1.4 Phylogenetic analysis
The maximum likelihood (ML), Bayesian inference (BI), maximum parsimony (MP) and neighbor-joining (NJ) methods were used for phylogenetic analysis. MAFFT software (Katoh & Standley, 2013) was used to align the complete chloroplast genome sequences of eight species of Cyatheaceae and one species of Cibotium , Cibotium barometz (Linn.) J. Sm. A phylogenetic tree was constructed using Cibotium barometz(Linn.) J. Sm. as an outgroup. When the ML, MP, and BI trees had been constructed, the whole chloroplast genome was screened in MrModelTest software to obtain the optimal nucleotide substitution model (GTR+I+G) selected based on the Akaike information criterion, and the relevant parameters were estimated. The ML tree was constructed by the software RAxML8.0.20 (Stamatakis, 2014), GTRGAMMAI was selected as the nucleotide substitution model, and the confidence of the branch was completed using the bootstrap analysis in autoMR. The BI tree was constructed by MrBayes v3.2.0 software (Ronquist et al., 2012) and was estimated by running 2,000,000 generations (Nst = 6, rates = invgamma). The MP tree was constructed in PAUP 4.0 software (Swofford, 2002) with the bootstrap value set to 1000. The NJ tree was constructed in MEGA7.0 software (Kumar et al., 2016), and the maximum composite likelihood algorithm was selected with the bootstrap value set to 1000 times. The resulting phylogenetic tree was viewed and edited in Figtree v 1.4.3 software.