Divergent X chromosome haplotype in Eurasians and East Africans

Yet another piece of evidence in favor of my idea that ancestral Africans were subdivided and did not form a single population. A widely divergent haplotype of the X chromosome was found in Eurasians and East Africans but not at all in the Sub-Saharan Africans of the CEPH Panel. If there was no population structure in Africa, then we would expect to see this hX haplotype in different African locations.

From the paper:

Designated hX, this haplotype was found once in Melanesia (Oceania) and 8 times in widespread locations in Eurasia, including the Orkney Islands, Pakistan, Algeria, Israel, and France. Contrary to the typical pattern found in many genes, in which the variation in non-African populations is a subset of the variation in sub-Saharan Africa, hX was not observed among the HGDP-CEPH males from sub-Saharan Africa (98 individuals).

...

One possible historical model that could generate this pattern supposes that differences between hX and other haplotypes arose in the presence of population structure that allowed for the divergence among Xp11.22 haplotypes. Even if we discount the possibility of a non-African archaic human population as the source of hX, the age and low frequency of the haplotype does suggest a history in which hX persisted and diverged in a separate refugium population (either a separate modern human population or possibly an archaic human population). Models of this type, which suppose the presence of old population strutcture among African populations, have been suggested based on evidence from other regions of the genome (Tishkoff et al. 1996Go; Harding et al. 1997Go; Labuda et al. 2000Go; Tishkoff et al. 2000Go; Zietkiewicz et al. 2003Go; Garrigan, Mobesher, Kingan, et al. 2005Go).

Molecular Biology and Evolution

Divergent Haplotypes and Human History as Revealed in a Worldwide Survey of X-Linked DNA Sequence Variation

Makoto K. Shimada et al.

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.

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