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).