From the original Figures 3 and 4 only one has been kept and the legend rewritten. In fact, the whole paragraph changed to: “The newly proposed phylum Thaumarchaeota appears to be non-monophyletic as an outlying strain Candidatus Caldiarchaeum subterranum was assigned to this phylum according to the NCBI taxonomy. The NCBI assignment might reflect its position in some phylogenetic tree based on concatenated proteins, e.g., Figure 2 in […]. However, in the original paper reporting the discovery of this strain […] and in recent 16S rRNA studies, e.g., […], Candidatus Caldiarchaeum subterranum was proposed to make a new phylum Aigarchaeota. CVTrees support the introduction of this new phylum. A lineage modification of Candidatus Caldiarchaeum subterranum from Thaumarchaeota to Aigarchaeota would lead to a monophyletic Thaumarchaeota{7}.”
L146: No need to explain the 6+2 if it is properly explained in the figure legend. Figure 3 is redundant. I would recommend to avoid presenting different versions of the same tree; just the final tree is OK (use final/valid labels) and all important explanations in the text or legend. Perhaps the whole reasoning in Lines 142–180 is not so relevant for the current objective of comparing CVT, LTP, Bergeys? Or, perhaps, define this objective more clearly.