Center for Biodiversity Science

Research Achievements

Peer-Reviewed Articles

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▪In English

Oyabu, A., Wu, L., Matsumoto, T., Kihara, N., Yamanaka, H., & Minamoto, T. (2024). The effect of artificial light at night on wild fish community: manipulative field experiment and species composition analysis using environmental DNA. Environmental Advances15, 100457. LINK
Sugiyama, Y., Matsuoka, S., Shimono, Y., Ushio, M., & Doi, H. (2024). Do aquatic fungal environmental DNA assemblages reflect the surrounding terrestrial sporocarp communities?. Fungal Ecology67, 101311. LINK
Zhu, M., Kuroki, M., Kobayashi, T., Yamakawa, T., Sado, T., Kodama, K., Horiguchi, T., & Miya, M. (2023). Comparison of fish fauna evaluated using aqueous eDNA, sedimentary eDNA, and catch surveys in Tokyo Bay, Central Japan. Journal of Marine Systems240, 103886. LINK
Kawakami, T., Yamazaki, A., Asami, M., Goto, Y., Yamanaka, H., Hyodo, S., Ueno, H., & Kasai, A. (2023). Evaluating the sampling effort for the metabarcoding-based detection of fish environmental DNA in the open ocean. Ecology and evolution13(3), e9921. LINK
Zhu, T., Sato, Y., Sado, T., Miya, M., & Iwasaki, W. (2023). MitoFish, MitoAnnotator, and MiFish pipeline: updates in 10 years. Molecular Biology and Evolution40(3), msad035. LINK
Miki, T., Yamanaka, H., Sogabe, A., Omori, K., Saito, Y., Minamoto, T., Uchii, K., Honjo, M. N., Suzuki, A. A., Kohmatsu, Y., & Kawabata, Z. I. (2023). Spatial epidemiology model can explain the seasonal dynamics of infectious disease Cyprinid herpesvirus 3 (CyHV-3) by thermoregulation behavior of the host, common carp (Cyprinus carpio). Theoretical Ecology16(3), 195-208. LINK
Kanbe, T., Mizumoto, H., Mitsuzuka, T., Nakajima, N., & Araki, H. (2023). Co-occurrence patterns of endangered Sakhalin taimen and introduced rainbow trout in Hokkaido, Japan, inferred by environmental DNA metabarcoding. Aquatic Conservation: Marine and Freshwater Ecosystems33(12), 1492-1500. LINK
Fukuzawa, T., Shirakura, H., Nishizawa, N., Nagata, H., Kameda, Y., & Doi, H. (2023). Environmental DNA extraction method from water for a high and consistent DNA yield. Environmental DNA5(4), 627-633. LINK
von der Heyden, S., Neef, G., Grevesse, T., Cwecwe, Y., Sado, T., Miya, M., Mosie, I., Creer, S., Skelton, P., & von Brandis, R. (2023). Environmental DNA biomonitoring in biodiversity hotspots: A case study of fishes of the Okavango Delta. Environmental DNA5(6), 1720-1731. LINK
Nishizawa, R., Nakao, R., Ushimaru, A., & Minamoto, T. (2023). Development of environmental DNA detection assays for snakes in paddy fields in Japan. Landscape and Ecological Engineering19(1), 3-10. LINK
Souma, R., Katano, I., Doi, H., Takahara, T., & Minamoto, T. (2023). Comparing environmental DNA with whole pond survey to estimate the total biomass of fish species in ponds. Freshwater Biology68(5), 727-736. LINK
Wu, Q., & Minamoto, T. (2023). Improvement of recovery yield of macro-organismal environmental DNA from seawater samples. Analytical Sciences39(5), 713-720. LINK
Wu, Q., Zhou, J., Komoto, T., Ishikawa, T., Goto, N., Sakata, M. K., Kitazawa, D., & Minamoto, T. (2023). Opposite trends in environmental DNA distributions of two freshwater species under climate change. Ecosphere14(9), e4651. LINK
Yano, N., Minamoto, T., Yamaguchi, H., Goto, T., & Nishikata, T. (2023). Comparison of Evolutionary Relationships between Branchiostoma floridae, Ciona intestinalis, and Homo sapiens Globins Provide Evidence of Gene Co-Option and Convergent Evolution. International Journal of Molecular Sciences24(21), 16009. LINK
Ushio, M., Sado, T., Fukuchi, T., Sasano, S., Masuda, R., Osada, Y., & Miya, M. (2023). Temperature sensitivity of the interspecific interaction strength of coastal marine fish communities. ELife12. LINK
Sakata, M. K., Takeshita, D., Nishizawa, R., Sato, T., & Minamoto, T. (2023). An efficient environmental DNA detection method for rare species: a case study of a small salamander (Hynobius boulengeri). Analytical Sciences39(5), 721-728. LINK
Okanishi, M., Kohtsuka, H., Wu, Q., Shinji, J., Shibata, N., Tamada, T., Nakano, T., & Minamoto, T. (2023). Development of two new sets of PCR primers for eDNA metabarcoding of brittle stars (Echinodermata, Ophiuroidea). Metabarcoding and Metagenomics7, 51-72. LINK
Yoneya, K., Miki, T., & Takabayashi, J. (2023). Initial herbivory and exposure to herbivory-induced volatiles enhance arthropod species richness by diversifying community assemblages. Frontiers in Ecology and Evolution10, 1031664. LINK
Yoneya, K., Ushio, M., & Miki, T. (2023). Non-destructive collection and metabarcoding of arthropod environmental DNA remained on a terrestrial plant. Scientific Reports13(1), 7125. LINK
Mori, K., Imamura, A., Hirayama, I., & Minamoto, T. (2023). Detection of Echinococcus multilocularis in repurposed environmental DNA samples from river water. PeerJ11, e15431. LINK
Yoshitake, K., Yanagisawa, K., Sugimoto, Y., Nakamura, H., Mizusawa, N., Miya, M., Hamasaki, K., Kobayashi, T., Watabe, S., Nishikiori, K., & Asakawa, S. (2023). Pilot study of a comprehensive resource estimation method from environmental DNA using universal D-loop amplification primers. Functional & Integrative Genomics23(2), 96. LINK
Nakane, K., Liu, X., Doi, H., Dur, G., Kuwae, M., Ban, S., & Tsugeki, N. (2023). Sedimentary DNA can reveal the past population dynamics of a pelagic copepod. Freshwater Biology68(11), 1917-1928. LINK
Aoshima, I., Nakao, R., Minamoto, T., Ushimaru, A., & Sato, M. (2023). Heterogeneous preference for biodiversity in Japanese urban blue spaces based on people’s nature experiences: Analysis using eDNA and satisfaction data. City and Environment Interactions18, 100101. LINK
Doi, H., Matsuoka, S., Matsuzaki, S. I. S., Nagano, M., Sato, H., Yamanaka, H., Matsuhashi, S., Yamamoto, S., Minamoto, T., Araki, H., Ikeda, K., Kato, A., Kumei, K., Maki, N., Mitsuzuka, T., Takahara, T., Toki, K., Ueda, N., Watanabe, T., Yamazoe, K., & Miya, M. (2023). Species traits and ecosystem characteristics affect species detection by eDNA metabarcoding in lake fish communities. Freshwater Biology68(8), 1346-1358. LINK
Doi, H., & Kelly, R. P. (2023). Ethical considerations for human sequences in environmental DNA. Nature Ecology & Evolution7(9), 1334-1335. LINK
Doi, H., & Nakamura, K. (2023). Dominant barriers and the solutions to the social application of environmental DNA. Landscape and Ecological Engineering19(2), 305-312. LINK
Huston, G. P., Lopez, M. L. D., Cheng, Y., King, L., Duxbury, L. C., Picard, M., Thomson-Laing, G., Myler, E., Helbing, C. C., Kinnison, M. T., Saros, J. E., Gregory-Eaves, I., Monchamp, M. E., Wood, S. A., Armbrecht, L., Ficetola, G. F., Kurte, L., Von Eggers, J., Brahney, J.,  Parent, G., Sakata, M. K., Doi, H., & Capo, E. (2023). Detection of fish sedimentary DNA in aquatic systems: A review of methodological challenges and future opportunities. Environmental DNA5(6), 1449-1472. LINK
