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.
Subscribe to Journal
Get full journal access for 1 year
only $18.75 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Rent or Buy article
Get time limited or full article access on ReadCube.
All prices are NET prices.
Hammer, M.F. & Zegura, S.L. The role of the Y chromosome in human evolutionary studies. Evol. Anthropol. 5, 116–134 (1996).
Oefner, P.J. & Underhill, P.A. DNA mutation detection using denaturing high-performance liquid chromatography. Current Protocols in Human Genetics. Suppl 19, 7.10.1– 7.10.12 (Wiley & Sons, New York, 1998).
Underhill, P.A. et al. Detection of numerous Y chromosome biallelic polymorphisms by denaturing high performance liquid chromatography (DHPLC). Genome Res. 7, 996–1005 (1997).
Shen, P. et al. Population genetic implications from sequence variation in four Y chromosome genes. Proc. Natl Acad. Sci. USA 97, 7354–7359 (2000).
Hammer, M.F. et al. Out of Africa and back again: nested cladistic analysis of human Y chromosome variation. Mol. Biol. Evol. 15, 427–441 (1998).
Tajima, F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism Genetics 123, 585–595 (1989).
Nachman, M.W. Y chromosome variation of mice and men. Mol. Biol. Evol. 15, 1744–1750 (1998).
Jaruzelska, J., Zietkiewicz, E. & Labuda, D. Is selection responsible for the low level of variation in the last intron of the ZFY locus? Mol. Biol. Evol. 16, 1633–1640 (1999).
Wyckoff, G.J., Wang, W. & Wu, C.I. Rapid evolution of male reproductive genes in the descent of man. Nature 403, 304–309 ( 2000).
Jorde, L.B. et al. The distribution of human genetic diversity: a comparison of mitochondrial, autosomal, and Y-chromosome data. Am. J. Hum. Genet. 66, 979–988 ( 2000).
Thomson, R. et al. Recent common ancestry of human Y chromosomes: Evidence from DNA sequence data. Proc. Natl Acad. Sci. USA 97, 7360–7365 (2000).
Pritchard, J.K., Seielstad, M.T., Perez-Lezaun, A. & Feldman, M.W. Population growth of human Y chromosomes: a study of Y chromosome microsatellites. Mol. Biol. Evol. 16, 1791–1798 (1999).
Klein, R.G. The Human Career: Human Biological and Cultural Origins (University of Chicago Press, Illinois, 1999).
Quintana-Murci, L. et al. Genetic evidence of an early exit of Homo sapiens sapiens from Africa through eastern Africa. Nature Genet. 23 , 437–441 (1999).
Rogers, A.R. Genetic evidence for a Pleistocene population explosion. Evolution 49, 608–615 ( 1995).
Vollrath, D. et al. The human Y chromosome: a 43-interval map based on naturally occurring deletions. Science 258, 52– 59 (1992).
Hammer, M.F. & Horai, S. Y chromosomal DNA variation and the peopling of Japan. Am. J. Hum. Genet. 56, 951–962 (1995).
Seielstad, M.T. et al. Construction of human Y-chromosome haplotypes using a new polymorphic A to G transition. Hum. Mol. Genet. 3, 2159–2161 (1994).
Hammer, M.F. et al. The geographic distribution of human Y chromosome variation . Genetics 145, 787–805 (1997).
Zerjal, T. et al. Genetic relationships of Asians and northern Europeans, revealed by Y-chromosomal DNA analysis. Am. J. Hum. Genet. 60 , 1174–1183 (1997).
Bergen, A.W. et al. An Asian-native American paternal lineage identified by RPS4Y resequencing and by microsatellite haplotyping. Ann. Hum Genet. 63, 63–80 ( 1999).
Bianchi, N.O. et al. Origin of Amerindian Y-chromosomes as inferred by the analysis of six polymorphic markers. Am. J. Phys. Anthropol. 102, 79–89 (1997).
Diamond, J. Guns, Germs, and Steel (Norton, New York, 1999).
Macaulay, V. et al. The emerging tree of west Eurasian mtDNAs: a synthesis of control-region sequences and RFLPs. Am. J. Hum. Genet. 64, 232–249 (1999).
Jin, L. et al. Distribution of haplotypes from a chromosome 21 region distinguishes multiple prehistoric human migrations. Proc. Natl Acad. Sci. USA 96, 3796–3800 ( 1999).
Cavalli-Sforza, L.L., Menozzi, P. & Piazza, A. The History and Geography of Human Genes (Princeton University Press, Princeton, New Jersey, 1994).
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.
About this article
Cite this article
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
The Y-chromosome F haplogroup contributes to the development of Barrett’s esophagus-associated esophageal adenocarcinoma in a white male population
Diseases of the Esophagus (2020)
Paternal genetic history of the Yong population in northern Thailand revealed by Y-chromosomal haplotypes and haplogroups
Molecular Genetics and Genomics (2020)
Theoretical Population Biology (2020)
BMC Evolutionary Biology (2020)
Current Biology (2020)