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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
Benchmarking multi-rate codon models
PLoS ONE, Volume 5, No. 7, Article e11587, Year 2010
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Description
The single rate codon model of non-synonymous substitution is ubiquitous in phylogenetic modeling. Indeed, the use of a non-synonymous to synonymous substitution rate ratio parameter has facilitated the interpretation of selection pressure on genomes. Although the single rate model has achieved wide acceptance, we argue that the assumption of a single rate of non-synonymous substitution is biologically unreasonable, given observed differences in substitution rates evident from empirical amino acid models. Some have attempted to incorporate amino acid substitution biases into models of codon evolution and have shown improved model performance versus the single rate model. Here, we show that the single rate model of non-synonymous substitution is easily outperformed by a model with multiple non-synonymous rate classes, yet in which amino acid substitution pairs are assigned randomly to these classes. We argue that, since the single rate model is so easy to improve upon, new codon models should not be validated entirely on the basis of improved model fit over this model. Rather, we should strive to both improve on the single rate model and to approximate the general time-reversible model of codon substitution, with as few parameters as possible, so as to reduce model over-fitting. We hint at how this can be achieved with a Genetic Algorithm approach in which rate classes are assigned on the basis of sequence information content. © 2010 Delport et al.
Authors & Co-Authors
Delport, Wayne
United States, La Jolla
University of California, San Diego
Scheffler, Konrad
South Africa, Stellenbosch
Stellenbosch University
Gravenor, Mike B.
United Kingdom, Swansea
Swansea University Medical School
Muse, Spencer V.
United States, Raleigh
Nc State University
Pond, Sergei L.Kosakovsky
United States, La Jolla
University of California, San Diego
Statistics
Citations: 11
Authors: 5
Affiliations: 4
Identifiers
Doi:
10.1371/journal.pone.0011587
e-ISSN:
19326203
Research Areas
Genetics And Genomics