Ito, G., Yamauchi, H., Shigeyoshi, M., Ashino, K., Yonashiro, C., Asami, M., Goto, Y., Duda, J. J., & Yamanaka, H. (2023). Using eDNA metabarcoding to establish targets for freshwater fish composition following river restoration. Global Ecology and Conservation43, e02448. LINK
Sakata, A., Sado, T., Oka, S. I., Ushio, M., & Miya, M. (2023). Collection of environmental DNA from stemflow for monitoring arboreal biodiversity: Preliminary validation using lichens. MethodsX11, 102448. LINK
Tanaka, A., Katano, I., Doi, H., Iguchi, M., & Koike, S. (2023). Applicability of environmental DNA metabarcoding for the hyporheic zone of a stream bed. Environmental DNA5(6), 1667-1678. LINK
Wu, L., Wu, Q., Inagawa, T., Okitsu, J., Sakamoto, S., & Minamoto, T. (2023). Estimating the spawning activity of fish species using nuclear and mitochondrial environmental DNA concentrations and their ratios. Freshwater Biology, 68(1), 103-114. LINK
Jo, T. S. (2023). Correlation between the number of eDNA particles and species abundance is strengthened by warm temperature: simulation and meta-analysis. Hydrobiologia, 850(1), 39-50. LINK
Takahara, T., Doi, H., Kosuge, T., Nomura, N., Maki, N., Minamoto, T., & Watanabe, K. (2023). Effective environmental DNA collection for an endangered catfish species: testing for habitat and daily periodicity. Ichthyological Research70(4), 409-418. LINK
Takahara, T., Fukui, K., Hiramatsu, D., Doi, H., Fujii, M., & Minamoto, T. (2023). Development of primer–probe sets for environmental DNA-based monitoring of pond smelt Hypomesus nipponensis and Japanese icefish Salangichthys microdon. Landscape and Ecological Engineering, 19(1), 11-19. LINK
Ogata, S., Nishiwaki, A., Yamazoe, K., Sugai, K., & Takahara, T. (2023). Discovery of unknown new ponds occupied by the endangered giant water bug Kirkaldyia deyrolli (Hemiptera: Heteroptera: Belostomatidae) by combining environmental DNA and capture surveys. Entomological Science, 26(1), e12540. LINK
Ogata, S., Doi, H., Igawa, T., Komaki, S., & Takahara, T. (2023). Environmental DNA methods for detecting two invasive alien species (American bullfrog and red swamp crayfish) in Japanese ponds. Ecological Research, 37(6), 701-710. LINK
Ito, G., & Koya, Y. (2022). Phylogeographic structure of an endemic lineage of the eight-barbel loach Lefua echigonia around the Suzuka and Yoro Mountains, central Honshu, Japan. Biogeography24, 39-45.LINK
Wu, L., Yamamoto, Y., Yamaguchi, S., & Minamoto, T. (2022). Spatiotemporal changes in environmental DNA concentrations caused by fish spawning activity. Ecological Indicators, 142, 109213. LINK
Wakiya, R., Itakura, H., Hirae, T., Igari, T., Manabe, M., Matsuya, N., Sakata, M.K., Minamoto, T., Yada, T., & Kaifu, K. (2022). Slower growth of farmed eels stocked into rivers with higher wild eel density. Journal of Fish Biology, 101(3), 613-627. LINK
Tsugeki, N., Nakane, K., Doi, H., Ochi, N., & Kuwae, M. (2022). Reconstruction of 100-year dynamics in Daphnia spawning activity revealed by sedimentary DNA. Scientific Reports, 12(1), 1741. LINK
Jo, T., Tsuri, K., Hirohara, T., & Yamanaka, H. (2022). Warm temperature and alkaline conditions accelerate environmental RNA degradation. Environmental DNA. LINK
Jo, T., & Yamanaka, H. (2022). Meta-analyses of environmental DNA downstream transport and deposition in relation to hydrogeography in riverine environments. Freshwater Biology, 67(8), 1333-1343. LINK
Jo, T., & Yamanaka, H. (2022). Fine-tuning the performance of abundance estimation based on environmental DNA (eDNA) focusing on eDNA particle size and marker length. Ecology and Evolution, 12(8), e9234. LINK
Asai, T., Sugiyama, M., Omatsu, T., Yoshikawa, M., & Minamoto, T. (2022). Isolation of extended-spectrum β-lactamase-producing Escherichia coli from Japanese red fox (Vulpes vulpes japonica). MicrobiologyOpen, 11(5), e1317. LINK
Shiozuka, N., Katano, I., Doi, H., Nakamura, M., Shirako, T., & Ichiyanagi, H. (2022). Diurnal detection of environmental DNA of the semi-aquatic water shrew Chimarrogale platycephala using 25-h water sampling in streams. Landscape and Ecological Engineering, 19(1), 69-77. LINK
Nagayama, S., Oota, M., Fujita, T., Kitamura, J. I., Minamoto, T., Mori, S., Kato, M., Takeyama, N., Takino, F., Yonekura, R., & Yamanaka, H. (2022). Autumn dispersal and limited success of reproduction of the deepbody bitterling (Acheilognathus longipinnis) in terrestrialized floodplain. Knowledge & Management of Aquatic Ecosystems, (423), 4. LINK
Sakata, M. K., Sato, M., Sato, M. O., Watanabe, T., Mitsuishi, H., Hikitsuchi, T., Kobayashi, J., & Minamoto, T. (2022). Detection and persistence of environmental DNA (eDNA) of the different developmental stages of a vector mosquito, Culex pipiens pallens. Plos one, 17(8), e0272653. LINK
Oka, S. I., Miya, M., & Sado, T. (2022). Gravity filtration of environmental DNA: A simple, fast, and power-free method. MethodsX, 9, 101838. LINK
Nakagawa, H., Fukushima, K., Sakai, M., Wu, L., & Minamoto, T. (2022). Relationships between the eDNA concentration obtained from metabarcoding and stream fish abundance estimated by the removal method under field conditions. Environmental DNA, 4(6), 1369-1380. LINK
Kimura, M., Yamanaka, H., & Nakashima, Y. (2022). Application of Machine Learning to Environmental DNA Metabarcoding. IEEE Access, 10, 101790-101794. LINK
Miya, M., Sado, T., Oka, S. I., & Fukuchi, T. (2022). The use of citizen science in fish eDNA metabarcoding for evaluating regional biodiversity in a coastal marine region: A pilot study. Metabarcoding and Metagenomics, 6, e80444. LINK
Miya, M. (2022). Environmental DNA metabarcoding: a novel method for biodiversity monitoring of marine fish communities. Annual Review of Marine Science, 14, 161-185. LINK
Minamoto, T. (2022). Environmental DNA analysis for macro-organisms: species distribution and more. DNA Research, 29(3), dsac018. LINK
Matsuoka, S., Sugiyama, Y., Nagano, M., & Doi, H. (2022). Influence of DNA extraction kits on freshwater fungal DNA metabarcoding. PeerJ, 10, e13477. LINK
Kuwae, M., Finney, B. P., Shi, Z., Sakaguchi, A., Tsugeki, N., Omori, T., Agusa, T., Suzuki, Y., Yokoyama, Y., Hinata, H., Hatada, Y., Inoue, J., Matsuoka, K., Shimada, M., Takahara, H., Takahashi, S., Ueno, D., Amano, A., Tsutsumi, J., Yamamoto, M., Takemura, K., Yamada, K., Ikehara, K., Haraguchi, T., Tims, S., Froehlich, M., Fifield, L. K., Aze, T., Sasa, K., Takahashi, T., Matsumura, M., Tani, Y., Leavitt, P. R., Doi, H., Irino, T., Moriya, K., Hayashida, A., Hirose, K., Suzuki, H., & Saito, Y. (2022). Beppu Bay, Japan, as a candidate Global Boundaries Stratotype Section and Point for an Anthropocene series. The Anthropocene Review, 20530196221135077. LINK
Jo, T., Sato, M., Minamoto, T., & Ushimaru, A. (2022). Valuing the cultural services from urban blue-space ecosystems in Japanese megacities during the COVID‐19 pandemic. People and Nature, 4(5), 1176-1189. LINK
Jo, T. S., Tsuri, K., & Yamanaka, H. (2022). Can nuclear aquatic environmental DNA be a genetic marker for the accurate estimation of species abundance?. The Science of Nature, 109(4), 38. LINK
