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.