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研究業績

学術論文(英文のもの)

  1. Kana Hayami, Masayuki K. Sakata, Takashi Inagawa, Jiro Okitsu, Izumi Katano, Hideyuki Doi, Katsuki Nakai, Hidetaka Ichiyanagi, Ryo O. Gotoh, Masaki Miya, Hirotoshi Sato, Hiroki Yamanaka, Toshifumi Minamoto. (accepted) Effects of sampling seasons and locations on fish environmental DNA metabarcoding in dam reservoirs. Ecology and Evolution. LINK
  2. Satsuki Tsuji, Atsushi Maruyama, Masaki Miya, Masayuki Ushio, Hirotoshi Sato, Toshifumi Minamoto, Hiroki Yamanaka. (accepted) Environmental DNA analysis shows high potential as a tool for estimating intraspecific genetic diversity in a wild fish population. Molecular Ecology Resources. LINK
  3. Akihide Kasai, Shingo Takada, Aya Yamazaki, Reiji Masuda, Hiroki Yamanaka. (accepted) The effect of temperature on degradation of environmental DNA of Japanese eel. Fisheries Science. LINK
  4. Masayuki K. Sakata, Satoshi Yamamoto, Ryo O. Gotoh, Masaki Miya, Hiroki Yamanaka, Toshifumi Minamoto. (accepted) Sedimentary eDNA provides different information on timescale and fish species composition compared with aqueous eDNA. Environmental DNA. LINK
  5. Satsuki Tsuji, Masaki Miya, Masayuki Ushio, Hirotoshi Sato, Toshifumi Minamoto, Hiroki Yamanaka. (2019) Evaluating intraspecific genetic diversity using environmental DNA and denoising approach: A case study using tank water. Environmental DNA 2: 42-52. LINK
  6. Kimiko Uchii, Hideyuki Doi, T Okahash, Izumi Katano, Hiroki Yamanaka, Masayuki K Sakata, Toshifumi Minamoto. (accepted) Comparison of inhibition resistance among PCR reagents for detection and quantification of environmental DNA. Environmental DNA 1: 359-367. . LINK
  7. Satsuki Tsuji, Teruhiko Takahara, Hideyuki Doi, Naoki Shibata, Hiroki Yamanaka. (2019) The detection of aquatic macroorganisms using environmental DNA analysis—A review of methods for collection, extraction, and detection. Environmental DNA 1: 99-108. LINK
  8. Qianqian Wu, Ken Kawano, Toshiyuki Ishikawa, Masayuki K. Sakata, Ryohei Nakao, Masayoshi K. Hiraiwa, Satsuki Tsuji, Hiroki Yamanaka, Toshifumi Minamoto. (2019) Habitat selection and migration of the common shrimp, Palaemon paucidens in Lake Biwa, Japan—An eDNA‐based study. Environmental DNA 1: 54-63. LINK
  9. Kazuya Fujii, Hideyuki Doi, Shunsuke Matsuoka, Mariko Nagano, Hirotoshi Sato, Hiroki Yamanaka. (2018) Environmental DNA metabarcoding for fish community analysis in backwater lakes: A comparison of capture methods. PLoS ONE 14:e0210357. LINK
  10. Atsushi Maruyama, Kousuke Sugatani, Kazuki Watanabe, Hiroki Yamanaka, Akio Imamura. (2018) Environmental DNA analysis as a non‐invasive quantitative tool for reproductive migration of a threatened endemic fish in rivers. Ecology and Evolution 8:11964-11974. LINK
  11. Hiroki Yamanaka, Daiki Takao, Atsushi Maruyama, Akio Imamura. (2018) Species-specific detection of the endangered piscivorous cyprinid fish Opsariichthys uncirostris uncirostris, three-lips, using environmental DNA analysis. Ecological Research 33:1-4. LINK
  12. Qianqian Wu, Ken Kawano, Yoshitoshi Uehara, Noboru Okuda, Masamichi Hongo, Satsuki Tsuji, Hiroki Yamanaka, Toshifumi Minamoto. (2018) Environmental DNA reveals non-migratory individuals of Palaemon paucidens overwintering in Lake Biwa shallow waters. Freshwater Science. LINK
  13. Masayuki Ushio, Hiroaki Murakami, Reiji Masuda, Tetsuya Sado, Masaki Miya, Sho Sakurai, Hiroki Yamanaka, Toshifumi Minamoto, Michio Kondoh. (2018) Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing. Metabarcoding & Metagenomics2:e23297. LINK
  14. Hiroki Yamanaka, Motomi Genkai-kato, Yukihiro Kohmatsu. (2017) Effects of water temperature, dissolved oxygen and body mass on the metabolic scope of larvae and juveniles of the nigorobunacarp, Carassius auratus grandoculis. Kuroshio Science.
