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).