University Of Tasmania
Browse
638 Woodhams.pdf (294.92 kB)
Download file

A new hierarchy of phylogenetic models consistent with heterogeneous substitution rates

Download (294.92 kB)
journal contribution
posted on 2023-05-18, 09:37 authored by Woodhams, MD, Fernandez-Sanchez, J, Jeremy SumnerJeremy Sumner
When the process underlying DNA substitutions varies across evolutionary history, some standard Markov models underlying phylogenetic methods are mathematically inconsistent. The most prominent example is the general time reversible model (GTR) together with some, but not all, of its submodels. To rectify this deficiency, nonhomogeneous Lie Markov models have been identified as the class of models that are consistent in the face of a changing process of DNA substitutions regardless of taxon sampling. Some well-known models in popular use are within this class, but are either overly simplistic (e.g. the Kimura two-parameter model) or overly complex (the general Markov model). On a diverse set of biological data sets, we test a hierarchy of Lie Markov models spanning the full range of parameter richness. Compared against the benchmark of the ever-popular GTR model, we find that as a whole the Lie Markov models perform well, with the best performing models having eight to ten parameters and the ability to recognise the distinction between purines and pyrimidines.

History

Publication title

Systematic Biology

Volume

64

Issue

4

Pagination

638-650

ISSN

1063-5157

Department/School

School of Natural Sciences

Publisher

Taylor & Francis Inc

Place of publication

325 Chestnut St, Suite 800, Philadelphia, USA, Pa, 19106

Rights statement

© The 2015 Author(s) Licensed under Creative Commons Attribution 4.0 International (CC BY 4.0) http://creativecommons.org/licenses/by/4.0/

Repository Status

  • Open

Socio-economic Objectives

Expanding knowledge in the mathematical sciences