Publications

Peer-reviewed Articles 

Submitted

• Hori, K., Takahashi, D., He, Y.H., Shin T., & Suyama Y. (submitted). Arachniodes ×tohtomiensis hyb.nov. (Dryopteridaceae) from Japan.

• Trovó M., Cabrini M., Ramos R., Suyama Y., Takahashi D., & Lira, C. (submitted). Genomic and spatial data on the conservation of the critically endangered Paepalanthus longiciliatus (Eriocaulaceae).

• Fukasawa, Y., Akai, D., Takehi, T., Takahashi, D., & Osada, Y. (submitted). Electrical information flows across the sporocarps of two ectomycorrhizal fungi in the field.

• Izumi, S., Kobayashi, K., Matsuoka, S., Ishihara, M., Inoue, M., Sakaguchi, S., Sakai, M., Takahashi, D., Takayanagi, A., Nagasawa, K., Fukushima, K., Fujiki, D., Masuda, K., Yamasaki, M., & Shiojiri, K. (submitted). Effects of deer-exclusion fences on population stability and abundance of the dragonfly Mnais pruinosa.

• Marthick, J.R., Phipps, A.J., Jordan, G.J., Takahashi, D., Suyama, Y., & Worth, J.R.P. (submitted). Stand structure and genetic diversity in one of the world’s oldest conifer clones, Lagarostrobos franklinii at Mt Read, western Tasmania.

Published/Accepted

1. Cabrini, M., Trovó, M., Takahashi, D., Suyama, Y., Ramos, R., & Lira C. (2025). Lithobiomes heterogeneity and geographic distance shape the landscape genomics within Brazilian mountain systems. Ecology and Evolution, 15(11), e72476.

2. Hori, K., Takahashi, D., Yoneoka, K., He Y.H., Suyama, Y., Murakami, N., & Ebihara A. (2025). Hybrid origin of Arachniodes hiugana (Dryopteridaceae). Bulletin of the National Museum of Nature and Science Series B (Botany), 51(4), 137–146.

3. Sun, S.S., Xu, S.H., Yi, W.J., Chen, S.L., Li P., Takahashi, D., Abe, H., Ma, X.L., & Fu, P.C. (2026). Incomplete lineage sorting, hybridization and polyploidization blurred phylogenetic relationships of gentians from the Qinghai-Tibetan Plateau. Molecular Phylogenetics and Evolution, 214, 108476.

4. Aihara, T., Cheng, C.H., Chen, C.P., Wang C.T., Uchiyama, K., Takahashi, D., Suyama, Y., & Tsumura, Y. (2025). The historical biogeography of divergence in the relict cypress Chamaecyparis obtusa, and the implications for conservation and management in East Asia. Ecology and Evolution, 15, no.10: e72240.

5. Takahashi, D., Suyama, Y., Ishikawa, N., Yamamoto, M., Fukuda, T., Ito, T., Magota, K., Yonekura, K., & Yahara, T. (Accepted). Taxonomic revision of Hypericum (Hypericaceae) in Yakushima, Japan with a new miniaturised species, H. yaedakense. Acta Phytotaxonomica et Geobotanica.

6. Vasques, D.T., Takahashi, D., Ishikawa, N., Kurata, S., Nanami, N., & Ikeda, H. (2025). Genome-wide analysis confirms the independent origin of the Japanese and Korean Adonis amurensis Regel & Radde (Ranunculaceae). Plant Systematics and Evolution, 311, 16.

7. Michimoto, K., Yokota, M., Abe, A., Fujii, S., Takahashi, D., Kakishima, S., Yu, C.C., Ito, T., & Maki, M. (2025). New species of Thalictrum (Ranunculaceae) from Okinawa Island in Japan and its phylogenetic implications. Phytotaxa, 696(1), 055–070.

