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

journal contribution
posted on 2023-05-17, 11:42 authored by Jeremy SumnerJeremy Sumner, Peter JarvisPeter Jarvis, Fernandez-Sanchez, J, Kaine, BT, Woodhams, MD, Barbara HollandBarbara Holland

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.

Funding

Australian Research Council

History

Publication title

Systematic Biology

Volume

61

Issue

6

Pagination

1069-1074

ISSN

1063-5157

Department/School

School of Natural Sciences

Publisher

Oxford University Press

Place of publication

United Kingdom

Rights statement

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

Repository Status

  • Restricted

Socio-economic Objectives

Expanding knowledge in the mathematical sciences

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