Contributions of ILS and introgression to genetic variation
QuIBL analysis indicated evidence of introgression at 32% (34/105) of trios and 46% (227/489) of SNPs (Table S4). In addition, Patterson’sD and f4 inferred multiple significant interspecies introgression events. The most frequently introgressed species wereS. barbata and S. taiwanensis , which introgressed with 5 and 4 species, respectively (Fig. S4). By contrast, fb statistics revealed only one introgression event, which occurred between S. barbata and the ancestor of the group containing S. indicaS. austrotaiwanensisS. tashiroi , S. hsiehii, and S. playfairii (Fig. 3B). The fb statistics showed significant signals of gene flow in LYC , OPCL1 , andPHYB (Fig. 3A; Table 1). These genes were associated with two [BIO2 (mean diurnal range) and BIO18 (precipitation of warmest quarter)], six [BIO2, BIO4 (temperature seasonality), BIO5 (maximum temperature of warmest month), BIO6 (minimum temperature of coldest month), BIO17 (temperature annual range) and BIO18], and one (BIO2) environmental variables related to precipitation and temperature, respectively (Table 1). A recent admixture between S. tashiroiand S. hsiehii was inferred by TreeMix (Fig. 3B; Fig. S5). Finally, the results of PhyloNetworks analysis indicated that the data were best fit with the lowest BIC by the model containing one reticulation event, and all bootstrap replications supported the introgression between the ancestor of S. playfairii and S. taiwanensis (Fig. 3B).