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MBE Advance Access published online on October 13, 2004
Molecular Biology and Evolution, doi:10.1093/molbev/msi013
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2004; all rights reserved
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Accepted October 4, 2004

Letter

Evidence for Archaic Asian Ancestry on the Human X Chromosome

Daniel Garrigan 1, Zahra Mobasher 1, Tesa Severson 1, Jason A. Wilder 1, and Michael F. Hammer 2*

1 Division of Biotechnology, University of Arizona, Tucson, AZ USA 85721
2 Division of Biotechnology, University of Arizona, Tucson, AZ USA 85721; Dept. EEB, University of Arizona, Tucson, AZ USA 85721

* To whom correspondence should be addressed. E-mail: mfh{at}u.arizona.edu.


  Abstract

The human RRM2P4 pseudogene has a pattern of nucleotide polymorphism that is unlike any locus published to date. A gene tree constructed from a 2.4 kb fragment of the RRM2P4 locus sequenced in a sample of 41 worldwide humans clearly roots in East Asia and has a most recent common ancestor ~2 million years before the present. The presence of this basal lineage exclusively in Asia results in higher nucleotide diversity among non-Africans than Africans. A global survey of a single nucleotide polymorphism that is diagnostic for the basal, Asian lineage in 570 individuals shows that it occurs at frequencies up to 53% in south China, while only one of 177 surveyed Africans carries this archaic lineage. We suggest that this ancient lineage is a remnant of introgressive hybridization between expanding anatomically modern humans emerging from Africa and archaic populations in Eurasia.

Keywords: hybridization; human origins; polymorphism; population subdivision; pseudogene.
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