European Journal of Human Genetics (2010) 18, 479–484; doi:10.1038/ejhg.2009.194; published online 4 November 2009

Separating the post-Glacial coancestry of European and Asian Y chromosomes within haplogroup R1a

Peter A Underhill1, Natalie M Myres2, Siiri Rootsi3,4, Mait Metspalu3,4, Lev A Zhivotovsky5, Roy J King1, Alice A Lin1, Cheryl-Emiliane T Chow6, Ornella Semino7, Vincenza Battaglia7, Ildus Kutuev3,8, Mari Järve3, Gyaneshwer Chaubey3, Qasim Ayub9, Aisha Mohyuddin10, S Qasim Mehdi11, Sanghamitra Sengupta12, Evgeny I Rogaev13, Elza K Khusnutdinova8, Andrey Pshenichnov3,14, Oleg Balanovsky3,14, Elena Balanovska14, Nina Jeran3,15, Dubravka Havas Augustin3,15, Marian Baldovic3,16, Rene J Herrera17, Kumarasamy Thangaraj18, Vijay Singh18, Lalji Singh18, Partha Majumder19, Pavao Rudan15, Dragan Primorac20, Richard Villems3 and Toomas Kivisild21

  1. 1Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, USA
  2. 2Sorenson Molecular Genealogy Foundation, Salt Lake City, UT, USA
  3. 3Department of Evolutionary Biology, University of Tartu, Tartu, Estonia
  4. 4Estonian Biocentre, Tartu, Estonia
  5. 5N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
  6. 6Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
  7. 7Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy
  8. 8Institute of Biochemistry and Genetics, Ufa Research Center, Russian Academy of Sciences, Ufa, Russia
  9. 9The Sulston Laboratories, The Wellcome Trust Sanger Institute, Hinxton, UK
  10. 10Shifa College of Medicine, Islamabad, Pakistan
  11. 11Centre for Human Genetics and Molecular Medicine, Sindh Institute of Urology and Transplantation, Karachi, Pakistan
  12. 12Department of Biochemistry, University of Calcutta, Kolkata, India
  13. 13Department of Psychiatry, Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, MA, USA
  14. 14Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moscow, Russia
  15. 15Institute for Anthropological Research, Zagreb, Croatia
  16. 16Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
  17. 17Department of Human and Molecular Genetics, College of Medicine, Florida International University, Miami, FL, USA
  18. 18Centre for Cellular and Molecular Biology, Hyderabad, India
  19. 19Human Genetics Unit, Indian Statistical Institute, Calcutta, India
  20. 20MZOS, Zagreb, Croatia
  21. 21Leverhulme Centre for Human Evolutionary Studies, Department of Biological Anthropology, University of Cambridge, Cambridge, UK

Correspondence: Dr PA Underhill, Division of Child and Adolescent Psychiatry and Child Development, Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, 1201 Welch Road, Stanford, CA 94304-5485, USA. Tel: +1 650 723 5805; Fax: +1 650 498 7761; E-mail:

Received 26 June 2009; Revised 23 September 2009; Accepted 24 September 2009; Published online 4 November 2009.



Human Y-chromosome haplogroup structure is largely circumscribed by continental boundaries. One notable exception to this general pattern is the young haplogroup R1a that exhibits post-Glacial coalescent times and relates the paternal ancestry of more than 10% of men in a wide geographic area extending from South Asia to Central East Europe and South Siberia. Its origin and dispersal patterns are poorly understood as no marker has yet been described that would distinguish European R1a chromosomes from Asian. Here we present frequency and haplotype diversity estimates for more than 2000 R1a chromosomes assessed for several newly discovered SNP markers that introduce the onset of informative R1a subdivisions by geography. Marker M434 has a low frequency and a late origin in West Asia bearing witness to recent gene flow over the Arabian Sea. Conversely, marker M458 has a significant frequency in Europe, exceeding 30% in its core area in Eastern Europe and comprising up to 70% of all M17 chromosomes present there. The diversity and frequency profiles of M458 suggest its origin during the early Holocene and a subsequent expansion likely related to a number of prehistoric cultural developments in the region. Its primary frequency and diversity distribution correlates well with some of the major Central and East European river basins where settled farming was established before its spread further eastward. Importantly, the virtual absence of M458 chromosomes outside Europe speaks against substantial patrilineal gene flow from East Europe to Asia, including to India, at least since the mid-Holocene.


Y chromosome; haplogroup R1a; human evolution; population genetics