DOI: 10.1101/460121Nov 2, 2018Paper

The Prevalence and Impact of Model Violations in Phylogenetics

BioRxiv : the Preprint Server for Biology
Suha Naser-KhdourRobert Lanfear


In phylogenetic inference, we commonly use models which assume that sequence evolution is stationary, reversible and homogeneous (SRH). Although such assumptions are often criticized, the extent of SRH violations and their effects on phylogenetic inference are not well understood. Here, we extend the matched-pairs test of symmetry to assess the scale and impact of SRH model violations on 3,572 partitions from 35 published phylogenetic datasets. We show that many partitions (39.5%) reject the SRH assumptions, and that in most datasets, phylogenies inferred from all partitions differ significantly from those inferred using the subset of partitions that do not reject the SRH assumptions. These results suggest that the extent and effects of model violation in phylogenetics may be substantial. They highlight the importance of testing for model violations and possibly excluding partitions that violate models prior to tree reconstruction. They also suggest that further effort in developing models that do not require SRH assumptions could lead to large improvements in the accuracy of phylogenomic inference. The scripts necessary to perform the analysis are available in, and the new tests we describe ...Continue Reading

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