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MBE Advance Access published online on July 25, 2007
Molecular Biology and Evolution, doi:10.1093/molbev/msm152
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© The Author 2007. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Article

The Nonsynonymous/Synonymous Substitution Rate Ratio Versus the Radical/Conservative Replacement Rate Ratio in the Evolution of Mammalian Genes

Kousuke Hanada1,2, Shin-Han Shiu2 and Wen-Hsiung Li1,*

1 Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637
2 Department of Plant Biology, Michigan State University, East Lansing, MI 48824

* Corresponding author. Wen-Hsiung Li, Department of Ecology and Evolution, University of Chicago 1101 East 57th Street, Chicago, IL, 60637, USA. Tel: +1- 773-702-3104. Fax: +1-773-702-9740. E-mail: whli{at}uchicago.edu

Received for publication May 12, 2007. Revision received July 10, 2007. Accepted for publication July 16, 2007.

There are two ways to infer selection pressures in the evolution of protein-coding genes: the nonsynonymous and synonymous substitution rate ratio (KA/KS) and the radical and conservative amino acid replacement rate ratio (KR/KC). Since the KR/KC ratio depends on the definition of radical and conservative changes in the classification of amino acids, we develop an amino acid classification that maximizes the correlation between KA/KS and KR/KC. An analysis of 3,375 orthologous gene groups among five mammalian species shows that our classification gives a significantly higher correlation coefficient between the two ratios than those of existing classifications. However, there are many orthologous gene groups with a low KA/KS but a high KR/KC ratio. Examining the functions of these genes, we found an overrepresentation of functional categories related to development. To determine if the over-representation is stage specific, we examined the expression patterns of these genes at different developmental stages of the mouse. Interestingly, these genes are highly expressed in the early middle stage of development (Blastocyst to Amnion). It is commonly thought that developmental genes tend to be conservative in evolution, but some molecular changes in developmental stages should have contributed to morphological divergence in adult mammals. Therefore, we propose that the relaxed pressures indicated by the KR/KC ratio but not by KA/KS in the early middle stage of development may be important for the morphological divergence of mammals at the adult stage, while purifying selection detected by KA/KS occurs in the early middle developmental stage.

Key Words: positive selection • radical substitution • conservative substitution • classification of amino acids • development


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