Jo, T. S. (2022). A higher DNA damage rate in aqueous eDNA particles suggests intra-cellular eDNA degradation in cellular environments. Environmental DNA, 5(2), 343-349. LINK
Fukuzawa, T., Kameda, Y., Nagata, H., Nishizawa, N., & Doi, H. (2022). Filtration extraction method using a microfluidic channel for measuring environmental DNA. Molecular Ecology Resources, 22(7), 2651-2661. LINK
Fujiwara, Y., Tsuchida, S., Kawato, M., Masuda, K., Sakaguchi, S. O., Sado, T., Miya, M., & Yoshida, T. (2022). Detection of the Largest Deep-Sea-Endemic Teleost Fish at Depths of Over 2,000 m Through a Combination of eDNA Metabarcoding and Baited Camera Observations. Frontiers in Marine Science, 9, 945758. LINK
Banerjee, P., Stewart, K. A., Dey, G., Antognazza, C. M., Sharma, R. K., Maity, J. P., Saha, S., Doi, H., de Vere, N., Chan, M. W.,, Lin, P. Y., Chao, H. C., & Chen, C. Y. (2022). Environmental DNA analysis as an emerging non-destructive method for plant biodiversity monitoring: a review. AoB Plants, 14(4), plac031. LINK
Banerjee, P., Stewart, K. A., Antognazza, C. M., Bunholi, I. V., Deiner, K., Barnes, M. A., Saha, S., Verdier H., Doi, H., Maity, J. P., Chan, M. W., & Chen, C. Y. (2022). Plant–animal interactions in the era of environmental DNA (eDNA)—A review. Environmental DNA, 4(5), 987-999. LINK
Tsuji, S., Nakao, R., Saito, M., Minamoto, T., & Akamatsu, Y. (2022). Pre-centrifugation before DNA extraction mitigates extraction efficiency reduction of environmental DNA caused by the preservative solution (benzalkonium chloride) remaining in the filters. Limnology, 23(1), 9-16. LINK
Miya, M. (2022). Environmental DNA Metabarcoding: A novel method for biodiversity monitoring of marine fish communities. Annual Review of Marine Science, 14,161-185. LINK
Uchii, K., Wakimura, K., Kikko, T., Yonekura, R., Kawaguchi, R., Komada, H., Yamanaka, H., Kenzaka, T., & Tani, K. (2022). Environmental DNA monitoring method of the commercially important and endangered fish Gnathopogon caerulescens Limnology, 23(1), 49-56. LINK
Jo, T., Takao, K., & Minamoto, T. (2022). Linking the state of environmental DNA to its application for biomonitoring and stock assessment: Targeting mitochondrial/nuclear genes, and different DNA fragment lengths and particle sizes. Environmental DNA, 4(2), 271-283. LINK
de Santana, C. D., Parenti, L. R., Dillman, C. B., Coddington, J. A., Bastos, D. A., Baldwin, C. C., Zuanon, J., Torrente-Vilara, G., Covain, R., Menezes, N, A., Datovo, A., & Miya, M. (2021). The critical role of natural history museums in advancing eDNA for biodiversity studies: a case study with Amazonian fishes. Scientific reports, 11(1), 1-22. LINK
Yoneya, K., Miki, T., Van den Wyngaert, S., Grossart, H. P., & Kagami, M. (2021). Non-random patterns of chytrid infections on phytoplankton host cells: mathematical and chemical ecology approaches. Aquatic Microbial Ecology, 87,1-15. LINK
Yasashimoto, T., Sakata, M. K., Sakita, T., Nakajima, S., Ozaki, M., & Minamoto, T. (2021). Environmental DNA detection of an invasive ant species (Linepithema humile) from soil samples. Scientific reports, 11(1), 1-12. LINK
Wu, Q., Sakata, M. K., Wu, D., Yamanaka, H., & Minamoto, T. (2021). Application of environmental DNA metabarcoding in a lake with extensive algal blooms. Limnology, 22(3), 363-370. LINK
Tenma, H., Tsunekawa, K., Fujiyoshi, R., Takai, H., Hirose, M., Masai, N., Sumi, K., Takihana, Y., Yanagisawa, S., Tsuchida, K., Ohara, K., Jo, T.,Takagi, M., Ota, A., Iwata. H., Yaoi, Y., & Minamoto, T. (2021). Spatiotemporal distribution of Flavobacterium psychrophilum and ayu Plecoglossus altivelis in rivers revealed by environmental DNA analysis. Fisheries science, 87(3), 321-330. LINK
Takasaki, K., Aihara, H., Imanaka, T., Matsudaira, T., Tsukahara, K., Usui, A., Osaki, S., & Doi, H. (2021). Water pre-filtration methods to improve environmental DNA detection by real-time PCR and metabarcoding. Plos one, 16(5), e0250162. LINK
Takahashi, S., Takada, S., Yamanaka, H., Masuda, R., & Kasai, A. (2021). Intraspecific genetic variability and diurnal activity affect environmental DNA detection in Japanese eel. PloS one, 16(9), e0255576. LINK
Saito, T., & Doi, H. (2021). Degradation modeling of water environmental DNA: Experiments on multiple DNA sources in pond and seawater. Environmental DNA, 3(4), 850-860. LINK
Saito, T., & Doi, H. (2021). A model and simulation of the influence of temperature and amplicon length on environmental DNA degradation rates: a meta-analysis approach. Frontiers in Ecology and Evolution, 9,623831. LINK
Rodriguez‐Ezpeleta, N., Morissette, O., Bean, C. W., Manu, S., Banerjee, P., Lacoursière‐Roussel, A., Beng, K, C., Elizabeth Alter, S., Roger, F., Holman, L, E., Stewart, K, A., Monaghan, M, T., Mauvisseau, Q., Mirimin, L., Wangensteen, O, S., Antognazza, C, M., Helyar, S, J., de Boer, H., Monchamp, M. E., Nijland, R., Abbott, C. L., Doi, H., Barnes, M, A., Leray, M., Hablützel, P. I., & Deiner, K. (2021). Trade‐offs between reducing complex terminology and producing accurate interpretations from environmental DNA: Comment on “Environmental DNA: What’s behind the term?” by Pawlowski et al.,(2020). Molecular Ecology, 30(19), 4601-4605. LINK
Osathanunkul, M., & Minamoto, T. (2021). eDNA‐based detection of a vulnerable crocodile newt (Tylototriton uyenoi) to influence government policy and raise public awareness. Diversity and Distributions, 27(10), 1958-1965. LINK
Osathanunkul, M., & Minamoto, T. (2021). Molecular detection of giant snakeheads, Channa micropeltes (Cuvier, 1831), one of the most troublesome fish species. Scientific Reports, 11(1), 1-7. LINK
Ogata, M., Masuda, R., Harino, H., Sakata, M. K., Hatakeyama, M., Yokoyama, K., Yamashita, Y., & Minamoto, T. (2021). Environmental DNA preserved in marine sediment for detecting jellyfish blooms after a tsunami. Scientific Reports, 11(1), 1-14. LINK
Nakao, R., Inui, R., Akamatsu, Y., Goto, M., Doi, H., & Matsuoka, S. (2021). Illumina iSeq 100 and MiSeq exhibit similar performance in freshwater fish environmental DNA metabarcoding. Scientific reports, 11(1), 1-10. LINK
Matsuoka, S., Sugiyama, Y., Shimono, Y., Ushio, M., & Doi, H. (2021). Evaluation of seasonal dynamics of fungal DNA assemblages in a flow‐regulated stream in a restored forest using eDNA metabarcoding. Environmental Microbiology, 23(8), 4797-4806. LINK
Jo, T., Sakata, M. K., Murakami, H., Masuda, R., & Minamoto, T. (2021). Universal performance of benzalkonium chloride for the preservation of environmental DNA in seawater samples. Limnology and Oceanography: Methods, 19(11), 758-768. LINK
Jo, T., & Minamoto, T. (2021). Complex interactions between environmental DNA (eDNA) state and water chemistries on eDNA persistence suggested by meta‐analyses. Molecular Ecology Resources, 21(5), 1490-1503. LINK
