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. 2002 May;161(1):269–274. doi: 10.1093/genetics/161.1.269

Larger genetic differences within africans than between Africans and Eurasians.

Ning Yu 1, Feng-Chi Chen 1, Satoshi Ota 1, Lynn B Jorde 1, Pekka Pamilo 1, Laszlo Patthy 1, Michele Ramsay 1, Trefor Jenkins 1, Song-Kun Shyue 1, Wen-Hsiung Li 1
PMCID: PMC1462113  PMID: 12019240

Abstract

The worldwide pattern of single nucleotide polymorphism (SNP) variation is of great interest to human geneticists, population geneticists, and evolutionists, but remains incompletely understood. We studied the pattern in noncoding regions, because they are less affected by natural selection than are coding regions. Thus, it can reflect better the history of human evolution and can serve as a baseline for understanding the maintenance of SNPs in human populations. We sequenced 50 noncoding DNA segments each approximately 500 bp long in 10 Africans, 10 Europeans, and 10 Asians. An analysis of the data suggests that the sampling scheme is adequate for our purpose. The average nucleotide diversity (pi) for the 50 segments is only 0.061% +/- 0.010% among Asians and 0.064% +/- 0.011% among Europeans but almost twice as high (0.115% +/- 0.016%) among Africans. The African diversity estimate is even higher than that between Africans and Eurasians (0.096% +/- 0.012%). From available data for noncoding autosomal regions (total length = 47,038 bp) and X-linked regions (47,421 bp), we estimated the pi-values for autosomal regions to be 0.105, 0.070, 0.069, and 0.097% for Africans, Asians, Europeans, and between Africans and Eurasians, and the corresponding values for X-linked regions to be 0.088, 0.042, 0.053, and 0.082%. Thus, Africans differ from one another slightly more than from Eurasians, and the genetic diversity in Eurasians is largely a subset of that in Africans, supporting the out of Africa model of human evolution. Clearly, one must specify the geographic origins of the individuals sampled when studying pi or SNP density.

