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Link to original content: https://pubmed.ncbi.nlm.nih.gov/19888303
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. 2010 Apr;18(4):479-84.
doi: 10.1038/ejhg.2009.194. Epub 2009 Nov 4.

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

Peter A Underhill  1 , 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 Pshenichnov, Oleg 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
Affiliations

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

Peter A Underhill et al. Eur J Hum Genet. 2010 Apr.

Erratum in

  • Eur J Hum Genet. 2010 Sep;18(9):1074

Abstract

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.

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Figures

Figure 1
Figure 1
Geographic distribution of haplogroup R1a1a frequency. Spatial frequency map was obtained applying the frequencies from Supplementary Table S2 and for 8429 individuals representing 118 populations from literature., , , , , , , , , , , , , , , , , , , , , Dots on the map indicate the approximate locations of the sampled populations. The frequency data were converted to isofrequency maps in Surfer software (version 7, Golden Software Inc., Golden, CO, USA) following the Kriging procedure. The inset map illustrates the available data (Supplementary Table S2) for the regional expansion times in KYA (thousands of years ago) of M17 Y-chromosomes. We note that especially in the latter case the density of the data points is too low for any viable geostatistical analyses. Phylogenetic tree relating SNP markers that define haplogroup R1a and its subgroups is shown in the inset. Previously described SNP markers are underlined. Markers M56, M157, M64.2, M87, M204, P98 and PK5 shown in gray font were not typed as they were previously detected at nonpolymorphic frequencies in other studies. PCR amplicons for 12 SNPs from Hinds et al (M420, M448, M449, M459, M511, M513, M516 and rs17250901) and 2 from Repping et al (Page07 and Page68) were designed and tested for male specificity using female control DNA. The phylogenetic relationships of these SNPs were evaluated in a geographically diverse panel of 18 R1a1 samples and 2 R1b* samples ranging from Northwest Europe to South Asia using DHPLC technology, and confirmed by direct sequencing of representative samples. Detailed specifications for these markers are given in Supplementary Table S5.
Figure 2
Figure 2
Geographic distribution of haplogroup R1a1a7-M458 frequency. The spatial frequency map was obtained applying the frequencies from Supplementary Table S2 (dots on the map indicate the approximate locations of the sampled populations) to the Surfer software (version 7, Golden Software Inc., Golden, CO, USA) following the Inverse Distance to Power (Power 3.75; smoothness 0) procedure with added break lines indicated by dashed blue lines in the seas. Spatial distribution of the expansion times of the regional M458 derived Y-chromosomes is shown in the lower left inset map according to data in Supplementary Table S4. See text for discussion concerning the spread of M458 lineages with the major European river basins (shown in blue) and major Neolithic and Metal Age cultures.
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