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Many commonly used models of molecular evolution assume homogeneous nucleotide frequencies. A deviation from this assumption has been shown to cause problems for phylogenetic inference. However, some claim that only extreme heterogeneity affects phylogenetic accuracy and suggest that violations of other model assumptions, such as variable rates among sites, are more problematic. In order to explore the interaction between compositional heterogeneity and variable rates among sites, I reanalyzed 3 real heterogeneous datasets using several models. My Bayesian inference recovers accurate topologies under variable rates-among-sites models, but fails under some models that account for compositional heterogeneity. I also ran simulations and found that accounting for rates among sites improves topology accuracy in compositionally heterogeneous data. This indicates that in some cases, models accounting for among-site rate variation can improve outcomes for data that violates the assumption of compositional homogeneity.

The Interaction between Base Compositional Heterogeneity and Among-Site Rate Variation in Models of Molecular Evolution