In order to infer the evolutional history of Japanese alpine plants, we performed a phylogeographic study using molecular markers. We analyzed variations in chloroplast DNA (cpDNA) in several species of Japanese alpine plants, for example, Pedicularis chamissonis, Primula cuneifolia, Cardamine nipponica, Loiseleuria procumbens, and Anemone narcissiflora (Fujii et al. 1995, 1997, 1999, Fujii and Senni 2006). Phylogenetic analyses of these haplotypes suggested two or three major cpDNA clades; each clade had a clear disjunct distribution pattern in the northern and central parts of Japan. The southernmost clades were endemic to central Honshu in Japan and were found in all species (Central Honshu clade). We speculated that the common distribution patterns of the cpDNA clades observed in central Honshu were formed by dynamic climatic changes (e.g., glacial events during the Pleistocene), and the alpine regions of central Honshu acted as refugia for alpine plants during warm interglacial periods (Fujii and Senni, 2006).
Pedicularis L. (Orobanchaceae) is a lineage of hemi-parasitic flowering plants distributed throughout the Northern hemisphere, primarily in cold, high-latitude, or montane habitats. With more than 500 described species, it has been noted as one of the largest genera of angiosperms in the North Temperate Zone. This genus is characterized by dramatic floral morphological diversity, particularly in the galea. Of the 15 species of Pedicularis described in Japan, half are endemic to Japan, suggesting allopatric speciation. We have been conducting molecular phylogenetic analyses to clarify the origin of the Japanese Pedicularis. For example, it was suggested that the Japanese species originated from the Asian continental species in a study using Pedicularis ser. Gloriosa (Fujii 2007). Further, two major clades were distinguished between the Japan Sea side and the Pacific Ocean side.
From the above mentioned study, P. chamissonis sensu lato possessed two major cpDNA clades, the Northern clade and Central Honshu clade. Fujii et al. (2001) examined the plants of Mt. Gassan, Tohoku district, Japan, where the two clades occur sympatrically. An analysis based on cpDNA and nuclear ribosomal DNA (ITS region) showed that no gene flow existed between the plants in the two clades. The two clades on Mt. Gassan were distinguished from each other by several morphological characteristics and habitat, suggesting that the two clades should be treated as separate species. Based on an examination of herbarium specimens and taxonomical literature, we concluded that the Northern clade should be treated as P. chamissonis sense strict and the Central Honshu clade as P. japonica Miq. (Fujii et al. 2013).
Fagus crenata is dominant in the typical temperate forests of Japan. This species is widely distributed from Hokkaido to Kyushu. To elucidate the evolutionary history of Fagus forest, we investigated cpDNA variations in this species using 45 populations throughout the species' distribution range (Fujii et al. 2002). We could recognize 13 distinct cpDNA haplotypes, and each haplotype was found to be geographically structured. Furthermore, two major clades were revealed in phylogenetic analyses (Clade I and Clade II + III). We can speculate that there have been at least two major refugia and migration routes in F. crenata along the Japan Sea side and the Pacific Ocean side.
Many grassland plant species occur in the Aso region, located in the eastern area of Kumamoto Prefecture. Because of a reduction in the use of grassland of late, some of the grassland species have become endangered. According to the Red List of the Ministry of the Environment, Japan, more than 70 species are listed as endangered. Therefore, we must accumulate the ecological and genetic information of these species. We performed conservation genetics analysis of Silene kiusiana (Caryophyllaceae) using microsatellite markers (Yamasaki et al. 2013). Each population has maintained relatively high genetic diversity; however, the differentiation values among the populations were significantly larger than zero, suggesting a possibility of fragmentation among the populations due to a reduction in population size.
