European Journal of Human Genetics (2015) 23, 124–131; doi:10.1038/ejhg.2014.50; published online 26 March 2014

The phylogenetic and geographic structure of Y-chromosome haplogroup R1a

Peter A Underhill1, G David Poznik2, Siiri Rootsi3, Mari Järve3, Alice A Lin4, Jianbin Wang5, Ben Passarelli5, Jad Kanbar5, Natalie M Myres6, Roy J King4, Julie Di Cristofaro7, Hovhannes Sahakyan3,8, Doron M Behar3,9, Alena Kushniarevich3, Jelena Šarac3,10, Tena Šaric3,10, Pavao Rudan10,11, Ajai Kumar Pathak3, Gyaneshwer Chaubey3, Viola Grugni12, Ornella Semino12,13, Levon Yepiskoposyan8, Ardeshir Bahmanimehr14, Shirin Farjadian15, Oleg Balanovsky16, Elza K Khusnutdinova17,18, Rene J Herrera19, Jacques Chiaroni7, Carlos D Bustamante1, Stephen R Quake5,20,21, Toomas Kivisild3,22 and Richard Villems3,23

  1. 1Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
  2. 2Program in Biomedical Informatics and Department of Statistics, Stanford University, Stanford, CA, USA
  3. 3Estonian Biocentre and the Department of Evolutionary Biology, University of Tartu, Tartu, Estonia
  4. 4Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, USA
  5. 5Department of Bioengineering, Stanford University, Stanford, CA, USA
  6. 6Ancestry DNA, Provo, UT, USA
  7. 7UMR 7268 ADES, Aix-Marseille Université/EFS/CNRS, Marseille, France
  8. 8Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia
  9. 9Molecular Medicine Laboratory, Rambam Health Care Campus, Haifa, Israel
  10. 10Institute for Anthropological Research, Zagreb, Croatia
  11. 11Croatian Academy of Sciences and Arts, Zagreb, Croatia
  12. 12Dipartimento di Biologia e Biotecnologie ‘Lazzaro Spallanzani’, Università di Pavia, Pavia, Italy
  13. 13Centro Interdipartimentale ‘Studi di Genere’, Università di Pavia, Pavia, Italy
  14. 14Department of Medical Genetic, Shiraz University of Medical Sciences, Shiraz, Iran
  15. 15Department of Immunology, Allergy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
  16. 16Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moscow, Russia
  17. 17Institute of Biochemistry and Genetics, Ufa Scientific Center of Russian Academy of Sciences, Ufa, Russia
  18. 18Department of Biology, Bashkir State University, Ufa, Russia
  19. 19Department of Human and Molecular Genetics, College of Medicine, Florida International University, Miami, FL, USA
  20. 20Department of Applied Physics, Stanford University, Stanford, CA, USA
  21. 21Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
  22. 22Division of Biological Anthropology, University of Cambridge, Cambridge, UK
  23. 23Estonian Academy of Sciences, Tallinn, Estonia

Correspondence: Dr PA Underhill, Department of Genetics, Stanford University School of Medicine, 365 Lasuen Street, Room 315, Littlefield Center, MC 2069, Stanford, CA 94305-2069, USA. Tel: +1 650 723 5805; Fax: +1 650 723 3667; E-mail:

Received 31 October 2013; Revised 7 February 2014; Accepted 13 February 2014
Advance online publication 26 March 2014



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 16244 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 ~25000 (95% CI: 21300–29000) 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.