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Is the general time-reversible model bad for molecular phylogenetics?


Sumner, JG and Jarvis, PD and Fernandez-Sanchez, J and Kaine, BT and Woodhams, MD and Holland, BR, Is the general time-reversible model bad for molecular phylogenetics?, Systematic Biology, 61, (6) pp. 1069-1074. ISSN 1063-5157 (2012) [Refereed Article]

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Copyright The Author(s) 2012. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved.

DOI: doi:10.1093/sysbio/sys042


The general time-reversible (GTR) model (Tavaré 1986) has been the workhorse of molecular phylogenetics for the last decade. GTR sits at the top of the ModelTest hierarchy of models (Posada and Crandall 1998) and, usually with the addition of invariant sites and a gamma distribution of rates across sites, is currently by far the most commonly selected model for phylogenetic inference (see Table 1).

However, a recent publication (Sumner et al. 2012) shows that GTR, along with several other commonly used models, has an undesirable mathematical property that may be a cause of concern for the thoughtful phylogeneticist. In mathematical terms, the problem is simple: matrix multiplication of two GTR substitution matrices does not return another GTR matrix. It is the purpose of this article to give examples that demonstrate why this lack of closure may pose a problem for phylogenetic analysis and thus add GTR to the growing list of factors that are known to cause model misspecification in phylogenetics.

Item Details

Item Type:Refereed Article
Keywords:general time-reversible model, GTR, molecular phylogenetics, phylogenetic inference
Research Division:Mathematical Sciences
Research Group:Applied mathematics
Research Field:Biological mathematics
Objective Division:Expanding Knowledge
Objective Group:Expanding knowledge
Objective Field:Expanding knowledge in the mathematical sciences
UTAS Author:Sumner, JG (Dr Jeremy Sumner)
UTAS Author:Jarvis, PD (Dr Peter Jarvis)
UTAS Author:Kaine, BT (Mr Bodie Kaine)
UTAS Author:Woodhams, MD (Dr Michael Woodhams)
UTAS Author:Holland, BR (Professor Barbara Holland)
ID Code:77706
Year Published:2012
Funding Support:Australian Research Council (DP0877447)
Web of Science® Times Cited:31
Deposited By:Mathematics and Physics
Deposited On:2012-05-18
Last Modified:2017-11-15
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