Estimation of divergent times and phylogeographical
history
Dating analyses were conducted using Markov Chain Monte Carlo (MCMC)
methods in BEAST version 2.4 (Bouckaert et al. 2014), which was
performed at the CIPRES Science Gateway (http://www.phylo.org). The
setting parameters in BEAUti, we chose “BEAST model test” for “Site
model”, “Relaxed Clock Log Normal” for “Clock model”, and “Yule
Model” for speciation. Meanwhile, we selected two crown nodes for
calibrations from published data using the CladeAge package (Matschiner
et al. 2016). (1) The Lobelia thuliniana – L.
columnaris clade was 8.0 Mya (sigma 1.0, offset: 0.0), and (2)Lobelia laxiflora - L. columnaris clade was 21 Mya (sigma
2.0, offset: 0.0) (Chen et al. 2016; Knox 2014). For reconstructing the
phylogeographical history of L. columnaris , a plastome phylogeny
of the L. thuliniana – L. columnaris clade
including 22 samples of L. columnaris and five outgroups was
estimated in BEAST2 with “beast-classic package” of BEAUti. For each
dataset, MCMC ran 200,000,000 generations and sampled every 20,000
generations. The first 5,000 generations were removed as “Pre Burnin”.
Log output of the BEAST analysis was evaluated using Tracer version 1.6.
Effective sample sizes (ESS) of all parameters were more than 200,
indicating that the estimations were confident. Maximum clade
credibility (MCC) tree was generated using TreeAnnotator by setting
“Mean heights” for the “Node heights”. The MCC tree was visualized
using FigTree version 1.4.2
(http://tree.bio.ed.ac.uk/software/figtree/).