Hirohara, T., Tsuri, K., Miyagawa, K., Paine, R. T., & Yamanaka, H. (2021). The application of PMA (propidium monoazide) to different target sequence lengths of Zebrafish eDNA: a new approach aimed toward improving environmental DNA ecology and biological surveillance. Frontiers in Ecology and Evolution, 277. LINK
Fukuda, A., Usui, M., Ushiyama, K., Shrestha, D., Hashimoto, N., Sakata, M. K., Minamoto, T., Yoshida, O., Murakami, K., Tamura, Y., & Asai, T. (2021). Prevalence of antimicrobial-resistant Escherichia coli in migratory greater white-fronted geese (Anser albifrons) and their habitat in Miyajimanuma, Japan. The Journal of Wildlife Diseases, 57(4), 954-958. LINK
Fukaya, K., Murakami, H., Yoon, S., Minami, K., Osada, Y., Yamamoto, S., Masuda, R., Kasai, A., Miyashita, K., Minamoto, T., & Kondoh, M. (2021). Estimating fish population abundance by integrating quantitative data on environmental DNA and hydrodynamic modelling. Molecular Ecology, 30(13), 3057-3067. LINK
Doi, H., Watanabe, T., Nishizawa, N., Saito, T., Nagata, H., Kameda, Y., Maki, N., Ikeda, K., & Fukuzawa, T. (2021). On‐site environmental DNA detection of species using ultrarapid mobile PCR. Molecular Ecology Resources, 21(7), 2364-2368. LINK
Doi, H., Inui, R., Matsuoka, S., Akamatsu, Y., Goto, M., & Kono, T. (2021). Estimation of biodiversity metrics by environmental DNA metabarcoding compared with visual and capture surveys of river fish communities. Freshwater Biology, 66(7), 1257-1266. LINK
Deiner, K., Yamanaka, H., & Bernatchez, L. (2021). The future of biodiversity monitoring and conservation utilizing environmental DNA. Environmental DNA, 3(1), 3-7. LINK
Cheung, P. Y., Nozawa, Y., & Miki, T. (2021). Ecosystem engineering structures facilitate ecological resilience: A coral reef model. Ecological Research, 36(4), 673-685. LINK
Chang, C. W., Miki, T., Ushio, M., Ke, P. J., Lu, H. P., Shiah, F. K., & Hsieh, C. H. (2021). Reconstructing large interaction networks from empirical time series data. Ecology Letters, 24(12), 2763-2774. LINK
Kasai, A., Yamazaki, A., Ahn, H., Yamanaka, H., Kameyama, S., Masuda, R., Azuma, N., Kimura, S., Karaki, T., Kurokawa, Y., & Yamashita, Y. (2021). Distribution of Japanese eel Anguilla japonica revealed by environmental DNA. Frontiers Ecology And Evolution, 9, 83. LINK
Wada, K., Kishimoto, N., Somiya, I., Sato, T., & Ueno, K. (2021). Impact of Submerged Macrophytes on Behavior of Organic Carbon and Nutrients: An Experimental Study. Journal of Water and Environment Technology, 19(1), 35-47. LINK
Tsuri, K., Ikeda, S., Hirohara, T., Shimada, Y., Minamoto, T., & Yamanaka, H. (2021). Messenger RNA typing of environmental RNA (eRNA): A case study on zebrafish tank water with perspectives for the future development of eRNA analysis on aquatic vertebrates. Environmental DNA, 3(1), 14-21. LINK
Tomaru, Y., Yamaguchi, H., & Miki, T. (2021). Growth Rate-dependent Cell Death of Diatoms due to Viral Infection and Their Subsequent Coexistence in a Semi-continuous Culture System. Microbes and Environments, 36(1), ME20116. LINK
Minamoto, T., Miya, M., Sado, T., Seino, S., Doi, H., Kondoh, M., Nakamura, K., Takahara, T., Yamamoto, S., Yamanaka, H., Araki, H., Iwasaki, W., Kasai, A., Masuda, R., Uchii, K. (2021). An illustrated manual for environmental DNA research: Water sampling guidelines and experimental protocols. Environmental DNA, 3(1), 8-13. LINK
Jo, T.,Ikeda, S., Fukuoka, A., Inagawa, T., Okitsu, J.,Katano, I.,Doi, H.,Nakai, K.,Ichiyanagi,H.,& Minamoto,T. (2021) Utility of environmental DNA analysis for effective monitoring of invasive fish species in reservoirs. Ecosphere, 12, e03643. LINK
Hoshino, T., Nakao, R., Doi, H., & Minamoto, T. (2021). Simultaneous absolute quantification and sequencing of fish environmental DNA in a mesocosm by quantitative sequencing technique. Scientific reports, 11, 4372. LINK
Doi, H., Minamoto, T., Takahara, T., Tsuji, S., Uchii, K., Yamamoto, S., Katano, I.,& Yamanaka, H. (2021). Compilation of real-time PCR conditions toward the standardization of eDNA methods. Ecological Research, 36(3), 379-388. LINK
Chen, J., Chen, Z., Liu, S., Guo, W., Li, D., Minamoto, T., & Gao, T. (2021). Revealing an Invasion Risk of Fish Species in Qingdao Underwater World by Environmental DNA Metabarcoding. Journal of Ocean University of China, 20(1), 124-136. LINK
Oka, S. I., Doi, H., Miyamoto, K., Hanahara, N., Sado, T., & Miya, M. (2021). Environmental DNA metabarcoding for biodiversity monitoring of a highly diverse tropical fish community in a coral reef lagoon: Estimation of species richness and detection of habitat segregation. Environmental DNA, 3(1), 55-69. LINK
Okada, R., Tsuji, S., Shibata, N., Morita, K., Kitagawa, T., & Yamanaka, H. (2021). Environmental DNA analysis provides an overview of distribution patterns of two dojo loach species within the Naka-ikemi Wetland, Fukui Prefecture, Japan. Ichthyological Research, 68(1), 198-206. LINK
Kawatsu, K., Ushio, M., Van Veen, F.J.K. & Kondoh, M. (2021). Are networks of trophic interactions sufficient for understanding the dynamics of multi-trophic communities? Analysis of a tri-trophic insect food-web time-series. Ecology Letters, 24(3) 543-552. LINK
Doi, H., Akamatsu, Y., Goto, M., Inui, R., Komuro, T., Nagano, M., & Minamoto, T. (2021). Broad-scale detection of environmental DNA for an invasive macrophyte and the relationship between DNA concentration and coverage in rivers. Biological Invasions, 23(2), 507-520. LINK
Suetsugu, K., Matsuoka, S., Shutoh, K., Okada, H., Taketomi, S., Onimaru, K., Tanabe, A. S., & Yamanaka, H. (2021). Mycorrhizal communities of two closely related species, Pyrola subaphylla and P. japonica, with contrasting degrees of mycoheterotrophy in a sympatric habitat. Mycorrhiza, 31, 219-229. LINK
Sakata, M. K., Watanabe, T., Maki, N., Ikeda, K., Kosuge, T., Okada, H., Yamanaka, H., Sado, T., Miya, M., & Minamoto, T. (2021). Determining an effective sampling method for eDNA metabarcoding: a case study for fish biodiversity monitoring in a small, natural river. Limnology, 22, 221-235. LINK
Yonezawa, S., Ushio, M., Yamanaka, H., Miya, M., Takayanagi, A., & Isagi, Y. (2020). Environmental DNA metabarcoding reveals the presence of a small, quick-moving, nocturnal water shrew in a forest stream. Conservation Genetics, 21(6), 1079-1084. LINK
Yamamichi, M., Kyogoku, D., Iritani, R., Kobayashi, K., Takahashi, Y., Tsurui-Sato, K., Yamawo, A., Dobata, S., Tsuji, K., & Kondoh, M. (2020). Intraspecific adaptation load: a mechanism for species coexistence. Trends in Ecology & Evolution, 35(10), 897-907. LINK
Wada, T., Doi, H., Togaki, D., Kaida, R., Nagano, M., Katano, I., Suzuki, M., Ohtani, T., & Mitsuhashi, H. (2020). Exploring a legendary giant squid: an environmental DNA approach. Marine Biology, 167(11), 1-6. LINK
Tsuji, S., Maruyama, A., Miya, M., Ushio, M., Sato, H., Minamoto, T., & Yamanaka, H. (2020). Environmental DNA analysis shows high potential as a tool for estimating intraspecific genetic diversity in a wild fish population. Molecular ecology resources, 20(5), 1248-1258. LINK
