Faculty list

Dr. Ryuji Machida

Assistant Research Fellow
Ph.D. University of Tokyo
Research Fields
Marine ecology, phylogeography, genetic connectivity of marine metazoans.
Target taxon is not restricted but mainly invertebrate.
Major Research Achievements (2013-2017)
  • Population subdivision and speciation are interesting and important evolutionary mechanism, which further generate biodiversity. Using individual- and community-based genetic analyses, we are demonstrating the importance of marginal seas for establishment of new populations and species in marine planktonic animals.
  • Designing of universal primer is critically important to recover community composition using community-based analyses. To achieve the task, we have identified conserved genetic region within mitochondrial 12S and nuclear 18S and 28S ribosomal RNA genes using database datasets. We now have sets of primers, which most likely recover most of metazoan species from any communities.
  • Global scale environmental problems, such as climate change and ocean acidification are emerging issues we are facing now. We need to understand not only the mechanism leading to those environment problems, but also the effect those problems have on organisms and ecosystems. We have established the community based genetic analysis (metagenetics and/or metagenomic) to estimate and describe diversity of marine animals. Using the technique, we are trying to understand distribution of marine animals in various temporal and spatial scales.
Research Interests
  • Our work use molecular approaches to address fundamental marine ecology and evolutionary questions.
  • Key words of our group: Biodiversity, Evolution, Ecology, Metagenetics, Phylogeography, Genetic connectivity, Larval dispersal.
    Ongoing projects
    • Global scale genetic connectivity analyses of planktonic animals
    • Role of marginal seas for generation of zooplankton diversity
    • Metagenetic analyses of coral reef metazoan communities
    • Metagenetic analyses of marine zooplankton communities
      Publications (2011-2017)
      1. Machida RJ, Leray M, Ho SL, Knowlton N, to appear, “Metazoan mitochondrial gene sequence reference datasets for taxonomic assignment of environmental samples”, Scientific Data, , 4-170027.
      2. Machida RJ, Lin YY, to appear, “Occurrence of Mitochondrial CO1 Pseudogenes in Neocalanus plumchrus (Crustacea: Copepoda): Hybridization Indicated by Recombined Nuclear Mitochondrial Pseudogenes”, PLOS ONE, , 12(2)-e0172710. (SCI) (IF: 3.057; SCI ranking: 17.5%)
      3. Fujioka HA, Machida RJ, Tsuda A , 2015, “Early life history of Neocalanus plumchrus (Calanoida: Copepoda) in the western subarctic Pacific ”, PROGRESS IN OCEANOGRAPHY, 137, 196-208. (SCI) (IF: 3.512; SCI ranking: 8.2%)
      4. Machida R.J. and Lin Y.Y. , 2014, “Four Methods of Preparing mRNA 5′ End Libraries Using the Illumina Sequencing Platform”, PLoS One, 9(7), e101812. (SCI) (IF: 3.057; SCI ranking: 17.5%)
      5. Miyamoto H, Machida RJ, Nishida S , 2012, “Global phylogeography of the deep-sea pelagic chetognath Eukrohnia hamata”, Progress in Oceanography, 104, 99-109. (SCI) (IF: 3.512; SCI ranking: 8.2%)
      6. Machida RJ*, Kweskin M, Knowlton N , 2012, “PCR primers for metazoan mitochondrial 12S ribosomal DNA sequences”, PLoS One, 7(4), e35887. (SCI) (IF: 3.057; SCI ranking: 17.5%)
      7. Machida, RJ*, Knowlton N , 2012, “PCR primers for metazoan nuclear 18S and 28S ribosomal DNA sequences”, PLoS One, 7(9), e46180. (SCI) (IF: 3.057; SCI ranking: 17.5%)
      8. Machida, R. J. and N. Knowlton, in press, "Ways to mix multiple PCR amplicons into single 454 run." Methods in Molecular Biology.
      9. Bottger-Schnack, R. and R. J. Machida, 2011, "Comparison of morphological and molecular traits for species identification and taxonomic grouping of oncaeid copepods." Hydrobiologia 666(1): 111-125.
      10. Machida, R. J. and S. Nishida, 2010, "Amplified fragment length polymorphism analysis of the mesopelagic copepod Disseta palumbii in the equatorial western Pacific and adjacent waters: Role of marginal seas in the genetic isolation of mesopelagic animals." Deep-Sea Research Part II-Topical Studies in Oceanography 57(24-26): 2130-2134.
      11. Machida, R. J. and A. Tsuda, 2010, "Dissimilarity of species and forms of planktonic Neocalanus copepods using mitochondrial COI, 12S, nuclear ITS, and 28S gene sequences." PLoS ONE 5(4).
      12. Miyamoto, H., R. J. Machida, and S. Nishida, 2010, "Complete mitochondrial genome sequences of the three pelagic chaetognaths Sagitta nagae, Sagitta decipiens and Sagitta enflata." Comparative Biochemistry and Physiology D-Genomics & Proteomics 5(1): 65-72.
      13. Miyamoto, H., R. J. Machida, and S. Nishida, 2010, "Genetic diversity and cryptic speciation of the deep sea chaetognath Caecosagitta macrocephala (Fowler, 1904)." Deep-Sea Research Part Ii-Topical Studies in Oceanography 57(24-26): 2211-2219.
      14. Machida, R. J., Y. Hashiguchi, M. Nishida, and S. Nishida, 2009, "Zooplankton diversity analysis through single-gene sequencing of a community sample." BMC Genomics 10.
      15. Tsuda, A., H. Saito, R. J. Machida, and S. Shimode, 2009, "Meso- and microzooplankton responses to an in situ iron fertilization experiment (SEEDS II) in the northwest subarctic Pacific." Deep-Sea Research Part II-Topical Studies in Oceanography 56(26): 2767-2778.
      16. Nonomura, T., R. J. Machida, and S. Nishida, 2008, "Stage-V copepodites of Calanus sinicus and Calanus jashnovi (Copepoda : Calanoida) in mesopelagic zone of Sagami Bay as identified with genetic markers, with special reference to their vertical distribution." Progress in Oceanography 77(1): 45-55.
      17. Tsuda, A., S. Takeda, et al., 2007, "Evidence for the grazing hypothesis: Grazing reduces phytoplankton responses of the HNLC ecosystem to iron enrichment in the western subarctic pacific (SEEDS II)." Journal of Oceanography 63: 983-994.