New Statistical Criteria Detect Phylogenetic Bias Caused by Compositional Heterogeneity

Molecular Biology and Evolution
David A DuchêneSimon Y W Ho


In statistical phylogenetic analyses of DNA sequences, models of evolutionary change commonly assume that base composition is stationary through time and across lineages. This assumption is violated by many data sets, but it is unclear whether the magnitude of these violations is sufficient to mislead phylogenetic inference. We investigated the impacts of compositional heterogeneity on phylogenetic estimates using a method for assessing model adequacy. Based on a detailed simulation study, we found that common frequentist criteria are highly conservative, such that the model is often rejected when the phylogenetic estimates do not show clear signs of bias. We propose new criteria and provide guidelines for their usage. We apply these criteria to genome-scale data from 40 birds and find that loci with severely non-homogeneous base composition are uncommon. Our results show the importance of using well-informed diagnostic statistics when testing model adequacy for phylogenomic analyses.


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Sep 30, 2015·Molecular Biology and Evolution·Sebastián DuchêneEdward C Holmes

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Feb 27, 2018·Bioinformatics·David A DuchêneSimon Y W Ho
Nov 15, 2017·Molecular Biology and Evolution·Sebastian HöhnaJeremy M Brown
Oct 14, 2017·Systematic Biology·David A DuchêneMark D B Eldridge
May 23, 2018·Genome Biology and Evolution·David A DuchêneSimon Y W Ho
Sep 20, 2019·Genome Biology and Evolution·Suha Naser-KhdourRobert Lanfear
Oct 18, 2018·Systematic Biology·Daisy A Shepherd, Steffen Klaere
Feb 3, 2021·Molecular Biology and Evolution·Robert Literman, Rachel Schwartz
Sep 12, 2021·Systematic Biology·David A DuchêneSimon Y W Ho

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