*2.4. Contemporary Gene Flow*

In *H. chrysotricha* populations from the TIL region, the proportion of individuals that originated from within the same site ranged from 68% (IP04) to 81% (WM02), with an average value of 72% (see BAYESASS, Table S4). In contrast, rates of gene flow (or 'migration', *m*) between populations were low to moderate, and in the majority of populations no more than 5% of the individuals were exchanged with other populations (Table S4). Similarly, in the ZA region, populations largely consisted of individuals originating from the same site (73% on average) (see BAYESASS, Table S5). Nevertheless, the average rate of interpopulation gene flow in the ZA region (*m*ZA = 0.027) was significantly higher than in the TIL region (*m*TIL = 0.019; *p* = 0.003). The DIVMIGRATE method also suggested that the relative migration rate was significantly higher in the ZS region than in the TIL region (*rm*ZA = 0.349, *rm*TIL = 0.252, *p* < 0.01) (Tables S6 and S7). In addition, we observed significant asymmetric gene flow patterns in 10 out of the 16 populations in the TIL region, and 4 out of the 11 populations in the ZA region (Figures 3 and 4).

**Figure 2.** STRUCTURE analysis of 101 individuals (11 populations) of *Hedyotis chrysotricha* from the Zhoushan Archipelago (ZA) region, based on RAD-Seq-derived single nucleotide polymorphism (SNP) data. (**A**) Plots of the mean posterior probability [LnP(*D*)] values of each *K* and (**B**) the corresponding Δ*K* statistics. (**C**) Histogram of the STRUCTURE analysis for the model with *K* = 2 (showing the highest Δ*K*). A vertical bar represents a single individual, and each color corresponds to a suggested cluster (Cluster I: blue; Cluster II: orange). The *x*-axis corresponds to population codes. The *y*-axis presents the estimated membership coefficient (*Q*) for each individual in the two clusters.
