An Improved Codon Modeling Approach for Accurate Estimation of the Mutation Bias - Archive ouverte HAL Access content directly
Journal Articles Molecular Biology and Evolution Year : 2022

An Improved Codon Modeling Approach for Accurate Estimation of the Mutation Bias

Abstract

Phylogenetic codon models are routinely used to characterize selective regimes in coding sequences. Their parametric design, however, is still a matter of debate, in particular concerning the question of how to account for differing nucleotide frequencies and substitution rates. This problem relates to the fact that nucleotide composition in protein-coding sequences is the result of the interactions between mutation and selection. In particular, because of the structure of the genetic code, the nucleotide composition differs between the three coding positions, with the third position showing a more extreme composition. Yet, phylogenetic codon models do not correctly capture this phenomenon and instead predict that the nucleotide composition should be the same for all three positions. Alternatively, some models allow for different nucleotide rates at the three positions, an approach conflating the effects of mutation and selection on nucleotide composition. In practice, it results in inaccurate estimation of the strength of selection. Conceptually, the problem comes from the fact that phylogenetic codon models do not correctly capture the fixation bias acting against the mutational pressure at the mutation-selection equilibrium. To address this problem and to more accurately identify mutation rates and selection strength, we present an improved codon modeling approach where the fixation rate is not seen as a scalar, but as a tensor. This approach gives an accurate representation of how mutation and selection oppose each other at equilibrium and yields a reliable estimate of the mutational process, while disentangling the mean fixation probabilities prevailing in different mutational directions.
Fichier principal
Vignette du fichier
Mol. Biol. Evol.2022Latrille.pdf (869.52 Ko) Télécharger le fichier
Origin : Publisher files allowed on an open archive

Dates and versions

hal-03764538 , version 1 (30-08-2022)

Identifiers

Cite

Thibault Latrille, Nicolas Lartillot. An Improved Codon Modeling Approach for Accurate Estimation of the Mutation Bias. Molecular Biology and Evolution, 2022, 39, ⟨10.1093/molbev/msac005⟩. ⟨hal-03764538⟩
32 View
23 Download

Altmetric

Share

Gmail Facebook X LinkedIn More