Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

Y chromosome sequence variation and the history of human populations

Nature Genetics volume 26, pages 358–361 (2000)Cite this article

Abstract

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.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

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.

Similar content being viewed by others

Accession codes

Accessions

GenBank/EMBL/DDBJ

References

  1. Hammer, M.F. & Zegura, S.L. The role of the Y chromosome in human evolutionary studies. Evol. Anthropol. 5, 116–134 (1996).

    Article  Google Scholar 

  2. 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).

    Google Scholar 

  3. 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).

    Article  CAS  Google Scholar 

  4. Shen, P. et al. Population genetic implications from sequence variation in four Y chromosome genes. Proc. Natl Acad. Sci. USA 97, 7354–7359 (2000).

    Article  CAS  Google Scholar 

  5. 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).

    Article  CAS  Google Scholar 

  6. Tajima, F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism Genetics 123, 585–595 (1989).

    CAS  Google Scholar 

  7. Nachman, M.W. Y chromosome variation of mice and men. Mol. Biol. Evol. 15, 1744–1750 (1998).

    CAS  Google Scholar 

  8. 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).

    Article  CAS  Google Scholar 

  9. Wyckoff, G.J., Wang, W. & Wu, C.I. Rapid evolution of male reproductive genes in the descent of man. Nature 403, 304–309 ( 2000).

    Article  CAS  Google Scholar 

  10. 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).

    Article  CAS  Google Scholar 

  11. 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).

    Article  CAS  Google Scholar 

  12. 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).

    Article  CAS  Google Scholar 

  13. Klein, R.G. The Human Career: Human Biological and Cultural Origins (University of Chicago Press, Illinois, 1999).

    Google Scholar 

  14. 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).

    Article  CAS  Google Scholar 

  15. Rogers, A.R. Genetic evidence for a Pleistocene population explosion. Evolution 49, 608–615 ( 1995).

    Article  Google Scholar 

  16. Vollrath, D. et al. The human Y chromosome: a 43-interval map based on naturally occurring deletions. Science 258, 52– 59 (1992).

    Article  CAS  Google Scholar 

  17. Hammer, M.F. & Horai, S. Y chromosomal DNA variation and the peopling of Japan. Am. J. Hum. Genet. 56, 951–962 (1995).

    CAS  Google Scholar 

  18. 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).

    Article  CAS  Google Scholar 

  19. Hammer, M.F. et al. The geographic distribution of human Y chromosome variation . Genetics 145, 787–805 (1997).

    CAS  Google Scholar 

  20. 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).

    CAS  Google Scholar 

  21. 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).

    Article  CAS  Google Scholar 

  22. 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).

    Article  CAS  Google Scholar 

  23. Diamond, J. Guns, Germs, and Steel (Norton, New York, 1999).

    Google Scholar 

  24. 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).

    Article  CAS  Google Scholar 

  25. 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).

    Article  CAS  Google Scholar 

  26. Cavalli-Sforza, L.L., Menozzi, P. & Piazza, A. The History and Geography of Human Genes (Princeton University Press, Princeton, New Jersey, 1994).

    Google Scholar 

Download references

Acknowledgements

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.

Author information

Authors and Affiliations

  1. Department of Genetics, Stanford University, Stanford, California, USA

    Peter A. Underhill, Alice A. Lin, Giuseppe Passarino & L. Luca Cavalli-Sforza

  2. Stanford DNA Sequencing and Technology Center, Palo Alto, California, USA

    Peidong Shen, Wei H. Yang, Erin Kauffman, Ronald W. Davis & Peter. J. Oefner

  3. University of Texas-Houston, Human Genetics Center, Houston, Texas, USA

    Li Jin

  4. Sackler Faculty of Medicine, Human Genetics, Tel-Aviv University, Tel-Aviv, Israel

    Batsheva Bonné-Tamir

  5. Unitat de Biologia Evolutiva, Facultat de Ciències de la Salut i de la Vida, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain

    Jaume Bertranpetit

  6. Dipartimento di Zoologia e Antropologia Biologica, Università di Sassari, Sassari, Italy

    Paolo Francalacci

  7. Institute of Endemic Diseases, University of Khartoum, Sudan

    Muntaser Ibrahim

  8. Department of Human Genetics, School of Pathology, South African Institute for Medical Research and the University of Witwatersrand, Johannesburg, South Africa

    Trefor Jenkins

  9. Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA

    Judith R. Kidd

  10. Dr. A. Q. Khan Research Laboratories, Biomedical & Genetic Engineering Laboratories, Islamabad, Pakistan

    S. Qasim Mehdi

  11. Harvard School of Public Health, Program for Population Genetics, Boston, Massachusetts, USA

    Mark T. Seielstad

  12. Wellcome Trust Centre for Human Genetics, University of Oxford, Headington, UK

    R. Spencer Wells

  13. Department of Genetics, Department of Genetics, Biology and Biochemistry, University of Torino, Torino, Italy

    Alberto Piazza

  14. Department of Biological Sciences, Herrin Laboratories, Stanford University, California, USA

    Marcus W. Feldman

Authors
  1. Peter A. Underhill
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Peidong Shen
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Alice A. Lin
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Li Jin
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Giuseppe Passarino
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Wei H. Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Erin Kauffman
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Batsheva Bonné-Tamir
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Jaume Bertranpetit
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Paolo Francalacci
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Muntaser Ibrahim
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Trefor Jenkins
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Judith R. Kidd
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. S. Qasim Mehdi
    View author publications

    You can also search for this author in PubMed Google Scholar

  15. Mark T. Seielstad
    View author publications

    You can also search for this author in PubMed Google Scholar

  16. R. Spencer Wells
    View author publications

    You can also search for this author in PubMed Google Scholar

  17. Alberto Piazza
    View author publications

    You can also search for this author in PubMed Google Scholar

  18. Ronald W. Davis
    View author publications

    You can also search for this author in PubMed Google Scholar

  19. Marcus W. Feldman
    View author publications

    You can also search for this author in PubMed Google Scholar

  20. L. Luca Cavalli-Sforza
    View author publications

    You can also search for this author in PubMed Google Scholar

  21. Peter. J. Oefner
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Peter A. Underhill.

Supplementary information

Rights and permissions

Reprints and permissions

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

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/81685

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing