2.4 Divergence Time Estimate
There are currently no well-documented fossils in Liliaceae, and thus fossil constraints were limited to Liliales. We used 10 populations ofNotholirion plastomes and 137 other plastomes to calibrate the divergence time of Notholirion (Supplementary Table 2) . Referring to previous studies(H. T. Li et al., 2019; J. Li et al., 2022; D. F. Xie et al., 2020) and to minimize the effects of missing data, we only used combined single-copy CDS genes data set derived from 147 plastomes for the estimation of divergence time. The common CDS of 147 plastomes were extracted, respectively aligned, and then concatenated as the plastome CDS dataset, using PhyloSuite v1.2.2(D. Zhang et al., 2020). Estimations of divergence time were performed using an uncorrelated lognormal relaxed molecular clock method implemented in the BEAST 1.10.4 program(Suchard et al., 2018). BEAUti was used to set criteria for analyses where we used a GTR + G substitution model selected by ModelFinder and a Yule process(Gernhard, 2008). An optimal partitioning scheme was determined using the PartitionFinder 2 program(Lanfear, Frandsen, Wright, Senfeld, & Calcott, 2017) and six calibration points were used to calibrate time (Supplementary Table 3) . MCMC analyses were run for 100 million generations with parameters sampled every 10,000 generations after discarding the first 10% of generations as burnin. The convergence of the stationary distribution was accessed by ESS values (>200) using the Tracer v.1.7.11. Maximum clade credibility (MCC) trees were produced using TreeAnnotator v1.8.4(Helfrich, Rieb, Abrami, Lücking, & Mehler, 2018) and visualized in FigTree v1.4.2(Rambaut, 2014).