2.5 Phylogenetic relationships of ribotypes
Phylogenetic relationships for the identified ribotypes were
reconstructed with Maximum Likelihood (ML) and Bayesian Inference (BI)
using MEGA v.6.5 (Kumar et al. , 2008) and MrBayes v.3.2.6
(Ronquist et al. , 2012). Primulina pteropoda (W.T.Wang)
Yan Liu was used as outgroup with sequences of nrDNA (Gao et al. ,
2015, Genbank with accession number DQ872827).
We inferred the optimal model of nucleotide substitution using
MrModeltest 2.3 (Nylander, 2004), based on the AIC (Akaike Information
Criteria) (Akaike, 1981). The most suitable model (GTR+I+G) was used in
both Maximum Likelihood (ML) and Bayesian inference (BI) analysis. ML
analysis was conducted using MEGA v.6.5 with the optimal substitution
model, and 1000 bootstrap (BS) replicates were carried out to assess the
support of the resulting groups. BI analysis was conducted using MrBayes
v.3.2.6. The Markov Chain Monte Carlo (MCMC) was run for 10 million
generations, sampling every 10,000 generations across four independent
Bayesian runs. The first 2500 trees (25% of total trees) were discarded
as burn-in, and the remaining trees were summarized in a 50%
majority-rule consensus tree with the posterior probabilities (PP).
Chain convergence was assessed by checking the effective sample size
(ESS) that was bigger than 200 for each parameter in Tracer v.1.6
(Rambaut &+’ Drummond, 2007), and the length and PP of each branch were
visualized by FIGTREE v.1.4.2 (Rambaut, 2009).