Data from: Phylogenetic, population structure, and population demographic analyses reveal that Vicia sepium in Japan is native and not introduced

Vicia sepium (bush vetch) is a perennial legume widely distributed
throughout the Eurasian continent. However, its distribution in Japan is
limited to Mt. Ibuki and small parts of central and southern Hokkaido.
Therefore, each Japanese V. sepium lineage has been considered to have
been introduced separately from Europe. Here, we examined whether the
species was introduced or not on the basis of cpDNA sequences and
genome-wide SNPs from Japanese and overseas samples. Both the cpDNA
haplotype network and the nuclear DNA phylogenetic tree showed that
Japanese V. sepium is monophyletic. Furthermore, although the nuclear DNA
phylogenetic tree also showed that each lineage is clearly monophyletic,
genetic admixture of the genetic cluster dominated in the Hokkaido lineage
was also detected in the Mt. Ibuki lineage. Population divergence analysis
showed that the two lineages diverged during the last glacial period. The
Mt. Ibuki lineage showed a sudden population decline 300–400 years ago,
indicating that some anthropogenic activity might be involved, while the
Hokkaido lineage showed a gradual population decline from 5,000 years ago.
Consequently, these two lineages show low current genetic diversity
compared with overseas lineages. These results show that the Japanese V.
sepium is not introduced but is native.