We failed to find significant results on the impact of outgroup branch lengths and uncertainty in polarization on the neontological trees (Fig. 5A-C), except on some trees built from the symmetrical reference topology.
The effect of outgroup branch length appears to be much stronger on paleontological trees, perhaps because of the shorter branches in the ingroup. Tests on a non-ultrametric version of the equiprobable tree (Fig. 5D) with a variable outgroup branch lengths show that the performance of all methods decreases when outgroup branch length increases (Fig. 7; Table 2). Results of ordered parsimony and 3ta are very similar, with unordered parsimony performing much more poorly. 3ta is more sensitive to outgroup branch length, an effect that might be linked to reversal treatment, but that in any case confirms our second hypothesis. It is however surprising to see that an incorrect polarization has so little effect on resolving power and artefactual resolution.