Cases in which Parsimony or Compatibility Methods will be Positively Misleading

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.