We investigated the range expansion histories of Machilus thunbergii populations in the Kinki region of central Japan on the basis of nuclear microsatellite data. In the Kinki region, M. thunbergii is typically found along the sea coast area, with some fragmented populations inland, around Lake Biwa.

Phylogenetic and STRUCTURE analyses revealed that the lake populations have different genetic components between the west and east sides. The population located on the north side of the lake has an admixture of the two genetically differentiated lineages, contributing to an increase in the genetic diversity of the population. Populations around Lake Biwa had lost rare alleles. Additionally, magnitude of genetic drift ( Fst ) obtained from STRUCTURE analysis was higher in the lake populations than in the coastal populations. These results suggest that populations around Lake Biwa experienced a bottleneck due to a founder effect during the initial migration to the lake and that glacial refugia of M. thunbergii in the Kinki region existed along the sea coast.