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

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

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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.

Corresponding author

Correspondence to Peter A Underhill.

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DOI

https://doi.org/10.1038/ejhg.2014.50

Supplementary Information accompanies this paper on European Journal of Human Genetics website (http://www.nature.com/ejhg)

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