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Journal of Biomedicine and Biotechnology
Volume 2010 (2010), Article ID 202918, 9 pages
http://dx.doi.org/10.1155/2010/202918
Research Article

Features of Recent Codon Evolution: A Comparative Polymorphism-Fixation Study

1Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
2Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
3Bioinformatics Resource Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN 37203, USA
4Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA

Received 14 March 2010; Accepted 31 March 2010

Academic Editor: Momiao Xiong

Copyright © 2010 Zhongming Zhao and Cizhong Jiang. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

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 A∣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.