Publications

<2023>

• Hidaka S, Jo TS, Yamamoto S, Katsuhara KR, Tomita S, Miya M, Ikegami M, Ushimaru A, Minamoto T (2023)  Sensitive and efficient surveillance of Japanese giant salamander (Andrias japonicus) distribution in western Japan using multi-copy nuclear DNA marker. Limnology (Accepted)

• Doi H, Matsuoka S, Matsuzaki SS, 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 Biology 68:1346–1358 doi:https://doi.org/10.1111/fwb.14107

<2022>

• 馬場友希, 片山直樹, 山迫淳介, 山本哲史, 池田浩明, 伊藤健二 (2022) 環境DNA分析を用いた水田の昆虫多様性評価. 昆虫と自然 10月号 (non peer-reviewed article in Japanese)

• 山本哲史 (2022) 昆虫調査における環境DNA分析. 昆虫と自然 10月号 pp2–4 (non peer-reviewed article in Japanese)

<2021>

• Murakami M, Masuda R, Yamamoto S, Minamoto T, Yamashita Y (2021) Environmental DNA emission by two carangid fishes in single and mixed-species tanks. Fisheries Science 88:55–62. doi:10.1007/s12562-021-01565-y  [web]

• Schwentner M, Zahiri R, Yamamoto S, Husemann M, Kullmann B, Thiel R (2021) eDNA as a tool for non-invasive monitoring of the fauna of a turbid, well-mixed system, the Elbe estuary in Germany. PLOS ONE 16(4):e0250452. doi:10.1371/journal.pone.0250452 [web]

• 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 36:379– 388 doi:10.1111/1440-1703.12217 [web]

• Kadowaki K, Yamamoto S, Sato H, Tanabe SA, Toju H (2021) Aboveground herbivores drive stronger plant species-specific feedback than belowground fungi to regulate tree community assembly. Oecologia 195:773–784. doi:10.1007/s00442-021-04868-0 [web]

<2020>

• 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 (2020) An illustrated manual for environmental DNA research: Water sampling guidelines and experimental protocols. Environmental DNA 3:8– 13. doi: https://doi.org/10.1002/edn3.121 (This is commentary, not original article.)

• 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 modeling. Molecular Ecology 30:3057– 3067. doi: 10.1111/mec.15530 [web]

• Kudoh A, Minamoto T, Yamamoto S (2020) Detection of herbivory: eDNA detection from feeding marks on leaves. Environmental DNA 2:627–634. doi: 10.1002/edn3.113 [web]

• 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. doi: 10.1007/s10228-020-00756-4 [web]

• Itakura H, Wakiya R, Sakata MK, Hsu H, Chen S, Yang C, Huang Y, Han Y, Yamamoto S, Minamoto T (2020) Estimations of riverine distribution, abundance, and biomass of anguillid eels in Japan and Taiwan using environmental DNA analysis. Zoological Studies 59:17 [web (PDF)]

• Sakata MK, Yamamoto S, Gotoh RO, Miya M, Yamanaka H, Minamoto T. (2020) Sedimentary eDNA provides different information on timescale and fish species composition compared with aqueous eDNA. Environmental DNA 2:505–518. doi:10.1002/edn3.75 [web]

• Yamamoto S, Matsuhisa S. (2020) Population abundance gradient of Inurois punctigera along altitude. Entomological Science 23:23–27. doi: 10.1111/ens.12392 [web]

<2019>

• 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 Biology 95: 979–981. doi: 10.1111/jfb.14095 [web]

• 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 Ecosystems 29: 361–373 [web]

• Murakami H, Yoon S, Kasai A, Minamoto T, Yamamoto S, Sakata MK, Horiuchi T, Sawada H, Kondoh M, Yamashita Y, Masuda R. (2019) Dispersion and degradation of environmental DNA from caged fish in a marine environment. Fisheries Science 85:327–337 doi:10.1007/s12562-018-1282-6 [web]

• Takeuchi A, Watanabe S, Yamamoto S, Miller MJ, Fukuba T, Miwa T, Okino T, Minamoto T, Tsukamoto K. (2019) First attempt of an oceanic environmental DNA survey of the spawning ecology of the Japanese eel Anguilla japonica. Marine Ecology Progress Series 609:187–196 [web]

• 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 Evolution 9: 1135–1146 [web]

