Genetics, Vol. 161, 269-274, May 2002, Copyright © 2002

Larger Genetic Differences Within Africans Than Between Africans and Eurasians

Ning Yua, Feng-Chi Chena,b, Satoshi Otaa, Lynn B. Jordec, Pekka Pamilod, Laszlo Patthye, Michele Ramsayf, Trefor Jenkinse, Song-Kun Shyueg, and Wen-Hsiung Lia
a Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637,
b Department of Life Science, National Tsing Hua University, Hsinchu, 300 Taiwan,
c Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112,
d Department of Biology, University of Oulu, 90014 Oulu, Finland,
e Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, H-1518 Budapest, Hungary,
f Department of Human Genetics, South African Institute for Medical Research and University of the Witwatersrand, Johannesburg, 2050 South Africa
g Institute of Biomedical Sciences, Academia Sinica, Taipei, 115 Taiwan

Corresponding author: Wen-Hsiung Li, University of Chicago, 1101 E. 57th St., Chicago, IL 60637., whli{at}uchicago.edu (E-mail)

Communicating editor: Y.-X. FU

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 ~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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