We offer the phrase "short-branch exclusion" (SBE) to identify this associated artifact.
Similar trends were observed using long-branch exclusion, but patterns were neither as strong nor as clear.
A detailed investigation shows that this clade can be explained by what we call "short-branch exclusion," a phylogenetic artifact integrally associated with "long-branch attraction".
For Pinus chloroplast genomes, removal of variable sites appears to be more effective than long-branch exclusion for clarifying phylogenetic hypotheses.
I suggest that substitution of iron or vanadium for molybdenum to form the group III enzymes (probably independently [ 114]) can also accelerate evolution and cause similar long-branch exclusion.
For example, the strict application of long-branch exclusion serves to minimize long-branch attraction artefacts, yet phylogenetic hypotheses may still be misled by evolutionary patterns at highly variable sites since all sites are still included in the analysis.
When long-branch exclusion was used in combination with variable site removal (specifically partitions A136665 and A133065), trends were reflective of variable site removal alone for partition size A136665 in subsection Contortae and P. merkusii / P. latteri (Table 2).
At the same time, the impact of long-branch exclusion was less pronounced, suggesting that long-branch attraction artefacts are not prevalent at these levels of the Pinus phylogeny.
Maximum likelihood phylogenetic analyses were performed as described above for the full alignment for each strategy of long-branch exclusion on each of three partition sizes of interest (full alignment, A136665, A133065, as discussed in Results).
Based on the slopes of regression lines of corrected vs. uncorrected pairwise distances, saturation decreased similarly both with OV-based variable site removal and long-branch exclusion strategies (Table 3, Additional File 7).
Our approach is similar to previous efforts, but focused on two fundamental and complementary strategies, variable site removal and long-branch exclusion, and explored the dynamics of tree topology and support values to measure their impact on an infrageneric phylogenetic analysis.
