Fig. 6

Flowchart of rDNA consensus secondary structure sequence alignment and analyses. Step 1. Multiple alignment guided by secondary structure information detects paired, unpaired and regions of ambiguous alignment (RAAs). Step 2. The RAAs are excluded from the alignment for the first set of Bayesian and ML inferences. Two Bayesian analyses were run, considering either a single model for the concatenated loop and stems or separate substitution models for each of these partitions. Step 3. Bayes factors estimated by Harmonic Mean and AICM strongly favor the partitioned model. Step 4. Partitioned RAxML analyses were run. Step 5. Regions of ambiguous alignment (RAAs) were aligned individually using a gap opening cost of four and equally weighted gap extension and substitutions [48] and Markov chain stationary trees from Bayesian analyses as guide trees. Step 6. The resulting concatenated alignment was filtered using Aliscore. Step 7. Bayesian and ML analyses employing RAAs alignment as a third partition resulted in topologies largely congruent to those of the two partition analyses, but their nodal support was higher in most cases