Takeshita, D., Terui, S., Ikeda, K., Mitsuzuka, T., Osathanunkul, M., & Minamoto, T. (2020). Projection range of eDNA analysis in marshes: a suggestion from the Siberian salamander (Salamandrella keyserlingii) inhabiting the Kushiro marsh, Japan. PeerJ, 8, e9764. LINK
Takahashi, S., Sakata, M. K., Minamoto, T., & Masuda, R. (2020). Comparing the efficiency of open and enclosed filtration systems in environmental DNA quantification for fish and jellyfish. PloS one, 15(4), e0231718. LINK
Takahara, T., Taguchi, J., Yamagishi, S., Doi, H., Ogata, S., Yamanaka, H., & Minamoto, T. (2020). Suppression of environmental DNA degradation in water samples associated with different storage temperature and period using benzalkonium chloride. Limnology and Oceanography: Methods, 18(8), 437-445. LINK
Sugiura, K., Tomita, S., Minamoto, T., Mishina, T., Iwata, A., Abe, T., Yamamoto, S., & Watanabe, K. (2020). Characterizing the spatial and temporal occurrence patterns of the endangered botiid loach Parabotia curtus by environmental DNA analysis using a newly developed species-specific primer set. Ichthyological Research, 68, 152-157. LINK
Sakata, M. K., Yamamoto, S., Gotoh, R. O., Miya, M., Yamanaka, H., & Minamoto, T. (2020). Sedimentary eDNA provides different information on timescale and fish species composition compared with aqueous eDNA. Environmental DNA, 2(4), 505-518. LINK
Osathanunkul, M., & Minamoto, T. (2020). A molecular survey based on eDNA to assess the presence of a clown featherback (Chitala ornata) in a confined environment. PeerJ8, e10338. LINK
Muchebve, E., Takayama, Y., Akatsuka, M., Ito, K., & Minamoto, T. (2020). Feasibility Study for Seagrass Beds Monitoring Using Environmental DNA. Journal of Japan Society of Civil Engineers, Ser. B2 (Coastal Engineering)76(2), I_949-I_954. LINK
Metelmann, S., Sakai, S., Kondoh, M., & Telschow, A. (2020). Evolutionary stability of plant–pollinator networks: efficient communities and a pollination dilemma. Ecology Letters23(12), 1747-1755. LINK
Matsuoka,S., Doi, H., Masumoto, S., Kitagawa, R., Nishizawa, K., Tanaka, K., Hasegawa,M., Hobara, S., Osono, T., Mori, A., & Uchida M.(2020) Taxonomic, functional, and phylogenetic diversity of fungi in a forest-tundra ecotone in Quebec. Polar Science, 100594. LINK
Kuwae, M., Tamai, H., Doi, H., Sakata, M. K., Minamoto, T., & Suzuki, Y. (2020). Sedimentary DNA tracks decadal-centennial changes in fish abundance. Communications biology3558. LINK
Kudoh, A., Minamoto, T., & Yamamoto, S. (2020). Detection of herbivory: eDNA detection from feeding marks on leaves. Environmental DNA2(4), 627-634. LINK
Kasai, A., Takada, S., Yamazaki, A., Masuda, R., & Yamanaka, H. (2020). The effect of temperature on environmental DNA degradation of Japanese eel. Fisheries Science86, 465-471. LINK
Jo, T., Tomita, S., Kohmatsu, Y., Osathanunkul, M., Ushimaru, A., & Minamoto, T. (2020). Seasonal monitoring of Hida salamander Hynobius kimurae using environmental DNA with a genus-specific primer set. Endangered Species Research43, 341-352. LINK
Jo, T., Murakami, H., Masuda, R., & Minamoto, T. (2020). Selective collection of long fragments of environmental DNA using larger pore size filter. Science of the Total Environment735, 139462. LINK
Itakura, H., Wakiya, R., Sakata, M. K., Hsu, H. Y., Chen, S. C., Yang, C. C., Huang, Y. C., Han, Y. S., Yamamoto, S., & Minamoto, T. (2020). Estimations of riverine distribution, abundance, and biomass of Anguillid Eels in Japan and Taiwan using environmental DNA analysis. Zoological studies59, e17. LINK
Imamura, A., Hayami, K., Sakata, M. K., & Minamoto, T. (2020). Environmental DNA revealed the fish community of Hokkaido Island, Japan, after invasion by rainbow trout. Biodiversity data journal8, e56876. LINK
Hoshino, T., Doi, H., Uramoto, G. I., Wörmer, L., Adhikari, R. R., Xiao, N., Morono, Y., D’Hondt, S., Hinrichs, K. U., & Inagaki, F. (2020). Global diversity of microbial communities in marine sediment. Proceedings of the National Academy of Sciences117(44), 27587-27597. LINK
Hayami, K., Sakata, M. K., Inagawa, T., Okitsu, J., Katano, I., Doi, H., Nakai, K., Ichiyanagi, H., Gotoh, R. O., Miya, M., Sato, H., Yamanaka, H., & Minamoto, T. (2020). Effects of sampling seasons and locations on fish environmental DNA metabarcoding in dam reservoirs. Ecology and evolution, 10(12), 5354-5367. LINK
Fukaya, K., Murakami, H., Yoon, S., Minami, K., Osada, Y., Yamamoto, S., Masuda, R., Kasai, A., Miyashita, K., Minamoto, T., & Kondoh, M. (2020). Estimating fish population abundance by integrating quantitative data on environmental DNA and hydrodynamic modelling. Molecular ecology. LINK
Chen, Z., Minamoto, T., Lin, L., & Gao, T. (2020). An optional low-cost method of extracting environmental DNA of macro-organisms from filter membranes in large scale eDNA surveys. Pakistan Journal of Zoology53(1), 263-272. LINK
Chang, C. W., Ye, H., Miki, T., Deyle, E. R., Souissi, S., Anneville, O., Adrian, R., Chiang, Y. R., Ichise, S., Kumagai, M., Matsuzaki, S. S., Shiah, F. K., Wu, J. T., Hsieh, C.H., & Sugihara, G. (2020). Long‐term warming destabilizes aquatic ecosystems through weakening biodiversity‐mediated causal networks. Global Change Biology26(11), 6413-6423.  LINK
Frenken, T., Miki, T., Kagami, M., Van de Waal, D. B., Van Donk, E., Rohrlack, T., & Gsell, A. S. (2020). The potential of zooplankton in constraining chytrid epidemics in phytoplankton hosts. Ecology101(1), e02900. LINK
Togaki, D., Doi, H., & Katano, I. (2020). Detection of freshwater mussels (Sinanodonta spp.) in artificial ponds through environmental DNA: a comparison with traditional hand collection methods. Limnology21(1), 59-65. LINK
Takahara, T., Iwai, N., Yasumiba, K., & Igawa, T. (2020). Comparison of the detection of 3 endangered frog species by eDNA and acoustic surveys across 3 seasons. Freshwater Science39(1), 18-27. LINK
Yatsuyanagi, T., Ishida, R., Sakata, M. K., Kanbe, T., Mizumoto, H., Kobayashi, Y., Kamada, S., Namba, S., Nii, H., Minamoto, T., & Araki, H. (2020). Environmental DNA monitoring for short-term reproductive migration of endemic anadromous species, Shishamo smelt (Spirinchus lanceolatus). Environmental DNA2(2), 130-139. LINK
Tsuji, S., Miya, M., Ushio, M., Sato, H., Minamoto, T., & Yamanaka, H. (2020). Evaluating intraspecific genetic diversity using environmental DNA and denoising approach: A case study using tank water. Environmental DNA2(1), 42-52. LINK
Jo, T., Fukuoka, A., Uchida, K., Ushimaru, A., & Minamoto, T. (2020). Multiplex real-time PCR enables the simultaneous detection of environmental DNA from freshwater fishes: a case study of three exotic and three threatened native fishes in Japan. Biological Invasions22(2), 455-471. LINK
Jo, T., Arimoto, M., Murakami, H., Masuda, R., & Minamoto, T. (2020). Estimating shedding and decay rates of environmental nuclear DNA with relation to water temperature and biomass. Environmental DNA2(2), 140-151. LINK
Kong, W. L., Miki, T., Lin, Y. Y., Makino, W., Urabe, J., Gu, S. H., & Machida, R. J. (2019). Nuclear and mitochondrial ribosomal ratio as an index of animal growth rate. Limnology and Oceanography: Methods17(11), 575-584. LINK
