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According to previous phylogeographic studies, high mountains at low latitudes are important areas for the study of the evolutionary history of arctic–alpine plants in surviving the Pleistocene climatic oscillations. To evaluate this hypothesis, we elucidated the genetic structure of the arctic–alpine plant, Loiseleuria procumbens, in the Japanese archipelago, which corresponds to one of the southernmost limits of its distribution, using 152 individuals from 17 populations that covered the entire distribution of the Japanese archipelago and Sakhalin, in addition to samples from Sweden. Based on 854 bp of chloroplast DNA, we detected eight haplotypes. Along with haplotype distribution, strong genetic differentiation between populations in central and northern Japan was elucidated by a neighbour-joining tree (100%) and spatial analysis of molecular variance (79%), which is consistent with other alpine plants in Japan, regardless of the species' range. In addition, the southernmost populations from northern Japan showed specific genetic structure, although the remaining areas of northern Japan and Sakhalin harboured an homogenous genetic structure. Our results suggest that the populations in central Japan persisted for a long time during the Pleistocene climatic oscillation and that genetic divergence occurred in situ, supporting our hypothesis in conjunction with a previous study of another arctic–alpine plant, Diapensia lapponica subsp. obovata. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 97, 403–412.

Molecular phylogeography has inferred the history of differentiation between regions and/or among populations following the Pleistocene climatic oscillations, mostly based on the genetic structure of organelle DNA. However, such genetic structure only reflects the history of a single gene, and studies based on single-copy genes of nuclear DNA (nDNA) are required for phylogeography, although their efficiency remains unclear. To examine the utility of nDNA loci, the genetic structures of three genes from Cardamine nipponica, which is closely related to the model species Arabidopsis thaliana, were elucidated: the nDNA genes DET1, PHYA, PHYE, as well as chloroplast DNA (cpDNA). In 279 individuals collected from throughout the range of the species, strong genetic differentiation between northern and central Japan was found for all loci. This result suggested that populations in central Japan experienced a different history from those in northern Japan during the Pleistocene climatic oscillations. In addition, the evidence of refugia at the edges of the distribution, where the genetic structure was less influenced by colonization following range expansion, was shown for several loci. The specific genetic structure within the southernmost populations of northern Japan suggested that this region was also isolated during range expansion. Hence, the consistent history among loci and a more detailed history from several loci indicated that cpDNA can represent the history of vicariance and demonstrated the efficiency of single-copy nuclear genes in phylogeography.

Aim We aimed to elucidate how the current geographic distribution of alpine plants in the Japanese archipelago was shaped during Quaternary climatic oscillations, using Potentilla matsumurae as a case study. According to previous phylogeographic studies, post-glacial range fragmentation (vicariance scenario) and stepwise migration (dispersal scenario) are both possible. We thus aimed to assess which scenario is more probable for the distribution changes of alpine plants in the Japanese archipelago. Location The alpine zone in the Japanese archipelago. Methods Using amplified fragment length polymorphism we determined the genotype of 161 individuals of P. matsumurae from 22 populations. Relationships among individuals and populations were examined using principal coordinates analysis and a neighbour-joining (NJ) tree, respectively. To examine the genetic population structure, we performed analysis of molecular variance (amova) and structure analysis. Results Differentiation between central Honshu and northern Japan was not very strong based on the principal coordinates analysis among individuals, the NJ tree of populations (59% bootstrap support), or amova (12% of genetic variation). Moreover, structure analysis did not detect clear geographic differentiation across populations. Although the populations in central Honshu were structured geographically (Mantel test: r = 0.45, P

Previous phylogeographic studies of arctic-alpine plants have partly elucidated that alpine areas at the southernmost edges of their distribution have been one of the most important areas for the survival of populations through Quaternary climatic oscillations. To reveal the genetic structure of arctic-alpine plants near the southern edge of their range in East Asia, 159 samples of Diapensia lapponica subsp. obovata (Diapensiaceae) were collected from 22 populations in Japan. Based on 1,134 bp of chloroplast DNA (cpDNA), we determined 10 haplotypes. Neighbor-joining (NJ) analysis, including D. lapponica from Sweden and Schizocodon soldanelloides, revealed that all haplotypes in Japan were monophyletic. Genetic differentiation between populations of central Honshu and northern Japan was strongly supported by the NJ tree (100%), analysis of molecular variance (AMOVA, 68%), and Monmonier’s algorithm (>95%). The most ancestral haplotype rarely occurred in Japan, which implied that the extant genetic structure was not caused by genetic divergence during colonization. Thus, these results suggest that the arctic-alpine plant D. lapponica subsp. obovata survived climatic oscillations in central Honshu. This finding supports the hypothesis that high mountains in temperate regions were important for survival of arctic-alpine plants during Quaternary climatic oscillations.

