2.3 | Phylogenetic relationships
We inferred the optimal model of nucleotide substitution using MrModeltest v.2.3 (Nylander, 2004), based on the AIC (Akaike Information Criteria) (Akaike, 1981). The putative most suitable model (GTR+I+G) was used in inferring the phylogenetic relationships of the identified ribotypes, which was done through maximum likelihood (ML) and Bayesian inference (BI) trees (Gao et al., 2015; Genbank with accession number DQ872827). ML analysis of ribotypes was conducted using MEGA v.6.5 with the optimal substitution model and 1000 bootstrap replicates carried out to assess the support of the resulting groups. BI analysis of ribotypes was conducted using MrBayes v.3.2.6 (nst = 2, rates = equal) (Ronquist et al., 2012), using the optimal model of nucleotide substitutions inferred by AIC in PAUP v.4.0a164. The analysis began with a random tree using Markov Chain Monte Carlo (MCMC) chains with 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 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).