Evolutionary switches between two serine codon sets are driven by selection

Significance When a rare evolutionary event is observed, such as substitution of two adjacent nucleotides, the question emerges whether such rare changes are caused by mutational bias or by selection. Here we address this question through genome-wide analysis of double substitutions that lead to switch of the codon sets for the amino acid serine, the only one that is encoded by two disjoint sets of codons. We show that selection is the primary factor behind these changes. These findings suggest that short-term evolution of proteins is subject to stronger purifying selection than previously thought and has significant implications for methods of phylogenetic analysis.