Synonymous and Nonsynonymous Rates

Soojin Yi, University of Chicago, Chicago, Illinois, USA

Published online: December 2007

DOI: 10.1002/9780470015902.a0005110.pub2

When comparing protein-coding DNA sequences between species, it is useful to distinguish between synonymous (silent) substitutions and nonsynonymous (amino-acid changing) substitutions. Because the two types of change are under different intensities of selective constraints, comparing their rates provides insights into the mechanisms of evolution of the gene under study.

Keywords: coding regions; nucleotide substitution; degenerate code; functional constraints; positive selection

Figure 1. Phylogeny of lysozyme sequences from seven primate species, representing four major groups of species. The two numbers shown along each branch are the maximum likelihood estimates of the numbers of nonsynonymous and synonymous substitutions for the entire gene along that branch. A model of different for each branch of the tree, the so-called ‘free-ratio’ model, is used. Branches are drawn in proportion to estimates of their lengths. Adapted from Yang (1998) with premission from the Society for Molecular Biology and Evolution.
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 References
    Goldman N and Yang Z (1994) A codon-based model of nucleotide substitution for protein-coding DNA sequences. Molecular Biology and Evolution 11: 725–736.
    Li WH (1993) Unbiased estimation of the rates of synonymous and nonsynonymous substitution. Journal of Molecular Evolution 36: 96–99.
    book Li WH (1997) Molecular Evolution. Sutherland, MA: Sinauer Associates.
    Li WH, Wu CI and Luo CC (1985) A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Molecular Biology and Evolution 2: 150–174.
    Messier W and Stewart C-B (1997) Episodic adaptive evolution of primate lysozymes. Nature 385: 151–154.
    Nei M and Gojobori T (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Molecular Biology and Evolution 3: 418–426.
    book Nei M and Kumar S (2000) Molecular Evolution and Phylogenetics. New York, NY: Oxford University Press.
    Pamilo P and Bianchi O (1993) Evolution of the Zfx and Zfy genes: rates and interdependence between the genes. Molecular Biology and Evolution 19: 271–281.
    Yang Z (1998) Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Molecular Biology and Evolution 15: 568–573.
    Yang Z and Bielawski JP (2000) Statistical methods for detecting molecular adaptation. Trends in Ecology and Evolution 15: 496–503.
 Further Reading
    Chamary JV, Parmley JL and Hurst LD (2006) Hearing silence: non-neutral evolution at synonymous sites in mammals. Nature Reviews Genetics 7(2): 98–108.
    Schattner P and Diekhans M (2006) Regions of extreme synonymous codon selection in mammalian genes. Nucleic Acids Research 34: 1700–1710.
    Yang Z (2002) Inference of selection from multiple species alignments. Current Opinion in Genetics & Development 12: 688–694.

Related Sub-Topics:

Molecular Evolution | Protein Evolution | Evolution Rates | Evolution of Coding and Functional Modules
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Article Title: Synonymous and Nonsynonymous Rates
 
How to Cite close
Yi, Soojin(Dec 2007) Synonymous and Nonsynonymous Rates. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0005110.pub2]