Cases in which Parsimony or Compatibility Methods will be Positively Misleading

TLDR

The study aims to establish a rigorous framework for assessing the statistical consistency of phylogenetic inference methods. By examining simple three‑ and four‑species, two‑state character scenarios, the authors determine the conditions under which Camin‑Sokal parsimony, compatibility, and Farris’s unrooted Wagner tree parsimony fail to converge to the true tree as data increase. They find that these methods become statistically inconsistent whenever parallel changes outnumber informative nonparallel changes, and that inconsistency can arise even with unlikely changes if lineage rates differ markedly.

Abstract

For some simple three- and four-species cases involving a character with two states, it is determined under what conditions several methods of phylogenetic inference will fail to converge to the true phylogeny as more and more data are accumulated. The methods are the Camin-Sokal parsimony method, the compatibility method, and Farris's unrooted Wagner tree parsimony method. In all cases the conditions for this failure (which is the failure to be statistically consistent) are essentially that parallel changes exceed informative, nonparallel changes. It is possible for these methods to be inconsistent even when change is improbable a priori, provided that evolutionary rates in different lineages are sufficiently unequal. It is by extension of this approach that we may provide a sound methodology for evaluating methods of phylogenetic inference.