MBE Advance Access originally published online on August 17, 2005
Molecular Biology and Evolution 2005 22(12):2504-2507; doi:10.1093/molbev/msi240
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Research Article |
Human SNPs Reveal No Evidence of Frequent Positive Selection
* Department of Computer Science, Virginia Tech; and Departments of Ecology and Evolution, University of Chicago
E-mail: lqzhang{at}vt.edu.
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 humans and chimpanzees and between humans 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.
Key Words: tissue-specific genes • housekeeping genes • selective constraints • nonsynonymous polymorphisms • expression breadth
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