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Finally, we present phylogenetic informativeness profiles for seven selected markers, revealing that the markers contain phylogenetic signal that spans the whole tree including the deeper branches.
In the phylogenetic trees, the deeper branches segregate the KIR from different species (Figure 6B).
Although almost 2000bp of sequence data were analyzed for the taxa included here, phylogenetic relationships at deeper branches in the phylogeny remain only poorly resolved.
However, the homoplasy index for the phylogenetic tree is high (0.7331, excluding uninformative characters) and strong bootstrap support is absent for many of the deeper branches.
Interestingly, all weak RP divisions (RP<50%) are within the Bacterial domain toward the tips of our tree of life, but the deeper branches are all strongly supported (Figure 2).
In both cases, support falls for deeper branches in the trees.
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They began as tiny rifts, but soon grew longer and deeper, branched, and interconnected.
However, families of either repeat type have been identified in deeper branching phyla among which Termotogae and Planctomycetes, plausibly the deepest branching phylum within the bacterial domain [ 58].
The deeper branching of the Thermoplasmatales within the Euryarchaeota will place it closer to the Crenarchaeota.
Accumulation of additional QSOX sequences might reveal slightly deeper branching between closely related plants.
Within Crenarchaeota, Pyrobaculum was indicated to be a deeper branch, and Aeropyrum branched in between the Pyrobaculum and Sulfolobus.
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