The Quaternary was characterized by a cyclic pattern of cold and warm climatic periods, which caused fluctuations in the distributions of organisms. The Japanese Archipelago is unique in terms of geographical complexity, and many plant species change their distribution responding to the past climatic oscillations. Rhododendron weyrichii Maxim. (Ericaceae) is a shrub with a wide distribution in southwest Japan and Jeju Island, South Korea. The last glacial may have affected genetic diversity and structure in R. weyrichii, because the species is thought to have persisted in limited warm-temperate forests in the last glacial maximum (LGM). To estimate the effects of palaeodistribution on genetic diversity and structure, we sequenced nine coding regions of nDNA and two noncoding regions of cpDNA in individuals from 18 R. weyrichii populations. Additionally, we reconstructed LGM palaeodistribution of R. weyrichii by ecological niche modeling.

STRUCTURE analysis revealed each of four gene pools mainly distributed in overall Japanese range, Kii-Shikoku, Kyushu and Jeju, respectively. The LGM palaeodistribution reconstructed by ecological niche modeling showed four main refugia (Kii, Shikoku, Kyushu and Jeju) which were disconnected from each other.