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Originally published as Genetics Published Articles Ahead of Print on June 18, 2006.

Genetics, Vol. 174, 399-409, September 2006, Copyright © 2006
doi:10.1534/genetics.106.060301

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Nucleotide Variation and Haplotype Diversity in a 10-kb Noncoding Region in Three Continental Human Populations

Zhongming Zhao*,{dagger}, Ning Yu{ddagger}, Yun-Xin Fu§ and Wen-Hsiung Li{ddagger},1

* Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia 23298, {dagger} Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia 23284, {ddagger} Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637 and § Human Genetics Center, University of Texas Health Science Center, Houston, Texas 77030

1 Corresponding author: Department of Ecology and Evolution, University of Chicago, 1101 E. 57th St., Chicago, IL 60637.
E-mail: whli{at}uchicago.edu

Noncoding regions are usually less subject to natural selection than coding regions and so may be more useful for studying human evolution. The recent surveys of worldwide DNA variation in four 10-kb noncoding regions revealed many interesting but also some incongruent patterns. Here we studied another 10-kb noncoding region, which is in 6p22. Sixty-six single-nucleotide polymorphisms were found among the 122 worldwide human sequences, resulting in 46 genotypes, from which 48 haplotypes were inferred. The distribution patterns of DNA variation, genotypes, and haplotypes suggest rapid population expansion in relatively recent times. The levels of polymorphism within human populations and divergence between humans and chimpanzees at this locus were generally similar to those for the other four noncoding regions. Fu and Li's tests rejected the neutrality assumption in the total sample and in the African sample but Tajima's test did not reject neutrality. A detailed examination of the contributions of various types of mutations to the parameters used in the neutrality tests clarified the discrepancy between these test results. The age estimates suggest a relatively young history in this region. Combining three autosomal noncoding regions, we estimated the long-term effective population size of humans to be 11,000 ± 2800 using Tajima's estimator and 17,600 ± 4700 using Watterson's estimator and the age of the most recent common ancestor to be 860,000 ± 258,000 years ago.






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Copyright © 2006 by the Genetics Society of America.