  15. Masayuki Ushio, Hisato Fukuda, Toshiki Inoue, Makoto Kobayashi, Osamu Kishida, Keiichi Sato, Koichi Murata, Masato Nikaido, Tetsuya Sado, Yukuto Sato, Masamichi Takeshita, Wataru Iwasaki, Hiroki Yamanaka, Michio Kondoh, Masaki Miya. (2017) Environmental DNA enables detection of terrestrial mammals 6 from forest pond water. Molecular Ecology Resources 17:e63-e75. LINK
  16. Hirotoshi Sato, Yuki Sogo, Hideyuki Doi, Hiroki Yamanaka. (2017) Usefulness and limitations of sample pooling for environmental DNA metabarcoding of freshwater fish communities. Scientific Reports 7:14860. LINK
  17. Kimiko Uchii, Hideyuki Doi Hiroki Yamanaka, Toshifumi Minamoto. (2017) Distinct seasonal migration patterns of Japanese native and non-native genotypes of common carp estimated by environmental DNA.Ecology and Evolution 7:8515-8522. LINK
  18. Satsuki Tsuji, Masayuki Ushio, Sho Sakurai, Toshifumi Minamoto, Hiroki Yamanaka. (2017) Water temperature-dependent degradation of environmental DNA and its relation to bacterial abundance. PLOS ONE 12:e0176608. LINK
  19. Hiroki Yamanaka, Toshifumi Minamoto, Junichi Matsuura, Sho Sakurai, Satsuki Tsuji, Hiromu Hotozawa, Masamichi Hongo, Yuki Sogo, Naoki Kakimi, Iori Teramura, Masaki Sugita, Miki Baba, Akihiro Kondo. (2017) A simple method for preserving environmental DNA in water samples at ambient temperature by addition of cationic surfactant. Limnology 18:pp233-241. LINK
  20. Toshifumi Minamoto, Kimiko Uchii, Teruhiko Takahara, Takumi Kitayoshi, Satsuki Tsuji, Hiroki Yamanaka, Hideyuki Doi. (2017) Nuclear internal transcribed spacer-1 as a sensitive genetic marker for environmental DNA studies in common carp Cyprinus carpio. Molecular Ecology Resources17:324-333. LINK
  21. Hideyuki Doi, Kimiko Uchii, Saeko Matsuhashi, Hiroki Yamanaka, Toshifumi Minamoto. (2017) Isopropanol precipitation method for collecting fish environmental DNA. Limnology and Oceanography: Methods 15:p212-218. LINK
  22. Hideyuki Doi, Ryutei Inui, Yoshihisa Akamatsu, Kazuki Kanno, Hiroki Yamanaka, Teruhiko Takahara, Toshifumi Minamoto. (2017) Environmental DNA analysis for estimating the abundance and biomass of stream fish. Freshwater Biology 62: 30-39. LINK
  23. Satsuki Tsuji, Hiroki Yamanaka, Toshifumi Minamoto. (2017) Effects of water pH and proteinase K treatment on the yield of environmental DNA from water samples. Limnology 18: pp 1-7. LINK
  24. Masaki Miya, Toshifumi Minamoto, Hiroki Yamanaka, Shin-ichiro Oka, Satoshi Yamamoto, Tetsuya Sado, Hideyuki Doi. (2016) Use of a filter cartridge for filtration of water samples and extraction of environmental DNA. Journal of Visualized Experiments. LINK
  25. *Hiroki Yamanaka, *Hiromu Motozawa, Satsuki Tsuji, Ryohei C Miyazawa, Teruhiko Takahara, Toshifumi Minamoto. (2016) On-site filtration of water samples for environmental DNA analysis to avoid DNA degradation during transportation. Ecological Research 31:963-967. (*Both authors contributed equally to this work) LINK
  26. Satoshi Yamamoto, Kenji Minami, Keiichi Fukaya, Kohji Takahashi, Hideki Sawada, Hiroaki Murakami, Satsuki Tsuji, Hiroki Hashizume, Shou Kubonaga, Tomoya Horiuchi, Masamichi Hongo, Jo Nishida, Yuta Okugawa, Ayaka Fujiwara, Miho Fukuda, Shunsuke Hidaka, Keita W. Suzuki, Masaki Miya, Hitoshi Araki, Hiroki Yamanaka, Atsushi Maruyama, Kazushi Miyashita, Reiji Masuda, Toshifumi Minamoto, Michio Kondoh. (2016) Environmental DNA as a ‘snapshot’ of fish distribution: a case study of Japanese jack mackerel in Maizuru Bay, Sea of Japan. PLOS ONE 11: e1249786. LINK