Molecular phylogeographic studies have revealed the genetic patterns and glacial-interglacial history of many plant and animal species. To infer the Quaternary history of alpine plants in the Japanese archipelago, which is poorly known, we investigated 203 individuals of Potentilla matsumurae and its varieties from 22 populations. We found 11 haplotypes based on approximately 1400 bp of two intergenetic spacers in chloroplast DNA (trnT-L and rpl20-rps20). The distribution of these haplotypes was geographically structured, which was supported by haplotype composition, principal component analysis, and unweighted pair group method with arithmetic mean (UPGMA), and N(ST) (0.71) was significantly greater than G(ST) (0.68). In addition to the positive correlation between genetic and geographic distance (Mantel test, r = 0.497, P < 0.001), an abrupt genetic change was detected between mountains in central Honshu and the Tohoku region. This genetic boundary was further supported by analysis of molecular variance (AMOVA), and high variation (54.0%) was explained by differences on either side of this boundary. Moreover, haplotypes in central Honshu were thought to have diverged, based on an outgroup comparison. These results suggest that mountains in central Honshu served as refugia during the Quaternary climatic oscillation, although the results could not reveal the history of most mountains in the Tohoku region and Hokkaido. Nevertheless, following floristic studies, our results indicate that alpine plants in Japan experienced a history different from that in Europe; i.e. they retreated into refugia during warm periods to avoid forest development, rather than glaciers.

A preliminary synthesis of the geographic distribution patterns of intraspecific cpDNA variations in Japanese alpine plants is presented by studying five species, namely, Pedicularis chamissonis, Primula cuneifolia, Loiseleuria procumbens, Cardamine nipponica, and Anemone narcissiflora. Nucleotide sequences of the noncoding regions of cpDNA recognized multiple cpDNA haplotypes in these species. Phylogenetic analyses of these haplotypes suggest two or three major cpDNA clades; each clade has a clearly disjunct distribution pattern in the northern parts of Japan, and in the central parts of Japan. The southernmost clades endemic to central Honshu in Japan were found in all the species (Central Honshu clade). We estimate that the major clades of Pedicularis chamissonis and Primula cuneifolia separated from a common ancestor before the last glacial period (>0.6 and 0.47 million years ago, respectively). We speculate that the common distribution patterns of the cpDNA clades observed in central Honshu were formed by dynamic climatic changes (e.g., glacial events in the Pleistocene) and that the alpine regions of central Honshu acted as refugia for alpine plants during warm interglacial periods.

Molecular phylogeographic studies have revealed the genetic patterns and glacial-interglacial history of many plant and animal species. To infer the Quaternary history of alpine plants in the Japanese archipelago, which is poorly known, we investigated 203 individuals of Potentilla matsumurae and its varieties from 22 populations. We found 11 haplotypes based on approximately 1400 bp of two intergenetic spacers in chloroplast DNA (trnT-L and rpl20-rps20). The distribution of these haplotypes was geographically structured, which was supported by haplotype composition, principal component analysis, and unweighted pair group method with arithmetic mean (UPGMA), and N(ST) (0.71) was significantly greater than G(ST) (0.68). In addition to the positive correlation between genetic and geographic distance (Mantel test, r = 0.497, P0.001), an abrupt genetic change was detected between mountains in central Honshu and the Tohoku region. This genetic boundary was further supported by analysis of molecular variance (AMOVA), and high variation (54.0%) was explained by differences on either side of this boundary. Moreover, haplotypes in central Honshu were thought to have diverged, based on an outgroup comparison. These results suggest that mountains in central Honshu served as refugia during the Quaternary climatic oscillation, although the results could not reveal the history of most mountains in the Tohoku region and Hokkaido. Nevertheless, following floristic studies, our results indicate that alpine plants in Japan experienced a history different from that in Europe; i.e. they retreated into refugia during warm periods to avoid forest development, rather than glaciers.