Wu, Q., Takami, Y., Minamoto, T., & Ishikawa, T. (2019). The life history with seasonal migration of the lacustrine shrimp Palaemon paucidens in an ancient lake in Japan. Ecosphere10(4), e02628. LINK
Wu, Q., Kawano, K., Ishikawa, T., Sakata, M. K., Nakao, R., Hiraiwa, M. K., Tsuji, S., Yamanaka, H., & Minamoto, T. (2019). Habitat selection and migration of the common shrimp, Palaemon paucidens in Lake Biwa, Japan—An eDNA‐based study. Environmental DNA1(1), 54-63. LINK
Uchii, K., Doi, H., Okahashi, T., Katano, I., Yamanaka, H., Sakata, M. K., & Minamoto, T. (2019). Comparison of inhibition resistance among PCR reagents for detection and quantification of environmental DNA. Environmental DNA1(4), 359-367. LINK
Tsuji, S., Takahara, T., Doi, H., Shibata, N., & Yamanaka, H. (2019). The detection of aquatic macroorganisms using environmental DNA analysis—A review of methods for collection, extraction, and detection. Environmental DNA1(2), 99-108. LINK
Takeuchi, A., Watanabe, S., Yamamoto, S., Miller, M. J., Fukuba, T., Miwa, T., Okino, T., Minamoto, T., & Tsukamoto, K. (2019). First use of oceanic environmental DNA to study the spawning ecology of the Japanese eel Anguilla japonica. Marine Ecology Progress Series609, 187-196. LINK
Takeuchi, A., Sado, T., Gotoh, R. O., Watanabe, S., Tsukamoto, K., & Miya, M. (2019). New PCR primers for metabarcoding environmental DNA from freshwater eels, genus Anguilla. Scientific reports9(1), 1-11. LINK
Takahara, T., Ikebuchi, T., Doi, H., & Minamoto, T. (2019). Using environmental DNA to estimate the seasonal distribution and habitat preferences of a Japanese basket clam in Lake Shinji, Japan. Estuarine, Coastal and Shelf Science221, 15-20. LINK
Sato, Y., Mizuyama, M., Sato, M., Minamoto, T., Kimura, R., & Toma, C. (2019). Environmental DNA metabarcoding to detect pathogenic Leptospira and associated organisms in leptospirosis-endemic areas of Japan. Scientific reports9(1), 1-11. LINK
Sakai, Y., Kusakabe, A., Tsuchida, K., Tsuzuku, Y., Okada, S., Kitamura, T., Tomita, S., Mukai, T., Tagami, M., Takagi, M., Yaoi, Y., & Minamoto, T. (2019). Discovery of an unrecorded population of Yamato salamander (Hynobius vandenburghi) by GIS and eDNA analysis. Environmental DNA1(3), 281-289. LINK
Murakami, H., Yoon, S., Kasai, A., Minamoto, T., Yamamoto, S., Sakata, M. K., Hirouchi, T., Sawada, H., Kondoh, M., Yamashita, Y., & Masuda, R. (2019). Dispersion and degradation of environmental DNA from caged fish in a marine environment. Fisheries science85(2), 327-337. LINK
Morita, K., Sahashi, G., Miya, M., Kamada, S., Kanbe, T., & Araki, H. (2019). Ongoing localized extinctions of stream-dwelling white-spotted charr populations in small dammed-off habitats of Hokkaido Island, Japan. Hydrobiologia840(1), 207-213. LINK
Minamoto, T., Hayami, K., Sakata, M. K., & Imamura, A. (2019). Real‐time polymerase chain reaction assays for environmental DNA detection of three salmonid fish in Hokkaido, Japan: Application to winter surveys. Ecological Research34(1), 237-242. LINK
Matsuoka, S., Sugiyama, Y., Sato, H., Katano, I., Harada, K., & Doi, H. (2019). Spatial structure of fungal DNA assemblages revealed with eDNA metabarcoding in a forest river network in western Japan. Metabarcoding and Metagenomics3, e36335. LINK
Matsuhashi, S., Minamoto, T., & Doi, H. (2019). Seasonal change in environmental DNA concentration of a submerged aquatic plant species. Freshwater Science38(3), 654-660. LINK
Kyogoku, D., Kataoka, Y., & Kondoh, M. (2019). Who determines the timing of inflorescence closure of a sexual dandelion? Pollen donors versus recipients. Evolutionary Ecology33(5), 701-712. LINK
Kyogoku, D., Kondoh, M., & Sota, T. (2019). Does past evolutionary history under different mating regimes influence the demographic dynamics of interspecific competition?. Ecology and evolution9(15), 8616-8624. LINK
Komai, T., Gotoh, R. O., Sado, T., & Miya, M. (2019). Development of a new set of PCR primers for eDNA metabarcoding decapod crustaceans. Metabarcoding and Metagenomics3, e33835. LINK
Kakuda, A., Doi, H., Souma, R., Nagano, M., Minamoto, T., & Katano, I. (2019). Environmental DNA detection and quantification of invasive red-eared sliders, Trachemy scripta elegans, in ponds and the influence of water quality. PeerJ7, e8155. LINK
Jo, T., Murakami, H., Yamamoto, S., Masuda, R., & Minamoto, T. (2019). Effect of water temperature and fish biomass on environmental DNA shedding, degradation, and size distribution. Ecology and evolution9(3), 1135-1146. LINK
Jo, T., Arimoto, M., Murakami, H., Masuda, R., & Minamoto, T. (2019). Particle size distribution of environmental DNA from the nuclei of marine fish. Environmental Science & Technology53(16), 9947-9956. LINK
Iwai, N., Yasumiba, K., & Takahara, T. (2019). Efficacy of environmental DNA to detect and quantify stream tadpoles of Odorrana splendida. Royal Society open science6(1), 181798. LINK
Itakura, H., Wakiya, R., Yamamoto, S., Kaifu, K., Sato, T., & Minamoto, T. (2019). Environmental DNA analysis reveals the spatial distribution, abundance, and biomass of Japanese eels at the river‐basin scale. Aquatic Conservation: Marine and Freshwater Ecosystems29(3), 361-373. LINK
Ikeda, K., Doi, H., Terui, S., Kato, A., Mitsuzuka, T., Kawai, T., & Negishi, J. N. (2019). Estimating native and invasive crayfish distributions in relation to culvert barriers with environmental DNA. Freshwater Science38(3), 629-641. LINK
Igawa, T., Takahara, T., Lau, Q., & Komaki, S. (2019). An application of PCR-RFLP species identification assay for environmental DNA detection. PeerJ7, e7597. LINK
Horiuchi, T., Masuda, R., Murakami, H., Yamamoto, S., & Minamoto, T. (2019). Biomass‐dependent emission of environmental DNA in jack mackerel Trachurus japonicus juveniles. Journal of fish biology95(3), 979-981. LINK
Fornillos, R. J. C., Sato, M. O., Tabios, I. K. B., Sato, M., Leonardo, L. R., Chigusa, Y., Minamoto, T., Kikuchi, M., Legaspi, E. R., & Fontanilla, I. K. C. (2019). Detection of Schistosoma japonicum and Oncomelania hupensis quadrasi environmental DNA and its potential utility to schistosomiasis japonica surveillance in the Philippines. PloS one14(11), e0224617. LINK
Doi, H., Fukaya, K., Oka, S. I., Sato, K., Kondoh, M., & Miya, M. (2019). Evaluation of detection probabilities at the water-filtering and initial PCR steps in environmental DNA metabarcoding using a multispecies site occupancy model. Scientific reports9(1), 1-8. LINK
Calata, F. I. C., Caranguian, C. Z., Mendoza, J. E. M., Fornillos, R. J. C., Tabios, I. K. B., Fontanilla, I. K. C., Leonardo, L. R., Sunico, L. S., Kawai, S., Chigusa, Y., Kikuchi, M., Sato, M., Minamoto, T., Baoanan, Z. G., & Sato, M. O. (2019). Analysis of environmental DNA and edaphic factors for the detection of the snail intermediate host Oncomelania hupensis quadrasi. Pathogens8(4), 160. LINK
