Figure 3b link
C2 and NirS domain trees reconstructed exclusively from ORFs containing both domains inverts the relative placement of Chloroflexi, suggesting that sampling and phylogenetic noise are likely responsible for the observed differences in these phylogenies (Fig. S3, Fig. S4). Additionally, there are notable differences in placement among subclades within the Proteobacteria, suggesting that patterns unrelated to Chloroflexi evolution may be polarizing the relative placements of groups in the tree. This lack of robustness caused by alternative sampling, combined with poor support values within the polyphyletic clade or between this clade and the Proteobacteria, suggest that the differences in tree topology may be artefactual, and not reflective of gene reticulation events. There seems to be no reason to reject the null hypothesis that the C2 and NirS domains have the same evolutionary origins within Chloroflexi.
The inferred phylogeny for C1 shows a much different evolutionary history than the other two domains (Fig. 4). In contrast to the domain trees for C2 or NirS, the C1 tree shows sequences from Nitrospirae and Nitrospinae grouping together within a large clade of Chloroflexi C1 domains. Additional Chloroflexi sequences group with a small number of more distantly related Proteobacteria. However, the placement and taxonomic representation of Proteobacteria in the C1 tree is different from that seen in the other domain trees.