Multiclass Synonymous Substitution

Correcting for Global Synonymous Selection Improves the Accuracy of Episodic Positive Selection Inference

The ratio of nonsynonymous to synonymous substitution rates ({omega}) constitutes a fundamental parameter for inferring adaptive protein evolution, predicated upon the assumption that synonymous substitutions are selectively inert. This premise, however, is increasingly untenable given evidence of selection acting on synonymous substitutions, driven by various biological processes such as translational efficiency and mRNA stability. In this study, we demonstrate that unmodelled synonymous...