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Fig. S1 TCS networks of (a) chlorotypes and (b) general ITS ribotypes (see Table S2).

Fig. S2 Mismatch distribution analyses of the five cpDNA clades showing histogram of observed mismatch frequencies and best-fit curve of the sudden expansion model.

Table S1 Locations of populations of Hippophae rhamnoides sampled, sample sizes (n), numbers of different cpDNA haplotypes and ITS ribotypes recorded in each population, and estimates of gene diversity (h) and nucleotide diversity (π) in percent

Table S2 List of the general ITS types grouped by TCS after collapsing sequences that differ only by ambiguous sites

Table S3 The divergence times of major cpDNA and ITS phylogenetic nodes (Fig. 2)

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