Features of recent codon evolution: a comparative polymorphism-fixation study.

Zhao Z, Jiang C
J Biomed Biotechnol. 2010 2010: 202918

PMID: 20622912 · PMCID: PMC2896653 · DOI:10.1155/2010/202918

Features of amino-acid and codon changes can provide us important insights on protein evolution. So far, investigators have often examined mutation patterns at either interspecies fixed substitution or intraspecies nucleotide polymorphism level, but not both. Here, we performed a unique analysis of a combined set of intra-species polymorphisms and inter-species substitutions in human codons. Strong difference in mutational pattern was found at codon positions 1, 2, and 3 between the polymorphism and fixation data. Fixation had strong bias towards increasing the rarest codons but decreasing the most frequently used codons, suggesting that codon equilibrium has not been reached yet. We detected strong CpG effect on CG-containing codons and subsequent suppression by fixation. Finally, we detected the signature of purifying selection against Amid R:U dinucleotides at synonymous dicodon boundaries. Overall, fixation process could effectively and quickly correct the volatile changes introduced by polymorphisms so that codon changes could be gradual and directional and that codon composition could be kept relatively stable during evolution.

MeSH Terms (12)

Amino Acid Substitution Animals Base Composition Codon CpG Islands Evolution, Molecular Humans Mice Mutation Pan troglodytes Polymorphism, Genetic Species Specificity

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