Biologically inspired phylogenetic models strongly outperform the no common mechanism model

Abstract

But Tuffley and Steel (1997) introduced a model called No Common Mechanism (NCM), in which characters may - but are not required to - vary their relative rates independently, both within and between branches. Because the independent variation is taken only as a possibility, not as a requirement, NCM would apply to almost any situation, and so may be accepted as realistic. This is useful because Tuffley and Steel also showed that maximum likelihood under NCM selects the same trees as does parsimony. With the realistic NCM in the background, then, most parsimonious trees have greatest power to explain available observations. © 2011 The Author(s).