Aim: While many phylogeographical studies have focused on continental refugia, the function of islands as refugia has been long overlooked. In this study, we examined the biogeographic history of Microtropis japonica and its insular distribution to elucidate the hidden status of islands on the range expansion of plants.

Location: Two disjunct island areas of Japan (the Izu and Ryukyu Islands) and their adjacent areas (the Japanese mainlands Honshu and Kyushu, and Taiwan).

Taxon: Microtropis japonica (Celastraceae).

Methods: Phylogeographic and population genetic analyses were performed using chloroplast DNA (cpDNA) and nuclear single-nucleotide polymorphism (SNP) data. In addition, ecological niche modeling of current suitable habitats and those during the last glacial maximum were conducted using occurrence and climate data.

Results: Both cpDNA and nuclear SNP data showed genetic differentiation between two disjunct regions (mainly the Izu and Ryukyu Islands). However, at the intra-regional level, the genetic structures revealed by different markers showed different geographic patterns. While cpDNA data indicated genetic differentiation within the Ryukyu Islands but not within the Izu Islands, nuclear SNP data indicated genetic differentiation within both island groups. Ecological niche modeling showed that both the Izu and Ryukyu Islands have continuously been potential distribution areas regardless of historical climate oscillations.

Main conclusions: Genetic data suggest that the current disjunct distribution pattern of M. japonica strongly reflects the refugia locations during the last glacial period and the subsequent range expansion. Ecological niche modeling revealed the importance of islands as refugia in the disjunct distribution of M. japonica.