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

Peter A. Underhill, Natalie M. Myres, Siiri Rootsi, Mait Metspalu, Lev A. Zhivotovsky, Roy J. King, Alice A. Lin, Cheryl Emiliane T. Chow, Ornella Semino, Vincenza Battaglia, Ildus Kutuev, Mari Järve, Gyaneshwer Chaubey, Qasim Ayub, Aisha Mohyuddin, S. Qasim Mehdi, Sanghamitra Sengupta, Evgeny I. Rogaev, Elza K. Khusnutdinova, Andrey PshenichnovOleg Balanovsky, Elena Balanovska, Nina Jeran, Dubravka Havas Augustin, Marian Baldovic, Rene J. Herrera, Kumarasamy Thangaraj, Vijay Singh, Lalji Singh, Partha Majumder, Pavao Rudan, Dragan Primorac, Richard Villems, Toomas Kivisild

Research output: Contribution to journalArticlepeer-review

138 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)479-484
Number of pages6
JournalEuropean Journal of Human Genetics
Issue number4
StatePublished - Apr 2010

All Science Journal Classification (ASJC) codes

  • Genetics
  • Genetics(clinical)


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