<2018>

• Toju H, Sato H, Yamamoto S, Tanabe AS. (2018) Structural diversity across arbuscular mycorrhizal, ectomycorrhizal, and endophytic plant-fungus networks. BMC Plant Biology 18: 292 [web]

• Yamamoto S, Uchida K. (2018) A generalist herbivore requires a wide array of plant species to maintain its populations. Biological Conservation 228: 167–174. doi:10.1016/j.biocon.2018.10.018 [web]

• Kadowaki K, Yamamoto S, Sato H, Tanabe AS, Hidaka A, Toju H. (2018) Mycorrhizal fungi mediate the direction and strength of plant-soil feedbacks differently between arbuscular mycorrhizal and ectomycorrhizal communities. Communication Biology 1: Article number 196. (co-first author) [web]

• 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 Biology 63: 569–580. doi:10.1111/fwb.13094 [web]

• 山本哲史. (2018) 環境DNAで見た舞鶴湾：マアジの分布推定と魚類群集の検出. 海洋と生物 40: 28–34.（原著論文ではありません）

<2017>

• Jo T, Murakami H, Masuda R, Sakata M, Yamamoto S, Minamoto T. (2017) Rapid degradation of longer DNA fragments enables the improved estimation of distribution and biomass using environmental DNA. Molecular Ecology Resources 17: e25–e33. doi: 10.1111/1755-0998.12685 [web].

• Minamoto T, Fukuda M, Katsuhara KR, Fujiwara A, Hidaka S, Yamamoto S, Takahashi K, Masuda R. (2017) Environmental DNA reflects spatial and temporal jellyfish distribution. PLOS ONE 12:  e0173073. doi:10.1371/journal.pone.0173073 [web].

• Kouduka M, Tanabe AS, Yamamoto S, Yanagawa K, Nakamura Y, Akiba F, Tomaru H, Toju H, Suzuki Y. (2017) Eukaryotic diversity in late Pleistocene marine sediments around a shallow methane hydrate deposit in the Japan Sea. Geobiology 15: 715–727. 

• Yamamoto S, Masuda R, Sato Y, Sado T, Araki H, Kondoh M, Minamoto T, Miya M. (2017) Environmental DNA metabarcoding reveals local fish communities in a species-rich coastal sea. Scientific Reports 7: 40368. doi:10.1038/srep40368 [web]

<2016>

• Miya M, Minamoto T, Yamanaka H, Oka S, Sato K, Yamamoto S, Sado T, Doi H. (2016) Use of a Filter Cartridge for Filtration of Water Samples and Extraction of Environmental DNA. Journal of Visualized Experiments 117: e54741. doi:10.3791/54741 [web] 

• 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 KW, 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 ONE 11 (3): e0149786. doi:10.1371/journal.pone.0149786 [web] 

• Toju H, Yamamoto S, Tanabe AS, Hayakawa T, Ishii HS. (2016) Network modules and hubs in plant-root fungal biome. Journal of the Royal Society Interface 13: 20151097. doi: 10.1098/rsif.2015.1097 [web]

• Ino K, Kouduka M, Hirota A, Togo Y, Fukuda A, Komatsu D, Tsunogai U, Tanabe AS, Yamamoto S, Iwatsuki T, Mizuno T, Ito K, Suzuki Y. (2016) Deep microbial life in high-quality granitic groundwater from geochemically and geographically distinct underground boreholes. Environmental Microbiology Reports 8: 285–294. doi: 10.1111/1758-2229.12379 [web]

• Fujiwara A, Matsuhashi S, Doi H, Yamamoto S, Minamoto T. (2016) Use of environmental DNA to survey the distribution of an invasive submerged plant in ponds. Freshwater Science 35:748–754. doi: 10.1086/685882 [web]

• 源利文、山本哲史、笠井亮秀、近藤倫生. (2016) 環境DNAを用いた沿岸域における魚類モニタリング. 沿岸海洋研究 53: 173–178.（原著論文ではありません）

• Yamamoto S, Beljaev AE, Sota T. (2016) Phylogenetic analysis of the winter geometrid genus Inurois reveals repeated reproductive season shifts. Molecular Phylogenetics and Evolution 94: 47–54. doi: 10.1016/j.ympev.2015.08.016 [web]

<2015>

• 山本哲史. (2015) 季節性の違いによって生じる冬尺蛾の種分化. 『生物時計の生態学（種生物学会 編、新田梢・陶山佳久 責任編集）』 第9章（pp171–190） [web]（原著論文ではありません）

