MBE Advance Access published online on December 14, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msl196
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Research Article |
Divergent Haplotypes and Human History as Revealed in a Worldwide Survey of X-Linked DNA Sequence Variation
1 Department of Genetics, Rutgers the State University of New Jersey, Piscataway, NJ 08854, U.S.A
2 Japan Biological Information Research Center, Japan Biological Informatics Consortium, 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan
3 Department of Biology, University of Maryland, College Park, MD 20742, U.S.A
Corresponding Author: Jody Hey, Department of Genetics, Rutgers the State University of New Jersey, 604 Allison Road, Piscataway, NJ 08854, hey{at}biology.rutgers.edu, Phone 732-445-5272 Fax 732-445-5870
Accepted for publication December 11, 2006.
The population genetic history of a 10.1 kb non-coding region of the human X-chromosome was studied using the males of the 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 one highly divergent haplotype (hX) was observed at low frequency in widely scattered non-African populations and not at all in sub-Saharan African populations. Microsatellite (STR) 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 million years. The estimated age of the common ancestor of all hX copies was 5,230 years (95% CI: 2000 to 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 thoughout 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
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