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European Journal of Human Genetics
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The phylogenetic and geographic structure of Y-chromosome haplogroup R1a

European Journal of Human Geneticsvolume 23, pages124–131 (2015)Cite this article

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Abstract

R1a-M420 is one of the most widely spread Y-chromosome haplogroups; however, its substructure within Europe and Asia has remained poorly characterized. Using a panel of 16 244 male subjects from 126 populations sampled across Eurasia, we identified 2923 R1a-M420 Y-chromosomes and analyzed them to a highly granular phylogeographic resolution. Whole Y-chromosome sequence analysis of eight R1a and five R1b individuals suggests a divergence time of∼25 000 (95% CI: 21 300–29 000) years ago and a coalescence time within R1a-M417 of∼5800 (95% CI: 4800–6800) years. The spatial frequency distributions of R1a sub-haplogroups conclusively indicate two major groups, one found primarily in Europe and the other confined to Central and South Asia. Beyond the major European versus Asian dichotomy, we describe several younger sub-haplogroups. Based on spatial distributions and diversity patterns within the R1a-M420 clade, particularly rare basal branches detected primarily within Iran and eastern Turkey, we conclude that the initial episodes of haplogroup R1a diversification likely occurred in the vicinity of present-day Iran.

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Acknowledgements

AAL thanks Ancestry DNA for support. PAU thanks CDB and Professor Michael Snyder for support. GDP was supported by the National Science Foundation Graduate Research Fellowship under Grant No. DGE-1147470. This work was supported by the European Union European Regional Development Fund through the Centre of Excellence in Genomics, by the Estonian Biocentre and the University of Tartu, by the European Commission grant 205419 ECOGENE to the EBC, by the Estonian Basic Research Grant SF 0270177s08 and by Institutional Research Funding from the Estonian Research Council IUT24-1. JS and TS were supported by the Croatian Ministry of Science, Education, and Sports grant Population structure of Croatia—anthropogenic approach (No. 196-1962766-2751 to PR). AKP was supported by European Social Fund's Doctoral Studies and Internationalisation Programme DoRa. VG and OS were supported by the Italian Ministry of the University: Progetti Ricerca Interesse Nazionale 2012. SNPs not previously submitted have been deposited to dbSNP (http://www.cbi.nlm.nih.gov/SNP/; ss947849426–947850190).

Author information

Authors and Affiliations

  1. Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA

    Peter A Underhill & Carlos D Bustamante

  2. Program in Biomedical Informatics and Department of Statistics, Stanford University, Stanford, CA, USA

    G David Poznik

  3. Estonian Biocentre and the Department of Evolutionary Biology, University of Tartu, Tartu, Estonia

    Siiri Rootsi, Mari Järve, Hovhannes Sahakyan, Doron M Behar, Alena Kushniarevich, Jelena Šarac, Tena Šaric, Ajai Kumar Pathak, Gyaneshwer Chaubey, Toomas Kivisild & Richard Villems

  4. Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, USA

    Alice A Lin & Roy J King

  5. Department of Bioengineering, Stanford University, Stanford, CA, USA

    Jianbin Wang, Ben Passarelli, Jad Kanbar & Stephen R Quake

  6. Ancestry DNA, Provo, UT, USA

    Natalie M Myres

  7. UMR 7268 ADES, Aix-Marseille Université/EFS/CNRS, Marseille, France

    Julie Di Cristofaro & Jacques Chiaroni

  8. Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia

    Hovhannes Sahakyan & Levon Yepiskoposyan

  9. Molecular Medicine Laboratory, Rambam Health Care Campus, Haifa, Israel

    Doron M Behar

  10. Institute for Anthropological Research, Zagreb, Croatia

    Jelena Šarac, Tena Šaric & Pavao Rudan

  11. Croatian Academy of Sciences and Arts, Zagreb, Croatia

    Pavao Rudan

  12. Dipartimento di Biologia e Biotecnologie ‘Lazzaro Spallanzani’, Università di Pavia, Pavia, Italy

    Viola Grugni & Ornella Semino

  13. Centro Interdipartimentale ‘Studi di Genere’, Università di Pavia, Pavia, Italy

    Ornella Semino

  14. Department of Medical Genetic, Shiraz University of Medical Sciences, Shiraz, Iran

    Ardeshir Bahmanimehr

  15. Department of Immunology, Allergy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran

    Shirin Farjadian

  16. Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moscow, Russia

    Oleg Balanovsky

  17. Institute of Biochemistry and Genetics, Ufa Scientific Center of Russian Academy of Sciences, Ufa, Russia

    Elza K Khusnutdinova

  18. Department of Biology, Bashkir State University, Ufa, Russia

    Elza K Khusnutdinova

  19. Department of Human and Molecular Genetics, College of Medicine, Florida International University, Miami, FL, USA

    Rene J Herrera

  20. Department of Applied Physics, Stanford University, Stanford, CA, USA

    Stephen R Quake

  21. Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA

    Stephen R Quake

  22. Division of Biological Anthropology, University of Cambridge, Cambridge, UK

    Toomas Kivisild

  23. Estonian Academy of Sciences, Tallinn, Estonia

    Richard Villems

Authors
  1. Peter A Underhill
  2. G David Poznik
  3. Siiri Rootsi
  4. Mari Järve
  5. Alice A Lin
  6. Jianbin Wang
  7. Ben Passarelli
  8. Jad Kanbar
  9. Natalie M Myres
  10. Roy J King
  11. Julie Di Cristofaro
  12. Hovhannes Sahakyan
  13. Doron M Behar
  14. Alena Kushniarevich
  15. Jelena Šarac
  16. Tena Šaric
  17. Pavao Rudan
  18. Ajai Kumar Pathak
  19. Gyaneshwer Chaubey
  20. Viola Grugni
  21. Ornella Semino
  22. Levon Yepiskoposyan
  23. Ardeshir Bahmanimehr
  24. Shirin Farjadian
  25. Oleg Balanovsky
  26. Elza K Khusnutdinova
  27. Rene J Herrera
  28. Jacques Chiaroni
  29. Carlos D Bustamante
  30. Stephen R Quake
  31. Toomas Kivisild
  32. Richard Villems

Corresponding author

Correspondence toPeter A Underhill.

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Competing interests

PAU consulted for and has stock in, and CDB is on the advisory board of a project at 23andMe. CDB is on the scientific advisory boards of Personalis, Inc.; InVitae (formerly Locus Development, Inc.); and Ancestry DNA. The remaining authors declare no conflict of interest.

Additional information

Supplementary Information accompanies this paper on European Journal of Human Genetics website

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Underhill, P., Poznik, G., Rootsi, S.et al. The phylogenetic and geographic structure of Y-chromosome haplogroup R1a.Eur J Hum Genet23, 124–131 (2015). https://doi.org/10.1038/ejhg.2014.50

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