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Caryopteris incana is a perennial shrub distributed in the temperate zone of the East Asia. It is found in West Kyushu in Japan, where it is designated as an endangered species. Tsushima, Nagasaki, which experienced repeated connection and fragmentation between the Korean Peninsula and Japan, is an island on the route along which C. incana moved to Japan from continental Asia. We conducted field work and confirmed the genetic structure of populations using DNA sequence analysis to construct a detailed distribution map and clarify the intraspecific phylogenetic relationships of C. incana in Tsushima Island. We confirmed 72 populations in Tsushima. Using the leaves of individuals cultivated from seeds collected from each natural population, we analyzed the chloroplast and nuclear DNA sequence variations. Among the populations, sequence variations were confirmed in six regions of chloroplast DNA, and six haplotypes, including base substitutions, were distinguished. Two haplotypes were mainly divided at the border of the northern part of the southern island in Tsushima. One population in the northwestern part of the north island showed a haplotype derived from the southern part. This finding revealed that the distribution of C. incana had been artificially influenced. Several haplotypes were confirmed by sequence variations in the northern populations, but only one haplotype in the southern populations, suggesting that C. incana on the north island had separated early from the south island in Tsushima.

Intraspecific Phylogenetic Relationships of Caryopteris incana in the Tsushima Islands, Japan, Using DNA Sequence Analysis