Hideyuki Doi

Graduate School of Simulation Studies

University of Hyogo


Graduate School of Simulation Studies, University of Hyogo

7-1-28 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan

E-mail: hideyuki.doi (at) icloud.com

Office & Fax: 078-303-1986




  • 23 Jul. NEW PAPER: Our global project published a math-analysis paper in Nature Communications. Our global meta-analysis found adaptive phenological responses of animals, mainly birds, against global warming, but did not find the sufficient morphological responses to warming. LINK
  • 11 Jul. NEW PAPER: Using eDNA metabarcoding, we implied that information on the terrestrial and aquatic fungal compositions of watersheds, and therefore their spatial structure, can be obtained by investigating the fungal DNA assemblages in river water. LINK
  • 28 Jan. NEW PAPER: Our food-chain length paper was published in Communications Biology. We investigated how the sequence of species immigration affects food-chain length and whether the effect depends on productivity using microcosm experiments. LINK


  • 30 Sep. We had the first annual meeting of The eDNA Society (http://ednasociety.org).
  • 4 Jul. Our perspective paper "A macroecological perspective for phenological research under climate change" was nominated a groundbreaking article for Change the World 2018. LINK


  • 18 Oct. NEW PAPER: We published a a paper titled "Water sampling for environmental DNA surveys by using an unmanned aerial vehicle" in Limnology and Oceanography: Methods. LINK We applied UAV (i.e., Drone) for eDNA sampling, and the method can be applied for high-current streams and extreme environments.
  • 30 Sep. The poster presentation by Matsuoka et al. was honored as the Best Poster Presentation Award in the 82nd annual meeting of Japanese Society of Limnology!
  • 7 Sep. NEW PAPER: We published a a paper titled "Environmental DNA method for estimating the distribution of endangered aquatic heteropteran in the wetlands" in Royal Society Open Science. LINK We summarized the eDNA methods could be used to the distribution of macroorganisms, including aquatic insects in wetlands which have very low water depth, less than 10 cm.
  • 1 Jun. NEW PAPER: We published a a paper titled "Environmental DNA method for estimating salamander distribution in headwater streams, and a comparison of water sampling methods in PLOSONE. LINK Here, we concluded that eDNA methods could be used to determine the distribution of macroorganisms inhabiting headwater systems using samples from the surface of the water.


  • 15 Oct. NEW PAPER: We published a new paper titled "Environmental DNA analysis for estimating the abundance and biomass of stream fish." in Freshwater Biology  LINK In this study, we found eDNA can be applied to lotic systems to evaluate fish abundance and biomass. 
  • 1 Aug. Shunsuke Matsuoka, a post-doc, joined our group.
  • 1 Jul. Mariko Nagano, a post-doc, joined our group.
  • 21 Jun.We published a new paper for the environment DNA method to estimate the distribution of an endangered Japanese crayfish in headwater streams. LINK *Featured by Asahi-Shinbun (Digital), Mainichi-Shinbun, Nikkei-Shinbun, Shinano Mainichi-Shinbun, Hokkaido Kensetsu-Shinbun, Hokkaido Tsushin, Kobe-Shinbun Next news, Yahoo! news, 47News, ITmedia, MyNavi news, etc
  • 4 Feb. We published a simulation model paper to evaluate the effect of leaf phenological shift caused by climate change on forest productivity and nutrient cycling with considering plant-microbe-soil interactions. LINK


  • 30 Oct. We published a cross-system meta-analysis paper for summarizing experiments testing predation effects on prey communities. The paper was published in Oikos as Editor's ChoiceLINK
  • 8 Sep. We published a paper for eDNA method to detect the ratio of native/non-native common carp in Japan using SNP. LINK This study was featured by ScienceDailyEurekalert, Science News, Phys.org, Helpinus
  • 3 Jul. We published a paper for eDNA method to detect Amur minnow (Rhynchocypris logowskii steindachneri) in Agricultural drainage canals. LINK
  • 7 Apr. We published a paper about the advantage of digital droplet PCR to survey fish distribution using environmental DNA  in Environmental Science and Technology LINK.
  • 1 Apr. Our lab. was moved to Graduate School of Simulation Studies, University of Hyogo. 
  • 23 Mar. We published a paper about digital droplet PCR for estimating fish abundance and biomass using environmental DNA survey in PLOS ONE. LINK   This study was featured by ScienceDailyPhys.orgDNA barcoding Blog
  • 30 Jan. Our paper about frog radioactive-cesium concentration in Fukushima was just published in Environmental Pollution. LINK


  • 2 Dec. Our eDNA paper was just published online in Biological Conservation. The paper tested sampling process (e.g., freezing sample water) effects on fish eDNA detection in ponds. LINK


Research overview

Our research objective is to understand ecosystem and community dynamics in ecosystems. We are broadly interested in the ecology, especially, trophic interactions in food web and phenological dynamics of community. Also, we are interested in general biology and sciences, such as metabolic theory and biological stoichiometry, environmental pollution. Currently, our research themes are follows.


1) Food webs: spatial patterns of food webs, production, material cycling in aquatic ecosystems, food web analysis using multiple stable isotopes, food-chain length theory


2) Prey-predator interactions: microalgal communities and grazers interaction, habitat use of aquatic grazers, interactions between hosts and parasites


3) Environmental DNA: estimation of species distribution by eDNA,  biomass/abundance estimation by eDNA, high-thoughput sequencing for eDNA meta-barcording


4) Phenology and climate change: recent climate changes and the phenological timings of the organisms, mismatching in trophic interactions in response to climate change


5) Meta-analysis and big data analysis to synthesize ecological and biological themes: metabolic scaling and grow rate of organisms, predator effect on ecosystems, food-chain lengths and ecosystem history