DOI:10.1093/sysbio/syv008 Circumstances in Which Parsimony but not Compatibility will be Provably Misleading

Abstract.—Phylogenetic methods typically rely on an appropriate model of how data evolved in order to infer an accurate phylogenetic tree. For molecular data, standard statistical methods have provided an effective strategy for extracting phylogenetic information from aligned sequence data when each site (character) is subject to a common process. However, for other types of data (e.g., morphological data), characters can be too ambiguous, homoplastic, or saturated to develop models that are effective at capturing the underlying process of change. To address this, we examine the properties of a classic but neglected method for inferring splits in an underlying tree, namely, maximum compatibility. By adopting a simple and extreme model in which each character either fits perfectly on some tree, or is entirely random (but it is not known which class any character belongs to) we are able to derive exact and explicit formulae regarding the performance of maximum compatibility. We show that this method is able to identify a set of non-trivial homoplasy-free characters, when the number n of taxa is large, even when the number of random characters is large. In contrast, we show that a method that makes more uniform use of all the data—maximum parsimony—can provably estimate trees in which none of the origina