MBE Advance Access originally published online on December 14, 2006
Molecular Biology and Evolution 2007 24(3):687-698; doi:10.1093/molbev/msl196
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Research Articles |
Divergent Haplotypes and Human History as Revealed in a Worldwide Survey of X-Linked DNA Sequence Variation
* Department of Genetics, Rutgers University
Japan Biological Information Research Center, Japan Biological Informatics Consortium, Koto-ku, Tokyo, Japan
Department of Biology, University of Maryland
E-mail: hey{at}biology.rutgers.edu.
Accepted for publication December 11, 2006.
The population genetic history of a 10.1-kbp noncoding region of the human X chromosome was studied using the males of the HGDP-CEPH Human Genome Diversity Panel (672 individuals from 52 populations). The geographic distribution of patterns of variation was roughly consistent with previous studies, with the major exception that 1 highly divergent haplotype (haplotype X, hX) was observed at low frequency in widely scattered non-African populations and not at all observed in sub-Saharan African populations. Microsatellite (short tandem repeat) variation within the sequenced region was low among copies of hX, even though the estimated time of ancestry of hX and other sequences was 1.44 Myr. The estimated age of the common ancestor of all hX copies was 5,230 years (95% consistency index: 2,000–75,480 years). To further address the presence of hX in Africa, additional samples from Chad and Tanzania were screened. Five additional copies of hX were observed, consistent with a history in which hX was present in Africa prior to the migration of modern humans out of Africa and with eastern Africa being the source of non-African modern human populations. Taken together, these features of hX—that it is much older than other haplotypes and uncommon and patchily distributed throughout Africa, Europe, and Asia—present a cautionary tale for interpretations of human history.
Key Words: human populations • population genetics • microsatellite (STR) • HGDP-CEPH Diversity Panel • sequence variation • population structure • coalescent
Anne Stone, Associate Editor
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