Figure 3b shows a balanced tree, but the trees depicted here are unbalanced because the major branches do not contain an equal number of species (i.e., one branch from the root contains only one species, H, whereas the other branch includes species G, F, E, D, C, B, and A).
HemYs from Chloroflexus aurantiacus and Chloroflexus aggregans branch from the root of the plant PPO2 clade (fig. 4).
Also notable are the vertical swaths of failed tests centered near α = 0.9, 0.75, and 0.65 for A″ respectively located at distances 0.75, 0.5, and 0.25 along the branch from the root to A′.
One starts with a simple tree T 1 invariant under permutations of the gene assignments to tips (a palm tree, with a branch from the root to the last common ancestor of Q and branches of equal length from the last common ancestor to each member of Q).
Subfamilies were defined as the most internal branch from the root node that formed a monophyletic group which was supported by greater than >70% bootstrap support, shared identical taxon composition across all three phylogenetic methods, and contained a representative fungal NRPS.
Fungal NRPS subfamilies were characterized as monophyletic groups defined by the most internal branch from the root above a bootstrap cutoff level (we chose 70%) [ 115, 116] that also shared identical taxon composition across all three phylogenetic methods and had fungal NRPS representation (Additional file 6).
Mapping a quartet method to rooted three taxa trees is straightforward once the root in the reconstructed topology is treated as a special label or taxon with a "virtual" branch from the true root to this "root" taxon.
I therefore suggest that carotenoid biosynthetic pathway evolution might more representatively be envisioned as a "bramble", where interior nodes branching from the root are highly reticulated due to non-vertical modes of evolution.
- The branches from the root of (V, I) to V and I are relatively shorter than the branches from the root of (V, I) to other peripheral nodes.