Fujii, K., Doi, H., Matsuoka, S., Nagano, M., Sato, H., & Yamanaka, H. (2019). Environmental DNA metabarcoding for fish community analysis in backwater lakes: A comparison of capture methods. Plos one14(1), e0210357. LINK
Ushio, M., Hsieh, C. H., Masuda, R., Deyle, E. R., Ye, H., Chang, C. W., Sugihara, G., & Kondoh, M. (2018). Fluctuating interaction network and time-varying stability of a natural fish community. Nature554(7692), 360-363. LINK
Nakagawa, H., Yamamoto, S., Sato, Y., Sado, T., Minamoto, T., & Miya, M. (2018). Comparing local-and regional-scale estimations of the diversity of stream fish using eDNA metabarcoding and conventional observation methods. Freshwater Biology63(6), 569-580. LINK
Kawatsu, K., & Kondoh, M. (2018). Density-dependent interspecific interactions and the complexity–stability relationship. Proceedings of the Royal Society B: Biological Sciences285(1879), 20180698. LINK
Kato, Y., Kondoh, M., Ishikawa, N. F., Togashi, H., Kohmatsu, Y., Yoshimura, M., Yoshimizu, C., Haraguchi, T. F., Osada, Y., Ohta, N., Tokuchi, N., Okuda, N., Miki, T., & Tayasu, I. (2018). Using food network unfolding to evaluate food–web complexity in terms of biodiversity: theory and applications. Ecology letters21(7), 1065-1074. LINK
Kishimoto, N., & Okumura, M. (2018). Feasibility of Mercury-free Chemical Oxygen Demand (COD) Test with Excessive Addition of Silver Sulfate. Journal of Water and Environment Technology16(6), 221-232. LINK
Maruyama, A., Sugatani, K., Watanabe, K., Yamanaka, H., & Imamura, A. (2018). Environmental DNA analysis as a non-invasive quantitative tool for reproductive migration of a threatened endemic fish in rivers. Ecology and Evolution8(23), 11964-11974. LINK
Yamanaka, H., Takao, D., Maruyama, A., & Imamura, A. (2018). Species-specific detection of the endangered piscivorous cyprinid fish Opsariichthys uncirostris uncirostris, three-lips, using environmental DNA analysis. Ecological research33(5), 1075-1078. LINK
Tsuji, S., Iguchi, Y., Shibata, N., Teramura, I., Kitagawa, T., & Yamanaka, H. (2018). Real-time multiplex PCR for simultaneous detection of multiple species from environmental DNA: an application on two Japanese medaka species. Scientific reports8(1), 1-8. LINK
Wu, Q., Kawano, K., Uehara, Y., Okuda, N., Hongo, M., Tsuji, S., Yamanaka, H., & Minamoto, T. (2018). Environmental DNA reveals nonmigratory individuals of Palaemon paucidens overwintering in Lake Biwa shallow waters. Freshwater Science37(2), 307-314. LINK
Ushio, M., Murakami, H., Masuda, R., Sado, T., Miya, M., Sakurai, S., Yamanaka, H., Minamoto, T., & Kondoh, M. (2018). Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing. Metabarcoding and Metagenomics2, e23297. LINK
Ushio, M., Fukuda, H., Inoue, T., Kobayashi, M., Kishida, O., Sato, K., Murata, K., Nikaido, M., Sado, T., Sato, Y., Takeshita, M., Iwasaki, W., Yamanaka, H., Kondoh, M., & Miya, M. (2017). Environmental DNA enables detection of terrestrial mammals from forest pond water. Molecular Ecology Resources17(6), e63-e75. LINK
Sato, H., Sogo, Y., Doi, H., & Yamanaka, H. (2017). Usefulness and limitations of sample pooling for environmental DNA metabarcoding of freshwater fish communities. Scientific Reports7(1), 1-12. LINK
Uchii, K., Doi, H., Yamanaka, H., & Minamoto, T. (2017). Distinct seasonal migration patterns of Japanese native and non-native genotypes of common carp estimated by environmental DNA. Ecology and evolution7(20), 8515-8522. LINK
Tsuji, S., Ushio, M., Sakurai, S., Minamoto, T., & Yamanaka, H. (2017). Water temperature-dependent degradation of environmental DNA and its relation to bacterial abundance. PLoS One12(4), e0176608. LINK
Yamanaka, H., Minamoto, T., Matsuura, J., Sakurai, S., Tsuji, S., Motozawa, H., Hongo, M., Sogo, Y., Kakimi, N., Teramura, I., Sugita, M., Baba, M., & Kondo, A. (2017). A simple method for preserving environmental DNA in water samples at ambient temperature by addition of cationic surfactant. Limnology18(2), 233-241. LINK
Minamoto, T., Uchii, K., Takahara, T., Kitayoshi, T., Tsuji, S., Yamanaka, H., & Doi, H. (2017). Nuclear internal transcribed spacer-1 as a sensitive genetic marker for environmental DNA studies in common carp Cyprinus carpio. Molecular ecology resources17(2), 324-333. LINK
Doi, H., Uchii, K., Matsuhashi, S., Takahara, T., Yamanaka, H., & Minamoto, T. (2017). Isopropanol precipitation method for collecting fish environmental DNA. Limnology and Oceanography: Methods15(2), 212-218. LINK
Doi, H., Inui, R., Akamatsu, Y., Kanno, K., Yamanaka, H., Takahara, T., & Minamoto, T. (2017). Environmental DNA analysis for estimating the abundance and biomass of stream fish. Freshwater Biology62(1), 30-39. LINK
Tsuji, S., Yamanaka, H., & Minamoto, T. (2017). Effects of water pH and proteinase K treatment on the yield of environmental DNA from water samples. Limnology18(1), 1-7. LINK
Yamamoto, J., Kishimoto, N., Ichise, S., & Furuta, S. (2016). Effects of environmental factors on microalgal biomass production in wastewater using cyanobacteria Aphanothece clathrata and Microcystis wesenbergii. Environmental technology37(4), 466-471. LINK
Miya, M., Minamoto, T., Yamanaka, H., Oka, S. I., Sato, K., Yamamoto, S., Sado, T., & Doi, H. (2016). Use of a filter cartridge for filtration of water samples and extraction of environmental DNA. JoVE (Journal of Visualized Experiments), (117), e54741. LINK
Yamanaka, H., Motozawa, H., Tsuji, S., Miyazawa, R. C., Takahara, T., & Minamoto, T. (2016). On-site filtration of water samples for environmental DNA analysis to avoid DNA degradation during transportation. Ecological Research31(6), 963-967. LINK
Yamamoto, S., Minami, K., Fukaya, K., Takahashi, K., Sawada, H., Murakami, H., Tsuji, S., Hashizume, H., Kubonaga, S., Horiuchi, T., Hongo, M., Nishida, J., Okugawa, Y., Fujiwara, A., Fukuda, M., Hidaka, S., Suzuki, K. W., Miya, M., Araki, H., Yamanaka, H., Maruyama, A., Miyashita, K., Masuda, R., Minamoto, T., & Kondoh, M. (2016). Environmental DNA as a ‘snapshot’of fish distribution: A case study of Japanese jack mackerel in Maizuru Bay, Sea of Japan. PLoS One11(3), e0149786. LINK
Yamanaka, H., & Minamoto, T. (2016). The use of environmental DNA of fishes as an efficient method of determining habitat connectivity. Ecological Indicators62, 147-153. LINK
Ikegaya, H., Suzuki, S., Ichise, S., Furuta, S., Wakabayashi, S., Ohigashi, T., Bamba, D., Namba, H., Kihara, H., Kishimoto, N., & Takemoto, K. (2015). Estimation of organic carbon content of the Cyanobacterium Synechococcus sp. by soft X-ray microscopy. Geomicrobiology Journal32(9), 827-835. LINK
TORIHARA, K., & KISHIMOTO, N. (2015). Evaluation of growth characteristics of Euglena gracilis for microalgal biomass production using wastewater. Journal of Water and Environment Technology13(3), 195-205. LINK
KISHIMOTO, N., YAMAMOTO, C., SUZUKI, K., & ICHISE, S. (2015). Does a decrease in chlorophyll a concentration in Lake Biwa mean a decrease in primary productivity by phytoplankton?. Journal of Water and Environment Technology13(1), 1-14. LINK

▪In Chinese

陈治, 宋娜, 源利文, 邬倩倩, & 高天翔. (2020) 舟山近海水样环境DNA获取方法的建立. 水生生物学報 44, 1-7.