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Selected References

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  1. Armour J. A., Anttinen T., May C. A., Vega E. E., Sajantila A., Kidd J. R., Kidd K. K., Bertranpetit J., Päbo S., Jeffreys A. J. Minisatellite diversity supports a recent African origin for modern humans. Nat Genet. 1996 Jun;13(2):154–160. doi: 10.1038/ng0696-154. [DOI] [PubMed] [Google Scholar]
  2. Cargill M., Altshuler D., Ireland J., Sklar P., Ardlie K., Patil N., Shaw N., Lane C. R., Lim E. P., Kalyanaraman N. Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat Genet. 1999 Jul;22(3):231–238. doi: 10.1038/10290. [DOI] [PubMed] [Google Scholar]
  3. Chen F. C., Li W. H. Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees. Am J Hum Genet. 2001 Jan 15;68(2):444–456. doi: 10.1086/318206. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Don R. H., Cox P. T., Wainwright B. J., Baker K., Mattick J. S. 'Touchdown' PCR to circumvent spurious priming during gene amplification. Nucleic Acids Res. 1991 Jul 25;19(14):4008–4008. doi: 10.1093/nar/19.14.4008. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Fu Y. X. Statistical properties of segregating sites. Theor Popul Biol. 1995 Oct;48(2):172–197. doi: 10.1006/tpbi.1995.1025. [DOI] [PubMed] [Google Scholar]
  6. Halushka M. K., Fan J. B., Bentley K., Hsie L., Shen N., Weder A., Cooper R., Lipshutz R., Chakravarti A. Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis. Nat Genet. 1999 Jul;22(3):239–247. doi: 10.1038/10297. [DOI] [PubMed] [Google Scholar]
  7. Hammer M. F., Spurdle A. B., Karafet T., Bonner M. R., Wood E. T., Novelletto A., Malaspina P., Mitchell R. J., Horai S., Jenkins T. The geographic distribution of human Y chromosome variation. Genetics. 1997 Mar;145(3):787–805. doi: 10.1093/genetics/145.3.787. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Harding R. M., Fullerton S. M., Griffiths R. C., Bond J., Cox M. J., Schneider J. A., Moulin D. S., Clegg J. B. Archaic African and Asian lineages in the genetic ancestry of modern humans. Am J Hum Genet. 1997 Apr;60(4):772–789. [PMC free article] [PubMed] [Google Scholar]
  9. Harris E. E., Hey J. X chromosome evidence for ancient human histories. Proc Natl Acad Sci U S A. 1999 Mar 16;96(6):3320–3324. doi: 10.1073/pnas.96.6.3320. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Ingman M., Kaessmann H., Päbo S., Gyllensten U. Mitochondrial genome variation and the origin of modern humans. Nature. 2000 Dec 7;408(6813):708–713. doi: 10.1038/35047064. [DOI] [PubMed] [Google Scholar]
  11. Jaruzelska J., Zietkiewicz E., Batzer M., Cole D. E., Moisan J. P., Scozzari R., Tavaré S., Labuda D. Spatial and temporal distribution of the neutral polymorphisms in the last ZFX intron: analysis of the haplotype structure and genealogy. Genetics. 1999 Jul;152(3):1091–1101. doi: 10.1093/genetics/152.3.1091. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Jorde L. B., Watkins W. S., Bamshad M. J., Dixon M. E., Ricker C. E., Seielstad M. T., Batzer M. A. The distribution of human genetic diversity: a comparison of mitochondrial, autosomal, and Y-chromosome data. Am J Hum Genet. 2000 Mar;66(3):979–988. doi: 10.1086/302825. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Kaessmann H., Heissig F., von Haeseler A., Päbo S. DNA sequence variation in a non-coding region of low recombination on the human X chromosome. Nat Genet. 1999 May;22(1):78–81. doi: 10.1038/8785. [DOI] [PubMed] [Google Scholar]
  14. Nachman M. W., Crowell S. L. Contrasting evolutionary histories of two introns of the duchenne muscular dystrophy gene, Dmd, in humans. Genetics. 2000 Aug;155(4):1855–1864. doi: 10.1093/genetics/155.4.1855. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Nickerson D. A., Taylor S. L., Weiss K. M., Clark A. G., Hutchinson R. G., Stengård J., Salomaa V., Vartiainen E., Boerwinkle E., Sing C. F. DNA sequence diversity in a 9.7-kb region of the human lipoprotein lipase gene. Nat Genet. 1998 Jul;19(3):233–240. doi: 10.1038/907. [DOI] [PubMed] [Google Scholar]
  16. Rieder M. J., Taylor S. L., Clark A. G., Nickerson D. A. Sequence variation in the human angiotensin converting enzyme. Nat Genet. 1999 May;22(1):59–62. doi: 10.1038/8760. [DOI] [PubMed] [Google Scholar]
  17. Sachidanandam R., Weissman D., Schmidt S. C., Kakol J. M., Stein L. D., Marth G., Sherry S., Mullikin J. C., Mortimore B. J., Willey D. L. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature. 2001 Feb 15;409(6822):928–933. doi: 10.1038/35057149. [DOI] [PubMed] [Google Scholar]
  18. Tishkoff S. A., Dietzsch E., Speed W., Pakstis A. J., Kidd J. R., Cheung K., Bonné-Tamir B., Santachiara-Benerecetti A. S., Moral P., Krings M. Global patterns of linkage disequilibrium at the CD4 locus and modern human origins. Science. 1996 Mar 8;271(5254):1380–1387. doi: 10.1126/science.271.5254.1380. [DOI] [PubMed] [Google Scholar]
  19. Tishkoff S. A., Pakstis A. J., Stoneking M., Kidd J. R., Destro-Bisol G., Sanjantila A., Lu R. B., Deinard A. S., Sirugo G., Jenkins T. Short tandem-repeat polymorphism/alu haplotype variation at the PLAT locus: implications for modern human origins. Am J Hum Genet. 2000 Sep 13;67(4):901–925. doi: 10.1086/303068. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Underhill P. A., Shen P., Lin A. A., Jin L., Passarino G., Yang W. H., Kauffman E., Bonné-Tamir B., Bertranpetit J., Francalacci P. Y chromosome sequence variation and the history of human populations. Nat Genet. 2000 Nov;26(3):358–361. doi: 10.1038/81685. [DOI] [PubMed] [Google Scholar]
  21. Venter J. C., Adams M. D., Myers E. W., Li P. W., Mural R. J., Sutton G. G., Smith H. O., Yandell M., Evans C. A., Holt R. A. The sequence of the human genome. Science. 2001 Feb 16;291(5507):1304–1351. doi: 10.1126/science.1058040. [DOI] [PubMed] [Google Scholar]
  22. Vigilant L., Stoneking M., Harpending H., Hawkes K., Wilson A. C. African populations and the evolution of human mitochondrial DNA. Science. 1991 Sep 27;253(5027):1503–1507. doi: 10.1126/science.1840702. [DOI] [PubMed] [Google Scholar]
  23. Yu N., Zhao Z., Fu Y. X., Sambuughin N., Ramsay M., Jenkins T., Leskinen E., Patthy L., Jorde L. B., Kuromori T. Global patterns of human DNA sequence variation in a 10-kb region on chromosome 1. Mol Biol Evol. 2001 Feb;18(2):214–222. doi: 10.1093/oxfordjournals.molbev.a003795. [DOI] [PubMed] [Google Scholar]
  24. Zhao Z., Jin L., Fu Y. X., Ramsay M., Jenkins T., Leskinen E., Pamilo P., Trexler M., Patthy L., Jorde L. B. Worldwide DNA sequence variation in a 10-kilobase noncoding region on human chromosome 22. Proc Natl Acad Sci U S A. 2000 Oct 10;97(21):11354–11358. doi: 10.1073/pnas.200348197. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Zietkiewicz E., Yotova V., Jarnik M., Korab-Laskowska M., Kidd K. K., Modiano D., Scozzari R., Stoneking M., Tishkoff S., Batzer M. Nuclear DNA diversity in worldwide distributed human populations. Gene. 1997 Dec 31;205(1-2):161–171. doi: 10.1016/s0378-1119(97)00408-3. [DOI] [PubMed] [Google Scholar]

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