Natural selection versus primitive gene structure as determinant of codon usage

Different codons are not utilized equally in known gene sequences. One of the important biases of codon usage is observed in the from of an enrichment of RNY codons, especially within RNN codon families. Such biases could represent the residue of a primitive repeating‐RNY gene structure, or the outcome of natural selection, or both. Analyses based on the rates of silent substitutions, the requencies of base doublets, and synonymous codon rations for Escherichia coli, yeast, Drosophila and Xenopus proteins have been performed. The results rule out any significant support for a primitive repeating‐RNY or repeating‐RNY gene structure, and establish the important role of natural selection in determining the choice of codons. With strong intervention by natural selection, the relationship between primitive gene structure and codon usage necessarily becomes minimal.