title: A generalized mechanistic codon model.
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.
authors: Department of Ecology and Evolution, Biophore, University of Lausanne, 1015 Lausanne, SwitzerlandSwiss Institute of Bioinformatics, Genopode, Quartier Sorge, 1015 Lausanne, Switzerland.
authors: Maryam
authors: M
authors: Zaheri
authors: Department of Ecology and Evolution, Biophore, University of Lausanne, 1015 Lausanne, SwitzerlandSwiss Institute of Bioinformatics, Genopode, Quartier Sorge, 1015 Lausanne, Switzerland.
authors: Linda
authors: L
authors: Dib
authors: Department of Ecology and Evolution, Biophore, University of Lausanne, 1015 Lausanne, SwitzerlandSwiss Institute of Bioinformatics, Genopode, Quartier Sorge, 1015 Lausanne, Switzerland nicolas.salamin@unil.ch.
authors: Nicolas
authors: N
authors: Salamin
mesh_terms: D000465:Algorithms; D019943:Amino Acid Substitution; D003062:Codon / Q000235:genetics*; D003198:Computer Simulation; D019143:Evolution, Molecular; D016013:Likelihood Functions; D008390:Markov Chains; D008957:Models, Genetic; D059645:Mutation Rate
chemical_list: D003062:Codon
keywords: Kronecker product; Markov model; codon models; multiple substitutions; phylogenetics; positive selection