Y chromosome sequence variation and the history of human populations


Binary polymorphisms associated with the non-recombining region of the human Y chromosome (NRY) preserve the paternal genetic legacy of our species that has persisted to the present, permitting inference of human evolution, population affinity and demographic history1. We used denaturing high-performance liquid chromatography (DHPLC; ref. 2) to identify 160 of the 166 bi-allelic and 1 tri-allelic site that formed a parsimonious genealogy of 116 haplotypes, several of which display distinct population affinities based on the analysis of 1062 globally representative individuals. A minority of contemporary East Africans and Khoisan represent the descendants of the most ancestral patrilineages of anatomically modern humans that left Africa between 35,000 and 89,000 years ago.

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Figure 1: Maximum parsimony phylogeny of human NRY chromosome bi-allelic variation.
Figure 2: Maximum likelihood network inferred from the haplotype frequencies reported in Table 1.

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We thank the 1,062 men who donated DNA; R.G. Klein, J. Mountain and M. Ruhlen for helpful discussions; D. Vollrath, R. Hyman and F.S. Dietrich for Y-specific cosmid sequences; and J. Block, D. Soergel, K. Prince, C. Edmonds and A. Rojas for technical help. A.W. Bergen made the RPS4YC711T marker (M130) information available to us before its publication. This work was supported in part by the NIH, NIHGR and L.S.B. Leakey Foundation.

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Correspondence to Peter A. Underhill.

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Underhill, P., Shen, P., Lin, A. et al. Y chromosome sequence variation and the history of human populations. Nat Genet 26, 358–361 (2000). https://doi.org/10.1038/81685

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