Refugia of<i>Potentilla matsumurae</i>(Rosaceae) located at high mountains in the Japanese archipelago

<jats:title>Abstract</jats:title><jats:p>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<jats:italic>Potentilla matsumurae</jats:italic>and its varieties from 22 populations. We found 11 haplotypes based on approximately 1400 bp of two intergenetic spacers in chloroplast DNA (<jats:italic>trnT</jats:italic>‐<jats:italic>L</jats:italic>and<jats:italic>rpl20</jats:italic>–<jats:italic>rps20</jats:italic>). 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<jats:italic>N</jats:italic><jats:sub>ST</jats:sub>(0.71) was significantly greater than<jats:italic>G</jats:italic><jats:sub>ST</jats:sub>(0.68). In addition to the positive correlation between genetic and geographic distance (Mantel test,<jats:italic>r</jats:italic> = 0.497,<jats:italic>P</jats:italic> < 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 (<jats:sc>amova</jats:sc>), 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.</jats:p>