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.
indica , S. austrotaiwanensis , S. 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).