8. Sakaguchi, S., Choi, H.J., Yoichi, W., Takahashi, D., Hirota, S.K., Maki, M., Murakami, S., Harada, T., Kobayashi, N., Kurashige, Y., Song, J.H., Choi, H.J., & Kim S.C. (2025). Unraveling enigmatic disjunctions: population genetic analysis points to independent origins of rare rhododendrons in the Rhododendron keiskei complex (Ericaceae). Taxon, 74(1), 117-132.

9. Alencar, A.S., Suyama, Y., Takahashi, D., Mansano, V.D.F., & Lira C.D.F. (2025). Insights from genetic studies: SNP analyses confirm white clover naturalization in Brazil. Genetic Resources and Crop Evolution, 72, 919–933.

10. Dos Santos, A., Nunes-Freitas, A., Tompson, C., Barbosa, G., Takahashi, D., Suyama, Y., & Lira, C. (2024). Multidisciplinary assessment of a restored mangrove ecosystem in Guanabara Bay, Brazil: Linking science and conservation. Wetlands Ecology and Management, 32, 1003–1025.

11. Cabrini, M., Lira, C., Suyama, Y., Takahashi, D., Ishikawa, N., Paglia, I., & Trovǒ, M. (2024). Genomic and morphological data reveal a critically endangered new species from the Atlantic Forest, Paepalanthus salimenae (Eriocaulaceae). Phytotaxa, 655(3), 173-186.

12. Worth, J.R.P., Kikuchi, S., Kanetani, S., Takahashi, D., Aizawa, M., Marchuk, E., Choi, H.J., Polezhaeva, M., Sheiko, V., & Ueno, S. (2024). Chloroplast genome-based genetic resources for Japan’s threatened subalpine forests via genome skimming. Ecology and Evolution. 14, e11584.

13. Takahashi, D., Suyama, Y., Fukushima, K., Setoguchi, H., & Sakaguchi, S. (2024). Deer grazing drove an assemblage-level evolution of plant dwarfism in an insular system. Journal of Ecology, 112(6), 1383-1396. #Harper Prize 2024 Shortlist

14. Kadowaki, K., Honjo, M., Nakamura, N., Kitagawa, Y., Ishihara, M., Matsuoka, S., Tachiki, Y., Fukushima, K., Sakaguchi, S., Mizuki, I., Fujiki, D., Sakai, M., Takayanagi, A., Yamasaki, M., Tokuchi, N., Takahashi, D., Nagasawa, K., & Masuda, K. (2023). eDNA metabarcoding analysis reveals the consequence of creating ecosystem-scale refugia from deer grazing for the soil microbial communities. Environmental DNA, 5(6), 1732-1742.

15. Takahashi, D., & Suyama, Y. (2023). Demographic history and conservation aspects of two relict shrubs (Daphnimorpha spp., Thymelaeaceae) showing disjunct and restricted distribution in the southern part of Japan. Tree Genetics & Genomes, 19(5) 43.

16. Takahashi, D., Sakaguchi, S., Teramine, T., & Setoguchi, H. (2022). Comparative reproductive ecology of two sister Asarum species (Aristolochiaceae) in relation to the evolution of elongated floral appendage. Plant Biology, 24(6), 987-997.

17. Takahashi, D., Isagi, Y., Li, P., Qiu, Y.X., Setoguchi, H., Suyama, Y., Matsuo, A., Tunamoto, Y., & Sakaguchi, S. (2022). Stable persistence of relict populations involved evolutionary shifts of reproductive characters in the genus Tanakaea (Saxifragaceae). Journal of Systematics and Evolution, 60(6), 1405-1416.

18. Sakaguchi, S., Oishi, M., Takahashi, D., Matsuo, A., Hirota, K.S., Suyama, Y., & Setoguchi, H. (2022). Ribes fujisanense (Grossulariaceae): A new obligate epiphytic species of gooseberry in central Japan. Acta Phytotaxonomica et Geobotanica, 73(1), 49-56.

