The effect of ambiguous data on phylogenetic estimates obtained by maximum likelihood and Bayesian inference.

ABSTRACT: Although an increasing number of phylogenetic data sets are incomplete, the effect of ambiguous data on phylogenetic accuracy is not well understood. We use 4-taxon simulations to study the effects of ambiguous data (i.e., missing characters or gaps) in maximum likelihood (ML) and Bayesian frameworks. By introducing ambiguous data in a way that removes confounding factors, we provide the first clear understanding of 1 mechanism by which ambiguous data can mislead phylogenetic analyses. We find that in both ML and Bayesian frameworks, among-site rate variation can interact with ambiguous data to produce misleading estimates of topology and branch lengths. Furthermore, within a Bayesian framework, priors on branch lengths and rate heterogeneity parameters can exacerbate the effects of ambigu

SUBMITTER: Lemmon AR 

PROVIDER: S-EPMC7539334 | biostudies-literature | 2009 Feb

REPOSITORIES: biostudies-literature