Fujii, N., S. Takasawa, M. Yokogawa, T. Yamasaki, K. Harada, S. Kaneko & Y. Isagi. (2016) Novel nuclear microsatellite markers reveal genetic diversity and structure of Veronicastrum sibiricum var. zuccarinii (Plantaginaceae) in the Aso region, Kyushu, Japan. Acta Phytotax. Geobot. 67: 69-82.
Fujii, N., M. Teramoto, R. H. Ree, N. Shirai, C. Suyama, K. Ueda, H. Takahashi. (2014) Relict distribution in Pedicularis spicata Pall. (Orobanchaceae): a new locality in central Honshu, Japan. Acta Phytotax. Geobot. 65: 75-87.
(CiNii PDF: http://ci.nii.ac.jp/naid/110009832036/)
Fujii, N., K. Ueda, Y. Watano, T. Shimizu. (2013) Taxonomic revival of Pedicularis japonica from P. chamissonis (Orobanchaceae). Acta Phytotax. Geobot. 63: 87-97.
(CiNii PDF: http://ci.nii.ac.jp/naid/110009592964/)
Yamasaki, T., K. Ozeki, N. Fujii, M. Takehara, M. Yokogawa, S. Kaneko, Y. Isagi. (2013) Genetic diversity and structure of Silene kiusiana (Caryophyllaceae) in the Aso region, Kyushu, Japan, revealed by novel nuclear microsatellite markers. Acta Phytotax. Geobot. 63: 107-120.
(CiNii PDF: http://ci.nii.ac.jp/naid/110009596183/)
Ikeda, H., T. Carlsen, N. Fujii, C. Brochmann, H. Setoguchi. (2012) Pleistocene climatic oscillations and the speciation history of an alpine endemic and a widespread arctic-alpine plant. New Phytologist 194: 583-594.
Ikeda H., N. Fujii, H. Setoguchi (2011) Molecular evolution of cryptochrome genes and the evolutionary manner of photoreceptor genes in Cardamine nipponica (Brassicaceae). J. Plant Res. 124: 85-92.
Ikeda H., N. Fujii, H. Setoguchi (2009) Molecular evolution of phytochromes in Cardamine nipponica (Brassicaceae) suggests the involvement of PHYE in local adaptation, Genetics 182: 603-614.
Ikeda H., K. Senni, N. Fujii, H. Setoguchi (2009) High mountains of the Japanese archipelago as refugia for arctic-alpine plants: phylogeography of Loiseleuria procumbens (L.) Desvaux (Ericaceae). Biological Journal of the Linnean Society 97: 403-412.
Ikeda H., N. Fujii, H. Setoguchi (2009) Application of the Isolation with migration model demonstrates the pleistocene origin of geographic differentiation in Cardamine nipponica (Brassicaceae), an endemic Japanese alpine plant. Mol. Biol. Evol. 26: 2207-2216.
Ikeda H., N. Fujii, H. Setoguchi (2008) Post-glacial range fragmentation is responsible for the current distribution of Potentilla matsumurae Th. Wolf (Rosaceae) in the Japanese archipelago. J. Biogeogr. 35: 791-800.
Ikeda H., N. Fujii, H. Setoguchi (2008) Consistent geographic structure among multiple nuclear sequences and cpDNA polymorphisms of Cardamine nipponica Franch. et Savat. (Brassicaceae). Mol. Ecol. 17: 3178-3188.
Ikeda H., K. Senni, N. Fujii, H. Setoguchi (2008) Survival and genetic divergence of an arctic-alpine plant, Diapensia lapponica subsp. obovata (Fr. Schm.) Hulten (Diapensiaceae), in the high mountains of central Japan during climatic oscillations. Plant Syst. Evol. 272: 197-210.
Fujii N. (2007) Chloroplast DNA phylogeography of Pedicularis ser. Gloriosae (Orobanchaceae) in Japan. J. Plant Res. 120: 491-500.
Ikeda H., K. Senni, N. Fujii, H. Setoguchi (2006) Refugia of Potentilla matsumurae (Rosaceae) located at high mountains in the Japanese archipelago. Mol. Ecol. 15: 3731-3740.
Fujii N., K. Senni (2006) Phylogeography of Japanese alpine plants: biogeographic importance of alpine region of central Honshu in Japan. Taxon 55: 43-52.
Kobashi, S., N. Fujii, A. Nojima, N. Hori (2006) Distribution of chloroplast DNA haplotypes in the contact zone of Fagus crenata in the southwest of Kanto District, Japan. J. Plant Res.119: 265-269.
Okuyama Y., N. Fujii, M. Wakabayashi, A. Kawakita, M. Ito, M. Watanabe, N. Murakami, M. Kato (2005) Nonuniform concerted evolution and chloroplast capture: a gradient of observed introgression patterns in three molecular data partition phylogenies of Asian Mitella (Saxifragaceae). Mol. Biol. Evol. 22: 285-296.
Senni K., N. Fujii, H. Takahashi, T. Sugawara, M. Wakabayashi (2005) Intraspecific chloroplast DNA variation of the alpine plants in Japan. Acta Phytotax. Geobot. 56: 265-275. (PDF)
Sugawara T., N. Fujii, K. Senni, J. Murata (2005) Morphological and karyological characteristics and phylogenetic relationship of Asarum cordifolium C. E. C. Fisch. (Aristolochiaceae) occurring in Myanmar. Acta Phytotax. Geobot. 56: 247-255.
Fujii N. (2003) Chloroplast DNA phylogeography of Pedicularis resupinata (Scrophulariaceae) in Japan. Acta Phytotax. Geobot. 54: 163-175. (PDF)
Fujii N., N. Tomaru, K. Okuyama, T. Koike, T. Mikami, K. Ueda (2002) Chloroplast DNA phylogeography of Fagus crenata (Fagaceae) in Japan. Plant Syst. Evol. 232: 21-33.
Pfosser M. F., J. Guzy-Wrobelska, B. Y. Sun, T. F. Stuessy, T. Sugawara, N. Fujii (2002) The origin of species of Acer (Sapindaceae) endemic to Ullung Island, Korea. Syst. Bot. 27: 351-367.
Fujii N., K. Ueda, Y. Watano, T. Shimizu (2001) Two genotypes of Pedicularis chamissonis (Scrophulariaceae) distributed at Mt. Gassan, Japan: additional genetic and morphological studies. J. Plant Res. 114: 133-140.
Fujii N., K. Ueda, Y. Watano, T. Shimizu (1999) Further analysis of intraspecific sequence variation of chloroplast DNA in Primula cuneifolia Ledeb. (Primulaceae): implications for biogeography of the Japanese alpine flora. J. Plant Res. 112: 87-96.
Fujii N., K. Ueda, Y. Watano, T. Shimizu (1997) Intraspecific sequence variation of chloroplast DNA in Pedicularis chamissonis Steven (Scrophulariaceae) and geographic structuring of the Japanese "alpine" plants. J. Plant Res. 110: 195-207.
Fujii N., K. Ueda, T. Shimizu (1996) Intraspecific sequence variation of chloroplast DNA in Japanese alpine plants. J. Phytogeogr. Taxon. 44: 72-81.
Fujii N., K. Ueda, Y. Watano, T. Shimizu (1995) Intraspecific sequence variation in chloroplast DNA of Primula cuneifolia Ledeb. (Primulaceae). J. Phytogeogr. Taxon. 43: 15-24.
著書･総説等
藤井紀行. 2012. 日本産シオガマギク属（ハマウツボ科）. 新しい植物分類学II. pp. 220-229. 講談社.
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