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.