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A Genome-Wide Analysis of Populations from European Russia Reveals a New Pole of Genetic Diversity in Northern Europe

Author

Listed:
  • Andrey V Khrunin
  • Denis V Khokhrin
  • Irina N Filippova
  • Tõnu Esko
  • Mari Nelis
  • Natalia A Bebyakova
  • Natalia L Bolotova
  • Janis Klovins
  • Liene Nikitina-Zake
  • Karola Rehnström
  • Samuli Ripatti
  • Stefan Schreiber
  • Andre Franke
  • Milan Macek
  • Veronika Krulišová
  • Jan Lubinski
  • Andres Metspalu
  • Svetlana A Limborska

Abstract

Several studies examined the fine-scale structure of human genetic variation in Europe. However, the European sets analyzed represent mainly northern, western, central, and southern Europe. Here, we report an analysis of approximately 166,000 single nucleotide polymorphisms in populations from eastern (northeastern) Europe: four Russian populations from European Russia, and three populations from the northernmost Finno-Ugric ethnicities (Veps and two contrast groups of Komi people). These were compared with several reference European samples, including Finns, Estonians, Latvians, Poles, Czechs, Germans, and Italians. The results obtained demonstrated genetic heterogeneity of populations living in the region studied. Russians from the central part of European Russia (Tver, Murom, and Kursk) exhibited similarities with populations from central–eastern Europe, and were distant from Russian sample from the northern Russia (Mezen district, Archangelsk region). Komi samples, especially Izhemski Komi, were significantly different from all other populations studied. These can be considered as a second pole of genetic diversity in northern Europe (in addition to the pole, occupied by Finns), as they had a distinct ancestry component. Russians from Mezen and the Finnic-speaking Veps were positioned between the two poles, but differed from each other in the proportions of Komi and Finnic ancestries. In general, our data provides a more complete genetic map of Europe accounting for the diversity in its most eastern (northeastern) populations.

Suggested Citation

  • Andrey V Khrunin & Denis V Khokhrin & Irina N Filippova & Tõnu Esko & Mari Nelis & Natalia A Bebyakova & Natalia L Bolotova & Janis Klovins & Liene Nikitina-Zake & Karola Rehnström & Samuli Ripatti & , 2013. "A Genome-Wide Analysis of Populations from European Russia Reveals a New Pole of Genetic Diversity in Northern Europe," PLOS ONE, Public Library of Science, vol. 8(3), pages 1-9, March.
    • Handle: RePEc:plo:pone00:0058552
    DOI: 10.1371/journal.pone.0058552
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    References listed on IDEAS

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    1. John Novembre & Toby Johnson & Katarzyna Bryc & Zoltán Kutalik & Adam R. Boyko & Adam Auton & Amit Indap & Karen S. King & Sven Bergmann & Matthew R. Nelson & Matthew Stephens & Carlos D. Bustamante, 2008. "Genes mirror geography within Europe," Nature, Nature, vol. 456(7219), pages 274-274, November.
    2. Chao Tian & Robert M Plenge & Michael Ransom & Annette Lee & Pablo Villoslada & Carlo Selmi & Lars Klareskog & Ann E Pulver & Lihong Qi & Peter K Gregersen & Michael F Seldin, 2008. "Analysis and Application of European Genetic Substructure Using 300 K SNP Information," PLOS Genetics, Public Library of Science, vol. 4(1), pages 1-11, January.
    3. John Novembre & Toby Johnson & Katarzyna Bryc & Zoltán Kutalik & Adam R. Boyko & Adam Auton & Amit Indap & Karen S. King & Sven Bergmann & Matthew R. Nelson & Matthew Stephens & Carlos D. Bustamante, 2008. "Genes mirror geography within Europe," Nature, Nature, vol. 456(7218), pages 98-101, November.
    4. Nick Patterson & Alkes L Price & David Reich, 2006. "Population Structure and Eigenanalysis," PLOS Genetics, Public Library of Science, vol. 2(12), pages 1-20, December.
    5. Doron M. Behar & Bayazit Yunusbayev & Mait Metspalu & Ene Metspalu & Saharon Rosset & Jüri Parik & Siiri Rootsi & Gyaneshwer Chaubey & Ildus Kutuev & Guennady Yudkovsky & Elza K. Khusnutdinova & Oleg , 2010. "The genome-wide structure of the Jewish people," Nature, Nature, vol. 466(7303), pages 238-242, July.
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