Multiple glacial refugia during Pleistocene climatic oscillations shape the genetic pattern of Machilus thunbergii across East Asia

Abstract Pleistocene climatic oscillations caused periodic decline and rise of sea levels, leading to dispersion and retraction cycles of island flora. Yet, the role of island refugia in the current Sino-Japanese Floristic Region remains poorly understood. In this study, we investigated the population genetic structure of the widespread Sino-Japanese Floristic Region tree Machilus thunbergii to infer the potential impact of island refugia. We collected 1378 samples from 64 locations across the distribution ranges. Using chloroplast DNA and microsatellite markers, we found a pronounced genetic differentiation between mainland and island populations, which can be divided further into two and three groups, respectively. Furthermore, comparable numbers of private alleles and haplotypes are present in both mainland and island populations. No essential current gene flow was detected between mainland and island populations after their separation 14 000 years ago. Such patterns are hypothesized to result from the influence of multiple glacial island refugia during Pleistocene climatic oscillations, with limited pollen and seed dispersal of the species. Our findings underscore that the islands and submerged land bridge can act as refugia for plants during glacial periods and have essentially shaped the genetic structure of M. thunbergii populations.