A generalized mechanistic codon model.

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Serval ID
serval:BIB_5ADE075B1CFC
Type
Article: article from journal or magazin.
Collection
Publications
Title
A generalized mechanistic codon model.
Journal
Molecular Biology and Evolution
Author(s)
Zaheri M., Dib L., Salamin N.
ISSN
1537-1719 (Electronic)
ISSN-L
0737-4038
Publication state
Published
Issued date
2014
Volume
31
Number
9
Pages
2528-2541
Language
english
Abstract
Models of codon evolution have attracted particular interest because of their unique capabilities to detect selection forces and their high fit when applied to sequence evolution. We described here a novel approach for modeling codon evolution, which is based on Kronecker product of matrices. The 61 × 61 codon substitution rate matrix is created using Kronecker product of three 4 × 4 nucleotide substitution matrices, the equilibrium frequency of codons, and the selection rate parameter. The entities of the nucleotide substitution matrices and selection rate are considered as parameters of the model, which are optimized by maximum likelihood. Our fully mechanistic model allows the instantaneous substitution matrix between codons to be fully estimated with only 19 parameters instead of 3,721, by using the biological interdependence existing between positions within codons. We illustrate the properties of our models using computer simulations and assessed its relevance by comparing the AICc measures of our model and other models of codon evolution on simulations and a large range of empirical data sets. We show that our model fits most biological data better compared with the current codon models. Furthermore, the parameters in our model can be interpreted in a similar way as the exchangeability rates found in empirical codon models.
Keywords
codon models, phylogenetics, multiple substitutions, positive selection, Markov model, Kronecker product
Pubmed
Web of science
Open Access
Yes
Create date
20/11/2014 11:17
Last modification date
20/08/2019 15:13
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