Intragenomic variation in non-adaptive nucleotide biases causes underestimation of selection on synonymous codon usage.
Patterns of non-uniform usage of synonymous codons vary across genes in an organism and between species across all domains of life.This codon usage bias (CUB) is due to a combination of non-adaptive (e.g.mutation biases) and adaptive (e.g.natural selection for translation efficiency/accuracy) evolutionary forces.Most models quantify the effects of