  27. Hiroki Yamanaka, Toshifumi Minamoto. (2016) The use of environmental DNA of fishes as an efficient method of determining habitat connectivity. Ecological Indicators 62:147-153. LINK
  28. Masaki Miya, Yukuto Sato, Tsukasa Fukunaga, Tetsuya Sado, Jan Y Poulsen, Keiichi Sato, Toshifumi Minamoto, Satoshi Yamamoto, Hiroki Yamanaka, Hitoshi Araki, Michio Kondoh, Wataru Iwasaki. (2015) MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species. Royal Society Open Science 2:150088. LINK
  29. *Hideyuki Doi, *Teruhiko Takahara, Toshifumi Minamoto, Saeko Matsuhashi, Kimiko Uchii, and Hiroki Yamanaka. (2015) Droplet digital PCR outperforms real-time PCR in the detection of environmental DNA from an invasive fish species. Environmental Science & Technology 49:5601-5608. (*The both authors equally contributed) LINK
  30. Hideyuki Doi, Kimiko Uchii, Teruhiko Takahara, Saeko Matsuhashi, Hiroki Yamanaka, Toshifumi Minamoto. (2015) Use of Droplet Digital PCR for Estimation of Fish Abundance and Biomass in Environmental DNA Surveys. PLoS ONE, 10:e0122763. LINK
  31. Toshifumi Minamoto, Xiaoying Pu, Jie Xie, Yi Dong, Deyi Wu, Hainan Kong, Xiaoxia Yang, Teruhiko Takahara, Mie N. Honjo, Hiroki Yamanaka, Zen’ichiro Kawabata. (2015) Monitoring of fish pathogenic viruses in natural lakes in Yunnan, China. Limnology 16:69-77. LINK
  32. Atsushi Maruyama, Keisuke Nakamura, Hiroki Yamanaka, Michio Kondoh, Toshifumi Minamoto. (2014) The Release Rate of Environmental DNA from Juvenile and Adult Fish. PLoS ONE 9:e114639. LINK
  33. Hiroki Yamanaka. (2013) Hypoxic conditions enhance refuge effect of macrophyte zone for small prey fish from piscivorous predators. Fisheries Management and Ecology 20:465-472. LINK
  34. Hiroki Yamanaka, Teruhiko Takahara, Yukihiro Kohmatsu, Masahide Yuma. (2013) Body size and temperature dependence of routine metabolic rate and critical oxygen concentration in larvae and juveniles of the round crucian carp Carassius auratus grandoculis Temminck & Schlegel 1846. Journal of Applied
  35. *Toshifumi Minamoto, *Hiroki Yamanaka, Teruhiko Takahara, Mie N. Honjo, Zen’ichiro Kawabata. (2012) Surveillance of fish species composition using environmental DNA. Limnology 13:193-197. (*Both authors contributed equally to this work) LINK
  36. Toshifumi Minamoto, Mie N Honjo, Hiroki Yamanaka, Kimiko Uchii, Zen’ichiro Kawabata. (2012) Nationwide Cyprinid herpesvirus 3 contamination in natural rivers of Japan. Research in Veterinary Science 93:508-514. LINK
  37. Teruhiko Takahara, Yukihiro Kohmatsu, Atsushi Maruyama, Hideyuki Doi, Hiroki Yamanaka, Ryohei Yamaoka. (2012) Inducible defense behavior of an anuran tadpole: cue-detection range and cue types used against predator. Behavioral Ecology 23:863-868. LINK
  38. Hiroki Yamanaka, Toshifumi Minamoto, Deyi Wu, Hainan Kong, Zhi-hong Wei, Bin Liu, Zen’ichiro Kawabata. (2012) Spatial-temporal analysis of water temperatures during spring in Lake Erhai, China: implications for fisheries. Inland Waters 2:129-136. LINK
  39. Teruhiko Takahara, Toshifumi Minamoto, Hiroki Yamanaka, Hideyuki Doi, Zen’ichiro Kawabata. (2012) Estimation of Fish Biomass using Environmental DNA. PLoS ONE 7:e35868. LINK
