Biodiversity Research Center, Academia Sinica

Dr. Ryuji Machida Associate Research Fellow

Lab PI

Dr. Ryuji Machida

Associate Research Fellow

Ph.D. University of Tokyo

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Office: Greenhouse Builiding  200


Research Fields
  • Marine Molecular Ecology
  • Marine Metazoan Metagenomics
  • Evolutionary ecology

Research Directions

  • 1.Metagenomics for marine metazoans
    Metagenomics has transformed our understanding of microbial communities, and is beginning to be applied to metazoans. The majority of marine metazoan species are small and thus difficult to sample individually. Additionally, it is difficult to identify organisms based on the morphology of early developmental stages, such as eggs and larvae. Therefore, the application of metagenomic approaches to marine metazoans has the potential to transform our understanding of metazoan biodiversity.
  • 2.Evolutionary ecology of marine invertebrates
    Our lab is studying invertebrate marine ecology and its evolution, using information acquired from both individual- and community-based (metagenomic) genetic analyses. Such data facilitate our study of invertebrate distribution, population structure, larval dispersal, and related fields.
  • 3.Population subdivision in pelagic zooplankton
    Population subdivision and speciation are important evolutionary mechanisms, which contribute for generation of biodiversity of pelagic zooplankton. We are utilizing both individual- and community-based genetic analyses to study the pelagic gene flow barrier, which plays an important role in the establishment of new populations and species of marine planktonic animals.

Latest published paper

期刊論文 ( 2016 - 2021 )

  1. Leray M, Knowlton N*, Ho SL, Nguyen BN, Machida RJ*, 2020, “Reply to Locatelli et al.: Evaluating species-level accuracy of GenBank metazoan sequences will require experts’ effort in each group”, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 00. (SCIE) (IF: 9.412; SCIE ranking: 11.3%)
  2. Leray M, Machida RJ*, 2020, “Seabed mining could come at a high price for a unique fauna”, MOLECULAR ECOLOGY, 00. (SCIE) (IF: 5.163; SCIE ranking: 16.8%,11.2%,13.7%)
  3. Makino W, Machida RJ, Okitsu J, Nisikawa U, 2019, “Underestimated species diversity and hidden habitat preference in Moina (Crustacea, Cladocera) revealed by integrative taxonomy”, HYDROBIOLOGIA, 847, 857–878. (SCIE) (IF: 2.385; SCIE ranking: 20.6%)
  4. Leray M, Knowlton N, Ho SL, Nguyen BN, Machida RJ*, 2019, “GenBank is a reliable resource for 21st century biodiversity research”, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 116 (45), 22651-22656. (SCIE) (IF: 9.412; SCIE ranking: 11.3%) Link
  5. Kong WL, Miki T, Lin YY, Makino W, Urabe J, Gu SH, Machida RJ*, 2019, “Nuclear and mitochondrial ribosomal ratio as an index of animal growth rate”, LIMNOLOGY AND OCEANOGRAPHY-METHODS, 17: 575-584. (SCIE) (IF: 2.458; SCIE ranking: 35.8%,18.2%)
  6. Pearman JK, Leray M, Villalobos R, Machida RJ, Berumen ML, Knowlton N, Carvalho S, 2018, “Cross-shelf investigation of coral reef cryptic benthic organisms reveals diversity patterns of the hidden majority”, Scientific Reports, 8(1), 8090. (SCIE) (IF: 3.998; SCIE ranking: 23.9%) Link
  7. Leray M, Ho SL, Lin IJ, Machida RJ*, 2018, “MIDORI server: a webserver for taxonomic assignment of unknown metazoan mitochondrial-encoded sequences using a curated database ”, BIOINFORMATICS, 34(21), 3753-3754. (SCIE) (IF: 5.61; SCIE ranking: 5.1%,7.8%,12.8%) Link
  8. White KN, Machida RJ*, 2018, “Taiwanese Leucothoidae (Crustacea: Amphipoda), Including Three New Species from Dongsha Atoll”, ZOOLOGICAL STUDIES, 57, 47. (SCIE) (IF: 1.257; SCIE ranking: 46.2%) Link
  9. Machida RJ, Leray M, Ho SL, Knowlton N, 2017, “Metazoan mitochondrial gene sequence reference datasets for taxonomic assignment of environmental samples”, Scientific Data, 4, 170027. (SCIE) (IF: 5.541; SCIE ranking: 46.2%,84.8%) Link
  10. Machida RJ, Lin YY, 2017, “Occurrence of Mitochondrial CO1 Pseudogenes in Neocalanus plumchrus (Crustacea: Copepoda): Hybridization Indicated by Recombined Nuclear Mitochondrial Pseudogenes”, PLOS ONE, 12(2), e0172710. (SCIE) (IF: 2.74; SCIE ranking: 38%) Link