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A new hierarchy of phylogenetic models consistent with heterogeneous substitution rates
journal contribution
posted on 2023-05-18, 09:37 authored by Woodhams, MD, Fernandez-Sanchez, J, Jeremy SumnerJeremy SumnerWhen 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 BiologyVolume
64Issue
4Pagination
638-650ISSN
1063-5157Department/School
School of Natural SciencesPublisher
Taylor & Francis IncPlace of publication
325 Chestnut St, Suite 800, Philadelphia, USA, Pa, 19106Rights 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