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).