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MBE Advance Access published online on August 17, 2005
Molecular Biology and Evolution, doi:10.1093/molbev/msi240
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© The Author 2005. 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@oupjournals.org
Accepted August 15, 2005

Research Article

Human SNPs Reveal no Evidence of Frequent Positive Selection

Liqing Zhang 1* and Wen-Hsiung Li 2

1 Department of Computer Science, Virginia Tech
2 Departments of Ecology and Evolution, University of Chicago

* To whom correspondence should be addressed.
Liqing Zhang, E-mail: lqzhang{at}vt.edu


  Abstract

We compared the single nucleotide polymorphisms (SNPs) in humans in 182 housekeeping and 148 tissue-specific genes. SNPs were divided into rare and common polymorphisms based on their frequencies. We found that housekeeping genes tend to be less polymorphic than tissue-specific genes for both rare and common SNPs. Using mouse as a second species for computing sequence divergences, we found no evidence of positive selection: for both housekeeping and tissue-specific genes, the ratio of nonsynonymous to synonymous common SNPs per site showed no significant difference from that of divergence. Similarly, we observed no evidence of positive selection for the 289 and 149 genes that have orthologs available for divergence calculation between human and chimpanzee and between human and old world monkeys, respectively. A comparison with previous SNP studies suggests that ~ 20% of the nonsynonymous SNPs in the human population are nearly neutral and that positive selection in the human genome might not be as frequent as previously thought.

Keywords: tissue-specific genes; housekeeping genes; selective constraints; nonsynonymous polymorphisms; expression breadth.
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