• Miya M, Sato Y, Fukunaga T, Sado T, Poulsen JY, Sato K, Minamoto T, Yamamoto S, Yamanaka H, Araki H, Kondoh M, Iwasaki W. (2015) MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: Detection of >230 subtropical marine species. Royal Society Open Science 2: 150088. doi: 10.1098/rsos.150088 [web]

<2014>

• Konuma J, Yamamoto S, Sota T. (2014) Morphological integration and pleiotropy in the adaptive body shape of the snail-feeding carabid beetle Damaster blaptoides. Molecular Ecology 23: 5843–5854. doi: 10.1111/mec.12976 [web]

• Hata H, Tanabe SA, Yamamoto S, Toju H, Kohda M, Hori M. (2014) Diet disparity among sympatric herbivorous cichlids in the same ecomorphs in Lake Tanganyika: amplicon pyrosequences on algal farms and stomach contents. BMC Biology 12: 90. doi: 10.1186/s12915-014-0090-4 [web]

• Yamamoto S, Sato H, Tanabe AS, Hidaka A, Kadowaki K, Toju H. (2014) Speatial segregation and aggregation of ectomycorrhizal and root-endophytic fungi in the seedlings of two Quercus species. PLoS ONE 9: e96363. doi: 10.1371/journal.pone.0096363 [web]

• Kadowaki K, Sato H, Yamamoto S, Tanabe AS, Hidaka A, Toju H. (2014) Detection of the horizontal spatial structure of soil fungal communities in a natural forest. Population Ecology 56: 301–310. doi: 10.1007/s10144-013-0424-z [web]

<2013>

• Toju H, Yamamoto S, Sato H, Tanabe AS. (2013) Sharing of diverse mycorrhizal and root-endophytic fungi among plant species in an oak-dominated cool-temperate forest. PLoS ONE 8: e78248. doi: 10.1371/journal.pone.0078248 [web]

• Toju H, Yamamoto S, Sato H, Kadowaki K, Tanabe AS, Yazawa T, Nishimura O, Agata K. (2013) How are plant and fungal communities linked to each other in below-graund ecosystems? A massively-parallel pyrosequencing analysis of the association specificity of root-associated fungi and their host plants. Ecology and Evolution 3: 3112–3124. doi: 10.1002/ece3.706 [web]

• Toju H, Yamamoto S, Sato H, Tanabe AS, Gilbert G, Kadowaki K. (2013) Community composition of root-associated fungi in a Quercus-dominated temperate forest: “co-dominance” of mycorrhizal and root-endophytic fungi. Ecology and Evolution 3: 1281–1293. doi: 10.1002/ece3.546 [web]

• Sota T, Yamamoto S, Cooley JR, Hill KBR, Simon C, Yoshimura J. (2013) Independent divergence of 13- and 17-y life cycles among three periodical cicada lineages. Proceedings of the National Academy of Science U.S.A. 110: 6919–6924. doi: 10.1073/pnas.1220060110 [web]

<2012 and before>

• Toju H, Tanabe AS, Yamamoto S, Sato H. (2012) High-coverage ITS primers for the DNA-based identification of Ascomycetes and Basidiomycetes in environmental samples. PLOS ONE 7: e40863. doi: 10.1371/journal.pone.0040863 [web]

• Yamamoto S, Sota T. (2012) Parallel allochronic divergence in a winter moth due to disruption of reproductive period by winter harshness. Molecular Ecology 21: 174–183. doi: 10.1111/j.1365-294X.2011.05371.x [web]

• Sato A, Yamamoto S, Hayaishi S, Sota T. (2012) Characterization of six microsatellite loci in the mangrove cricket Apteronemobius asahinai. Entomological Science 15: 133–136. doi: 10.1111/j.1479-8298.2011.00475.x [web]

• Yamamoto S, Sota T. (2009) Incipient allochronic speciation by climatic disruption of the reproductive period. Proceedings of the Royal Society B 276: 2711-2719. doi: 10.1098/rspb.2009.0349 [web]

• Yamamoto S, Sota T. (2007) Phylogeny of the Geometridae and the evolution of winter moths inferred from a simultaneous analysis of mitochondrial and nuclear genes. Molecular Phylogenetics and Evolution 44: 711-723. doi: 10.1016/j.ympev.2006.12.027  [web]