2.3 Phylogenetic analyses
The phylogeny reconstruction based on two databases of haplotypes
(ITS and cpDNA sequences) were performed using Bayesian inference
(BI) and maximum likelihood (ML). Gaps were treated as missing data
during the tree searches. The two programs MrBayes version 3.2(Ronquist
et al., 2012) and RAxML
v.8(Stamatakis, 2014) were used to conduct BI and ML analyses. The best
model for ITS and cpDNA were both GTR+G (BI and ML) inferred by
ModelFinder(Kalyaanamoorthy, Minh, Wong, von Haeseler, & Jermiin, 2017)
based on the Akaike information criterion (AIC). Markov chain Monte
Carlo (MCMC) method was used for BI and set to run 10 million
generations, sample every 1,000 generations, discarde 25% of the trees
as burn-in. The convergence of MCMC inference was evaluated using Tracer
v.1.7.11 to ensure sufficient samples (ESS > 200) by
checking the ESS (Effective Sample Size) value. Besides, we ran RAxML onITS and cpDNA with 1000 bootstrap replicates. Finally, BI
posterior probabilities (BI PP) and ML bootstrap support (ML BS) were
presented at the nodes separately.