A Novel Test for Absolute Fit of Evolutionary Models Provides a Means to Correctly Identify the Substitution Model and the Model Tree

Assessment of Absolute Substitution Model Fit Accommodating Time-Reversible and Non-Time-Reversible Evolutionary Processes

The loss of information accompanying assessment of absolute fit of substitution models to phylogenetic data negatively affects the discriminatory power of previous methods and can make them insensitive to lineage-specific changes in the substitution process. As an alternative, I propose evaluating absolute fit of substitution models based on a novel statistic which describes the observed data without information loss and which is unlikely to become zero-inflated with increasing numbers of taxa. This method can accommodate gaps and is sensitive to lineage-specific shifts in the substitution process. In simulation experiments, it exhibits greater discriminatory power than previous methods. The method can be implemented in both Bayesian and Maximum Likelihood phylogenetic analyses, and used to screen any set of models. Recently, it has been suggested that model selection may be an unnecessary step in phylogenetic inference. However, results presented here emphasize the importance of model fit assessment for reliable phylogenetic inference.

Assessing topological congruence among concatenation-based phylogenomic approaches in empirical datasets

Assessing the effect of methodological decisions on the resulting hypotheses is critical in phylogenetics. Recent studies have focused on evaluating how model selection, orthology definition and confounding factors affect phylogenomic results. Here, we compare the results of three concatenated phylogenetic methods (Maximum Likelihood, ML; Bayesian Inference, BI; Maximum Parsimony, MP) in 157 empirical phylogenomic datasets. The resulting trees were very similar, with 96.7% of all nodes shared between BI and ML (90.6% for ML-MP and 89.1% for BI-MP). Differing nodes were predominantly those of lower support. The main conclusions of most of the studies agreed for the three phylogenetic methods and the discordance involved nodes considered as recalcitrant problems in systematics. The differences between methods were proportionally larger in datasets that analyze the relationships at higher taxonomic levels (particularly phyla and kingdoms), and independent of the number of characters included in the datasets. Note: a spanish version of this article is available in the Supplementary material (Supplementary material online).