Fundamental Sources of Codon Bias

Differences in genome-wide frequencies of synonymous codons have been attributed to various biophysical mechanisms such as tRNA concentration and ribosomal affinity. Main features in the bias appear to be due to a balance between protein production efficiency and accuracy. In an effort to develop a comprehensive theoretical model of this phenomenon, we have developed a quasi-species evolutionary model which captures several of these main influences and predicts the frequencies of genomic codons with high accuracy. The model consists of a deterministic description of the evolution of independent codons under the influence of biophysically-motivated forms of selection, and as a result, the model parameters hold physical interpretability.