  40. Zen’ichiro Kawabata, Toshifumi Minamoto, Mie N Honjo, Kimiko Uchii, Hiroki Yamanaka, Alata A Suzuki,Yukihiro Kohmatsu, Kota Asano, Tomoaki Itayama,Tomoaki Ichijo, Koji Omori, Noboru Okuda, Masayuki Kakehashi, Masao Nasu, Kazuaki Matsui,Masatomi Matsuoka, Hainan Kong, Teruhiko Takahara, Deyi Wu, Ryuji Yonekura. (2011) Environment-KHV-carp-human linkage as a model for environmental diseases. Ecological Research 26:1011-1016. LINK
  41. Teruhiko Takahara, Hiroki Yamanaka, Aalata A. Suzuki, Mie N. Honjo, Toshifumi Minamoto, Ryuji Yonekura, Tomoaki Itayama, Yukihiro Kohmatsu, Takafumi Ito, Zen’ichiro Kawabata. (2011) Stress response to daily temperature fluctuation in common carp Cyprinus carpio L. Hydrobiologia 675:65-73. LINK
  42. Toshifumi Minamoto, Mie N Honjo, Hiroki Yamanaka, Nobuyuki Tanaka, Tomoaki Itayama, Zen’ichiro Kawabata. (2011) Detection of cyprinid herpesvirus 3 DNA in lake plankton. Research in Veterinary Science 90:530-532. LINK
  43. Kimiko Uchii, Arndt Telschow, Toshifumi Minamoto, Hiroki Yamanaka, Mie N. Honjo, Kazuaki Matsui, Zen’ichiro Kawabata. (2011) Transmission dynamics of a wildlife emerging infectious disease through host reproductive cycles. The ISME Journal 5:244-251. LINK
  44. Hiroki Yamanaka, Atsushi Sogabe, Itsuki C Handoh, Zen’ichiro Kawabata. (2011) The effectiveness of clove oil as an anaesthetic on adult common carp, Cyprinus carpio L. Journal of Animal and Veterinary Advances 10:210-213. LINK
  45. Mayumi Sato, Yôichi Kawaguchi, Hiroki Yamanaka, Tomoyuki Okunaka, Jun Nakajima, Yasuhiro Mitani, Yukihiro Shimatani, Takahiko Mukai, Norio Onikura. (2010) Predicting the spatial distribution of the invasive piscivorous chub (Opsariichthys uncirostris uncirostris) in the irrigation ditches of Kyushu, Japan: a tool for the risk management of biological invasions. Biological Invasions 12(11):3677-3686. LINK
  46. Hiroki Yamanaka, Yukihiro Kohmatsu, Toshifumi Minamoto, Zen’ichiro Kawabata. (2010) Spatial variation and temporal stability of littoral water temperature relative to lakeshore morphometry: environmental analysis from the view of fish thermal ecology. Limnology 11(1):71-76. LINK
  47. Mie N. Honjo, Toshifumi Minamoto, Kazuaki Matsui, Kimiko Uchii, Hiroki Yamanaka, Alata A. Suzuki, Yukihiro Kohmatsu, Takaji Iida, Zen’ichiro Kawabata. (2010) Quantification of Cyprinid Herpesvirus 3 in Environmental Water by Using an External Standard Virus. Applied and Environmental Microbiology 76(1):161-168. LINK
  48. Ryuji Yonekura, Hiroki Yamanaka, Atushi Ushimaru, Kazuaki Matsui, Kimiko Uchii, Atsushi Maruyama. (2009) Allochthonous prey subsidies provide an asymmetric growth benefit to invasive bluegills over native cyprinids under the competitive conditions in a pond. Biological Invasions 11(6):1347-1355. LINK
  49. Toshifumi Minamoto, Mie N. Honjo, Kimiko Uchii, Hiroki Yamanaka, Alata A. Suzuki, Yukihiro Kohmatsu, Takaji Iida, Zen’ichiro Kawabata. (2009) Detection of cyprinid herpesvirus 3 DNA in river water during and after an outbreak. Veterinary Microbiology 135(3-4):261-266. LINK
  50. Hiroki Yamanaka, Yukihiro Kohmatsu and Masahide Yuma. (2007) Difference in the hypoxia tolerance of the round crucian carp and largemouth bass: implications for physiological refugia in the macrophyte zone. Ichthyological Research 54(3):308-312. LINK