The Effect of Ambiguous Data on Phylogenetic Estimates Obtained by Maximum Likelihood and Bayesian Inference

• DOI: 10.1093/sysbio/syp017
• Publication Date: 2009-05-23T00:36:28Z
• Authors: Alan R. Lemmon; Jeremy M. Brown; Kathrin Stanger-Hall; Emily Moriarty Le...
• Keywords: Divergence (linguistics); Phylogenetic comparative methods

Abstract Although an increasing number of phylogenetic data sets are incomplete, the effect ambiguous on accuracy is not well understood. We use 4-taxon simulations to study effects (i.e., missing characters or gaps) in maximum likelihood (ML) and Bayesian frameworks. By introducing a way that removes confounding factors, we provide first clear understanding 1 mechanism by which can mislead analyses. find both ML frameworks, among-site rate variation interact with produce misleading estimates topology branch lengths. Furthermore, within framework, priors lengths heterogeneity parameters exacerbate data, resulting strongly bipartition posterior probabilities. The magnitude direction bias function taxonomic distribution characters, strength topological support, whether model correctly specified. results this have major implications for all analyses rely accurate lengths, including divergence time estimation, ancestral state reconstruction, tree-dependent comparative methods, analysis, hypothesis testing, phylogeographic analysis.