsuya Sado;M. Vincent Hirt;Emmanuel Pasco-Viel

  • Structure and variation of the mitochondrial genome of fishes.

    Takashi P. Satoh;Takashi P. Satoh;Masaki Miya;Kohji Mabuchi;Mutsumi Nishida;Mutsumi Nishida

  • Environmental DNA as a 'snapshot' of fish distribution: A case study of Japanese jack mackerel in Maizuru Bay, Sea of Japan

    Satoshi Yamamoto;Kenji Minami;Keiichi Fukaya;Kohji Takahashi

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

    Yukuto Sato;Masaki Miya;Tsukasa Fukunaga;Tetsuya Sado

  • A mitogenomic perspective on the basal teleostean phylogeny: resolving higher-level relationships with longer DNA sequences.

    Jun G. Inoue;Masaki Miya;Katsumi Tsukamoto;Mutsumi Nishida

  • Evolutionary Origin and Phylogeny of the Modern Holocephalans (Chondrichthyes: Chimaeriformes): A Mitogenomic Perspective

    Jun G. Inoue;Masaki Miya;Kevin Lam;Boon-Hui Tay

  • Mitochondrial Genomics of Ostariophysan Fishes: Perspectives on Phylogeny and Biogeography

    Kenji Saitoh;Masaki Miya;Jun G. Inoue;Naoya B. Ishiguro

  • Basal euteleostean relationships: a mitogenomic perspective on the phylogenetic reality of the "Protacanthopterygii".

    Naoya B Ishiguro;Masaki Miya;Mutsumi Nishida

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

    Masaki Miya;Ryo O. Gotoh;Tetsuya Sado

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

    Yuki Minegishi;Jun Aoyama;Jun G. Inoue;Masaki Miya

Frequent Co-Authors

Mutsumi Nishida
Mutsumi Nishida University of the Ryukyus
Toshifumi Minamoto
Toshifumi Minamoto Kobe University
Hiroki Yamanaka
Hiroki Yamanaka Ryukoku University
Richard L. Mayden
Richard L. Mayden Saint Louis University
Katsumi Tsukamoto
Katsumi Tsukamoto University of Tokyo
Reiji Masuda
Reiji Masuda Kyoto University
Hideyuki Doi
Hideyuki Doi Kyoto University
Thomas J. Near
Thomas J. Near Yale University
Guillermo Ortí
Guillermo Ortí George Washington University
Norihiro Okada
Norihiro Okada National Cheng Kung University

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