Success of Parsimony in the Four‐Taxon Case: Long‐Branch Repulsion by Likelihood in the Farris Zone

Abstract

The accuracy of phylogenetic methods is reinvestigated for the four-taxon case with a two-edge rate and a three-edge rate. Unlike previous studies involving computer simulations, the two-edge rate relates to branches that are sister taxa in the model tree. As with previous studies, certain methods are found to behave inaccurately in a portion of the parameter space where the two-edge rate is proportionally large. This phenomenon, to which parsimony is immune, is termed "long-branch repulsion" and the region of poor performance is called the Farris Zone. Maximum likelihood methods are shown to be particularly prone to failure when closely related taxa have long branches. Long-branch repulsion is demonstrated with an empirical case involving Strepsiptera and Diptera.