▪In Japanese

伊藤玄, 北村淳一, 谷口倫太郎, & 熊谷正裕. (2023). 文献情報に基づく日本産タナゴ亜科魚類における国内外来種の分布状況. 保全生態学研究, 28(1), 2205. LINK
伊藤玄, 小山直人, 川瀬成吾, & 古屋康則. (2022). 大阪府淀川水系における国内外来ミナミアカヒレタビラの初確認と移入起源. 地域自然史と保全, 44(1), 45-50. LINK
堀江真子, & 伊藤玄. (2022). 岐阜県の野外水域における体外光メダカ (幹之メダカ) などの観賞魚メダカの標本にもとづく初記録. 伊豆沼・内沼研究報告, 16, 63-72. LINK
伊藤玄, 旗薫, 北村淳一, & 古屋康則. (2021). 宮城県鳴瀬川水系における国内外来ヤリタナゴ Tanakia lanceolata の確認と遺伝的特徴. 魚類学雑誌, 69, 57-62. LINK
岸本直之, 古田世子, 藤原直樹, 井上栄壮, 馬場大哉, & 武井直子. (2022). 琵琶湖産淡水シジミ(Corbicula sp.)のろ水速度および生育可能条件の評価. 水環境学会誌.
赤塚真依子, 高山百合子, 織田幸伸, & 源利文. (2022). 環境 DNA を活用した藻場モニタリングにおける流れの影響について. 土木学会論文集 B2 (海岸工学), 78(2), I_865-I_870. LINK
小出水規行, 源利文, 白子智康, & 中村匡聡. (2022). 農業水路における環境DNA調査の適用性と環境DNAの拡散距離. 農業農村工学会誌, 90(8), 11-14. LINK
福岡太一, 田邑龍, 大庭伸也, & 遊磨正秀. (2022). 野外におけるコガタノゲンゴロウ幼虫によるコオイムシ卵塊の捕食. 昆蟲. ニューシリーズ, 25(1), 14-17. LINK
渡邉崚, 中尾航平, 平石優美子, 釣健司, 山中裕樹, 遊磨正秀, & 丸山敦. (2021). 環境 DNA 分析によるゲンジボタル幼虫の検出と定量可能性. 応用生態工学, 23(2), 279-293. LINK
遊磨正秀, 小野田幸生, & 太田真人. (2021). 琵琶湖流入河川, 安曇川の河川水位と瀬切れ. 環境技術, 50(3), 142-149. LINK
遊磨正秀, & 太田真人. (2021). 琵琶湖流入の 14 河川 1 支流における瀬切れ記録. 環境技術, 50(5), 268-273. LINK
森脇優介, & 遊磨正秀. (2021). 光害と LED 照明が動植物に与える影響. 環境技術= Journal of environmental conservation engineering, 50(5), 276-280. LINK
福岡太一. (2021). クロゲンゴロウ幼虫の食性および餌選択性. 環動昆, 32(1), 1-7. LINK
平井惇也, 宮正樹, 藤木徹一, 吉田聡, 乙坂重嘉, 帰山秀樹, 加古真一郎, 片岡智哉, 松岡大祐, 日高弥子, 杉山大祐, & 小嶌不二夫. (2021). 海洋学の 10 年展望: 新たな手法と問題. 海の研究, 30, 227-253. LINK
瀬口雄一, 山本義彦, 竹門康弘, & 源利文. (2021). 淀川大堰湛水域における琵琶湖産アユの河川残留個体の存在. 魚類学雑誌, 68(2), 163-172. LINK
久保星, 福岡太一, 太田真人, & 遊磨正秀. (2022). 木津川下流域におけるコクチバス当歳魚の食性. 魚類学雑誌, 69(1), 69-74. LINK
久保星, & 遊磨正秀. (2021). 特定外来生物コクチバスによる小型哺乳類の捕食事例. Ichthy, Natural History of Fishes of Japan, 13, 40-42. LINK
太田真人, 泉香名, & 遊磨正秀. (2021). 琵琶湖流入河川におけるトウヨシノボリを用いた瀬切れ規模の評価. 応用生態工学, 24(1), 39-50. LINK
赤塚真依子, 高山百合子, 伊藤一教, 渡辺謙太, 桑江朝比呂, & 源利文. (2021). 藻場モニタリングのための環境 DNA 分析プロトコル作成に向けた検討. 土木学会論文集 B2 (海岸工学), 77(2), I_895-I_900. LINK
高山百合子, 赤塚真依子, 伊藤一教, & 源利文. (2019). 環境 DNA を活用した固着性水生生物モニタリング手法の成立性について. 土木学会論文集 B2 (海岸工学), 75(2), I_1087-I_1092. LINK
高原輝彦, 藤田大登, 吉田真明, & 秋吉英雄. (2019). オキサンショウウオ Hynobius okiensis 幼生の季節的な個体数変動と 分布制限要因の解明. 保全生態学研究, 24(1), 83-93. LINK
近藤倫生. (2019). 環境 DNA 分析技術が拓く新たな未来. 化学と生物, 57(8), 503-509. LINK
今村彰生, 速水花奈, 坂田雅之, & 源利文. (2019). 河川横断構造物とニジマスが北海道のイワナ属の生息に与える影響: 環境 DNA 分析の結果をもとに. 保全生態学研究, 24(1), 71-81. LINK
赤塚真依子, 高山百合子, 伊藤一教, 渡辺謙太, 桑江朝比呂, 大澤亮介, 森本哲平, & 源利文. (2019). 海草場を対象とした環境 DNA の季節変化・日変化・形態変化に関する基礎研究. 土木学会論文集 B2 (海岸工学), 75(2), I_1075-I_1080. LINK
丹羽英之, 坂田雅之, 源利文, & 清野未恵子. (2018). 河川における流程 500m 間隔での環境 DNA 分析と現地採集調査による魚類検出結果の比較. 保全生態学研究, 23(2), 257-264. LINK
高山百合子, 赤塚真依子, 伊藤一教, & 源利文. (2018). アマモ場のモニタリング手法における環境 DNA の活用について. 土木学会論文集 B2 (海岸工学), 74(2), I_1231-I_1236. LINK
近藤倫生. (2018). 環境 DNA 技術がもたらす未来: 高度生態情報社会に向けて (特集 環境 DNA が拓く魚類生態研究の未来). 海洋と生物, 40(1), 60-65. LINK
赤塚真依子, 高山百合子, 伊藤一教, 森本哲平, & 源利文. (2018). 海草場を対象とした環境 DNA 検出方法と三次元数値解析の適用性に関する検討. 土木学会論文集 B2 (海岸工学), 74(2), I_1225-I_1230. LINK
古田世子, 一瀬諭, 馬場大哉, & 岸本直之. (2017). 琵琶湖沿岸帯における底泥環境の評価. 日本水処理生物学会誌, 53(1), 23-32. LINK
古田世子, 池谷仁里, 池田将平, 藤原直樹, 岡本高弘, 一瀬諭, 馬場大哉, 岸本直之, & 今井章雄. (2014). 琵琶湖に棲息する緑藻 Staurastrum arctiscon (Desmidiaceae) の生分解特性に関する研究. 水環境学会誌, 37(3), 103-109. LINK
和田桂子, 岸本直之, 宗宮功, 佐藤寿彦, & 津野洋. (2014). 土壌浸透処理による赤玉土のリン除去性能および吸着特性の長期カラム実証評価. 水環境学会誌, 37(2), 55-62. LINK
奥村浩気, 岸本直之, 一瀬諭, 馬場大哉, & 田中仁志. (2014). 琵琶湖北湖東岸における湖岸形状と泥質化の関係. 水環境学会誌, 37(2), 45-53. LINK