19. Magota, K., Sakaguchi, S., Jungsim, L., Yamamoto, M., Takahashi, D., Nagano, J.A., & Setoguchi, H. (2021). Phylogeographic analysis of Saxifraga fortunei complex (Saxifragaceae) reveals multiple origins of morphological and ecological variations in the Japanese Archipelago. Molecular Phylogenetics and Evolution, 163, 107230. 

20. Takahashi, D., Sakaguchi, S., Feng, Y., Isagi, Y., Qiu, Y.X., Li, P., Lu, R.S., Lu, C.T., Chung, S.W., Lin, Y.S., Chen, Y.C., Nagano, J.A., Kawaguchi, L., & Setoguchi, H. (2021). Geographic and subsequent biotic isolations led to a diversity anomaly of section Heterotropa (genus Asarum; Aristolochiaceae) in insular versus continental regions of the Sino-Japanese Floristic Region. Journal of Biogeography, 48, 1917-1929. 

21. Sakaguchi, S., Abe, A., Nagasawa, K., Takahashi, D., Setoguchi, H., Maki, M., Kyan, R., Nishino, T., Ishikawa, N., Hirota, K.S., Suyama, Y., & Ito, M. (2021). Functional traits divergence in parallelly evolved rheophytic populations of Solidago virgaurea L. complex (Asteraceae). Acta Phytotaxonomica et Geobotanica, 72(2), 93–111.

22. Sakaguchi, S., Asaoka, Y., Takahashi, D., Isagi, Y., Imai, R., Nagano, J.A., Qiu, Y.X., Li, P., Lu, R.S., & Setoguchi, H. (2021). Inferring historical survivals of climate relicts: roles of climate changes, geography and population-specific factors on herbaceous hydrangeas. Heredity, 126(4) , 615–629.

23. 阪口翔太, 福本繁, 長澤耕樹, 増田和俊, 髙橋大樹, 瀬戸口浩彰, 古田卓, 岸本泰典, 平塚健一, 船津慧, & 石原正恵. (2020). 京都府芦生にてフガクスズムシソウ (ラン科) を記録する. 植物地理・分類研究, 68(2), 81-88.

24. Yamamoto, M., Takahashi, D., Yu, C.C., & Setoguchi, H. (2020). Development and characterization of EST-SSR markers in creeping mazus (Mazus miquelii), and cross-amplification in five related species. Taiwania, 65(2), 249-252.

25. Lu, R.S., Chen, Y., Tamaki, I., Sakaguchi, S., Ding, Y.Q., Takahashi, D., Li, P., Isagi, Y., Chen, J., & Qiu, Y.X. (2020). Pre-quaternary diversification and glacial demographic expansions of Cardiocrinum (Liliaceae) in temperate forest biomes of Sino-Japanese Floristic Region. Molecular Phylogenetics and Evolution, 143, 106693.

26. Yamamoto, M., Takahashi, D., Horita, K., & Setoguchi, H. (2020). Speciation and subsequent secondary contact in two edaphic endemic primroses driven by Pleistocene climatic oscillation. Heredity, 124(1), 93-107.

27. Takahashi, D., Teramine, T., Sakaguchi, S., & Setoguchi, H. (2019). Genetic data reveals a complex history of multiple admixture events in presently allopatric wild gingers (Asarum spp.) showing intertaxonomic clinal variation in calyx lobe length. Molecular Phylogenetics and Evolution, 137, 146-155.

28. Magota, K., Takahashi, D., & Setoguchi, H. (2019). Development and characterization of EST‐SSR markers for Saxifraga fortunei var. incisolobata (Saxifragaceae). Applications in plant sciences, 7(7), e11275.

29. Kameoka, S., Murai, Y., Ohashi, K., Sakio, H., Abe, H., Takahashi, D., Nagasawa, K., & Setoguchi, H. (2019). Relationships among flower color polymorphism, feeding by visiting insects, and seed production in Hepatica nobilis var. japonica. Bulletin of the National Museum of Nature and Science. Series B, Botany, 45(1), 17-27.

