Divergence time among Embothrium coccineum genetics
groups
To estimate divergence times among E. coccineum genetic groups,
we implemented a Bayesian multispecies coalescent model (Rannala and
Yang, 2003) using the DT_dataset. For this purpose, we calibrated the
molecular clock using the following data: 1) a crown age of the
Embothrieae tribe of 66 millions of years (My), with a lower limit of 56
My and an upper limit of 75 My (Sauquet et al., 2009) using a lognormal
distribution; 2) a generation time of 10 years per individuals
(following A. Bertin, personal observation). The analyses were conducted
with the coalescent simulator SNAPP v.1.3.0 (Bryant et al., 2012),
included in the package BEAST v.2.4.5 (Bouckaert et al., 2014). Species
trees were inferred directly with no prior grouping assignment. We used
SNAPP with four independent runs of 2,000,000 generations with a
sampling every 200 generations each. The results (i.e., ESS
> 300) were checked for mixing for all parameters with
Tracer v1.7 (Rambaut et al., 2018) and convergence of split frequencies
among runs (Supplementary Figure 2) with the R package rwty (Warren et
al. 2019). The final trees from each run (corresponding to the 95%
highest posterior density (HPD), after discarding a 10% burn-in of tree
topologies) were combined and subsequently summarized using a maximum
credibility tree with TreeSetAnalyser v.2.4.5. This species tree was
visualized as a cloudgram with DensiTree v.2.2.7 (Bouckaert, 2010).