Phylogenetic analyses
The whole chloroplast genome matrix was aligned using MAFFT version 7.1 (Yamada et al. 2016). Only one inverted repeat region was used in the phylogenetic analyses. Two matrixes were prepared, one including all gaps, and another removed gaps using trimAl (Capella-Gutiérrez et al. 2009) by “-gt 0.4 -st 0.001 -cons 40”. Maximum Likelihood (ML) and Bayesian Inference (BI) methods were used to reconstruct phylogenetic trees. No nucleotide positions were excluded from analyses. The ML tree analyses and bootstrap estimation of clade support were conducted with RAxML version 8.2.10 (Stamatakis et al. 2008). These analyses used the GTR substitution model with gamma-distributed rate heterogeneity among sites and the proportion of invariable sites estimated from the data. Support values for the node and clade were calculated from 1000 bootstrap replicates. Bootstrap support (BS) ≥ 70 is considered as well supported (Hillis & Bull 1993). The BI analyses were performed using MrBayes version 3.2.6 (Ronquist & Huelsenbeck 2003), with DNA substitution models selected for each gene partition by the Bayesian information criterion (BIC) using jModeltest version 2.1.10 (Darriba et al. 2012; Guindon & Gascuel 2003). Markov Chain Monte Carlo (MCMC) analyses were run in MrBayes for 10,000,000 generations, with two simultaneous runs, and each run comprising four incrementally heated chains. The BI analyses were started with a random tree and sampled every 1000 generations. The number of generations for the three datasets was sufficient because the average standard deviation of split frequencies for the datasets was lower than 0.005, and Potential Scale Reduction Factor (PSRF) of Convergence Diagnostic (Gelman & Rubin 1992) for the datasets was 1.00. The first 25% of the trees were discarded as burn-in, and the remaining trees were used to generate a majority-rule consensus tree. Posterior probability values (PP) ≥ 0.95 were considered as well supported (Alfaro et al. 2003; Erixon et al. 2003; Kolaczkowski & Thornton 2007). Both ML and BI analyses, as well as jModeltest, were performed at the CIPRES Science Gateway (http://www.phylo.org).