Synonymous and Nonsynonymous Rates


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 ω 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 with premission from the Society for Molecular Biology and Evolution.



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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.

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How to Cite close
Yi, Soojin(Dec 2007) Synonymous and Nonsynonymous Rates. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0005110.pub2]