30. Takahashi, D., Sakaguchi, S., Isagi, Y., & Setoguchi, H. (2018). Comparative chloroplast genomics of series Sakawanum in genus Asarum (Aristolochiaceae) to develop single nucleotide polymorphisms (SNPs) and simple sequence repeat (SSR) markers. Journal of Forest Research, 23(6), 387-392.

31. Yamamoto, M., Horita, K., Takahashi, D., Murai, Y., & Setoguchi, H. (2018). Floral morphology and pollinator fauna of sister species Primula takedana and P. hidakana in Hokkaido Island, Japan. Bulletin of the National Museum of Nature and Science. Series B, Botany, 44(2), 97-103.

32. Takahashi, D., Teramine, T., Sakaguchi, S., & Setoguchi, H. (2018). Relative contributions of neutral and non-neutral processes to clinal variation in calyx lobe length in the series Sakawanum (Asarum: Aristolochiaceae). Annals of Botany, 121(1), 37-46.

33. Sakaguchi, S., Takahashi, D., Setoguchi, H., & Isagi, Y. (2018). Genetic structure of the clonal herb Tanakaea radicans (Saxifragaceae) at multiple spatial scales, revealed by nuclear and mitochondrial microsatellite markers. Plant Species Biology, 33(1), 81-87.

34. Takahashi, D., & Setoguchi, H. (2018). Molecular phylogeny and taxonomic implications of Asarum (Aristolochiaceae) based on ITS and matK sequences. Plant Species Biology, 33(1), 28-41.

35. Sakaguchi, S., Ueno, S., Tsumura, Y., Setoguchi, H., Ito, M., Hattori, C., Nozoe, S., Takahashi, D., Nakamasu, R., Sakagami, T., Lannuzel, G., Fogliani, B., Wulff, AS., L'Huillier, L. & Isagi, Y. (2017). Application of a simplified method of chloroplast enrichment to small amounts of tissue for chloroplast genome sequencing. Applications in Plant Sciences, 5: 1700002.

36. Takahashi, D., Sakaguchi, S., & Setoguchi, H. (2017). Development and characterization of EST‐SSR markers in Asarum sakawanum var. stellatum and cross‐amplification in related species. Plant Species Biology, 32(3), 256-260.

査読なし

• 髙橋大樹. (2025). 九州における森林樹種の遺伝的多様性. 木科学情報, 32(1), 2-5.

• 髙橋大樹. (2024). 日本の森林樹木の地理的遺伝構造（47）シャクナンガンピ属（ジンチョウゲ科）. 森林遺伝育種, 13(4), 167-171.

• 髙橋大樹. (2024). 東アジア地域の植物多様性に分子生態学的アプローチで迫る. 植物地理・分類研究, 72(1), 1-9.  #日本植物分類学会奨励賞受賞記念論文.

Books

• 髙橋大樹. (2025). クラインと種分化. 種分化の生物学 生物多様性を生み出す進化のしくみ (eds 種生物学会), 文一総合出版. 分担執筆.

• 髙橋大樹. (2022). カンアオイ類の起源と日本列島における多様化過程. さらに知っておきたい日本の絶滅危惧植物図鑑 (eds 長澤淳一, 瀬戸口浩彰), 創元社. 分担執筆.

その他

• "屋久島 ミニチュア植物の謎" 朝日新聞 朝刊 2024年7月26日.

• ”屋久島の植物、なぜ小型化? 東北大などが奇妙な法則を解明” 毎日新聞 夕刊 2024年6月15日.

• "屋久島にミニチュア植物が80種類 小型化の原因はあの動物だった！" 朝日新聞デジタル 2024年6月9日.

• “屋久島の植物 シカ採食防ぐため小型化か” 河北新報 朝刊 2024年5月29日.

• “Hungry deer may have driven tiny plant evolution on Japanese island” New Scientist web article 2024年5月24日.

• “屋久島のミニチュア植物群の進化はシカの採食圧が原因だった！ 80種にわたる植物の大規模な収れん進化の解明” 東北大学プレスリリース 2024年5月10日.