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Fig. S1 Parsimony networks of alleles at each locus.

Fig. S2 Summaries of the Bayesian clustering implemented by STRUCTURE.

Fig. S3 Summaries of the Bayesian clustering implemented by InStruct.

Fig. S4 Maximum likelihood tree of Cardamine nipponica and its closely related species based on concatenated sequences of all sites of 10 nuclear genes.

Table S1 Locality information for the samples and alleles at each locus

Table S2 Accession numbers of ITS used for phylogenetic analysis

Table S3 Sequences of primers used for PCR and sequencing

Table S4 Maximum likelihood estimates (MLEs) of demographic parameters of the IM model between Cardamine nipponica and C.  bellidifolia

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