Effects of nucleotide composition bias on the success of the parsimony criterion in phylogenetic inference

Convergence in nucleotide composition (CNC) in unrelated lineages is a factor potentially affecting the performance of most phylogeny reconstruction methods. Such convergence has deleterious effects because unrelated lineages show similarities due to similar nucleotide compositions and not shared histories. While some methods (such as the LogDet/paralinear distance measure) avoid this pitfall, the amount of convergence in nucleotide composition necessary to deceive other phylogenetic methods has never been quantified. We examined analytically the relationship between convergence in nucleotide composition and the consistency of parsimony as a phylogenetic estimator for four taxa. Our results show that rather extreme amounts of convergence are necessary before parsimony begins to prefer the incorrect tree. Ancillary observations are that (for unweighted Fitch parsimony) transition/transversion bias contributes to the impact of CNC and, for a given amount of CNC and fixed branch lengths, data sets exhibiting substantial site-to-site rate heterogeneity present fewer difficulties than data sets in which rates are homogeneous. We conclude by reexamining a data set originally used to illustrate the problems caused by CNC. Using simulations, we show that in this case the convergence in nucleotide composition alone is insufficient to cause any commonly used methods to fail, and accounting for other evolutionary factors (such as site-to-site rate heterogeneity) can give a correct inference without accounting for CNC.