The genome-wide structure of the Jewish people (original) (raw)

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Gene Expression Omnibus

Data deposits

The array data described in this paper are deposited in the Gene Expression Omnibus under accession number GSE21478.

References

1. Ben-Sasson, H. H. A History of the Jewish People (Harvard Univ. Press, 1976)
   Google Scholar
2. De Lange, N. Atlas of the Jewish World (Phaidon Press, 1984)
   Google Scholar
3. Mahler, R. A History of Modern Jewry (Schocken, 1971)
   Google Scholar
4. Stillman, N. A. Jews of Arab Lands: A History and Source Book (Jewish Publication Society of America, 1979)
   Google Scholar
5. Della Pergola, S. in Papers in Jewish Demography 1997 (eds Della Pergola, S. & Even, J.) 11–33 (The Hebrew University of Jerusalem, 1997)
   Google Scholar
6. Cavalli-Sforza, L. L., Menozzi, A. & Piazza, A. in The History and Geography of Human Genes 4 (Princeton Univ. Press, 1994)
   MATH Google Scholar
7. Bauchet, M. et al. Measuring European population stratification with microarray genotype data. Am. J. Hum. Genet. 80, 948–956 (2007)
   Article CAS Google Scholar
8. Behar, D. M. et al. Counting the founders: the matrilineal genetic ancestry of the Jewish Diaspora. PLoS ONE 3, e2062 (2008)
   Article ADS Google Scholar
9. Hammer, M. F. et al. Jewish and Middle Eastern non-Jewish populations share a common pool of Y-chromosome biallelic haplotypes. Proc. Natl Acad. Sci. USA 97, 6769–6774 (2000)
   Article ADS CAS Google Scholar
10. Kopelman, N. M. et al. Genomic microsatellites identify shared Jewish ancestry intermediate between Middle Eastern and European populations. BMC Genet. 10, 80 (2009)
    Article Google Scholar
11. Need, A. C., Kasperaviciute, D., Cirulli, E. T. & Goldstein, D. B. A genome-wide genetic signature of Jewish ancestry perfectly separates individuals with and without full Jewish ancestry in a large random sample of European Americans. Genome Biol. 10, R7 (2009)
    Article Google Scholar
12. Olshen, A. B. et al. Analysis of genetic variation in Ashkenazi Jews by high density SNP genotyping. BMC Genet. 9, 14 (2008)
    Article Google Scholar
13. Ostrer, H. A genetic profile of contemporary Jewish populations. Nature Rev. Genet. 2, 891–898 (2001)
    Article CAS Google Scholar
14. Price, A. L. et al. Discerning the ancestry of European Americans in genetic association studies. PLoS Genet. 4, e236 (2008)
    Article Google Scholar
15. Seldin, M. F. et al. European population substructure: clustering of northern and southern populations. PLoS Genet. 2, e143 (2006)
    Article Google Scholar
16. Tian, C. et al. Analysis and application of European genetic substructure using 300 K SNP information. PLoS Genet. 4, e4 (2008)
    Article Google Scholar
17. Abdulla, M. A. et al. Mapping human genetic diversity in Asia. Science 326, 1541–1545 (2009)
    Article CAS Google Scholar
18. Li, J. Z. et al. Worldwide human relationships inferred from genome-wide patterns of variation. Science 319, 1100–1104 (2008)
    Article ADS CAS Google Scholar
19. Jakobsson, M. et al. Genotype, haplotype and copy-number variation in worldwide human populations. Nature 451, 998–1003 (2008)
    Article ADS CAS Google Scholar
20. Novembre, J. et al. Genes mirror geography within Europe. Nature 456, 98–101 (2008)
    Article ADS CAS Google Scholar
21. Reich, D., Thangaraj, K., Patterson, N., Price, A. L. & Singh, L. Reconstructing Indian population history. Nature 461, 489–494 (2009)
    Article ADS CAS Google Scholar
22. Biswas, S., Scheinfeldt, L. B. & Akey, J. M. Genome-wide insights into the patterns and determinants of fine-scale population structure in humans. Am. J. Hum. Genet. 84, 641–650 (2009)
    Article CAS Google Scholar
23. Tishkoff, S. A. et al. The genetic structure and history of Africans and African Americans. Science 324, 1035–1044 (2009)
    Article ADS CAS Google Scholar
24. Patterson, N., Price, A. L. & Reich, D. Population structure and eigenanalysis. PLoS Genet. 2, e190 (2006)
    Article Google Scholar
25. Hourani, A. A History of the Arab Peoples (Faber & Faber, 1991)
    Google Scholar
26. Weiss, K. M. & Long, J. C. Non-Darwinian estimation: my ancestors, my genes’ ancestors. Genome Res. 19, 703–710 (2009)
    Article CAS Google Scholar
27. Alexander, D. H., Novembre, J. & Lange, K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655–1664 (2009)
    Article CAS Google Scholar
28. Rasmussen, M. et al. Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463, 757–762 (2010)
    Article ADS CAS Google Scholar
29. Gao, X. & Martin, E. R. Using allele sharing distance for detecting human population stratification. Hum. Hered. 68, 182–191 (2009)
    Article Google Scholar
30. Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559–575 (2007)
    Article CAS Google Scholar

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Acknowledgements

We thank the individuals who provided DNA samples for this study, including the National Laboratory for the Genetics of Israeli Populations; Mari Nelis, Georgi Hudjashov and Viljo Soo for conducting the autosomal genotyping; Lauri Anton for computational help. R.V. and D.M.B. thank the European Commission, Directorate-General for Research for FP7 Ecogene grant 205419. R.V. thanks the European Union, Regional Development Fund through a Centre of Excellence in Genomics grant and the Swedish Collegium for Advanced Studies for support during the initial stage of this study. E.M. and Si.R. thank the Estonian Science Foundation for grants 7858 and 7445, respectively. K.S. thanks the Arthur and Rosalinde Gilbert Foundation fund of the American Technion Society. Sa.R. thanks the European Union for Marie Curie International Reintegration grant CT-2007-208019, and the Israeli Science Foundation for grant 1227/09. IPATIMUP is an Associate Laboratory of the Portuguese Ministry of Science, Technology and Higher Education and is partly supported by Fundação para a Ciência ea Tecnologia, the Portuguese Foundation for Science and Technology.

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Author notes

1. Doron M. Behar, Bayazit Yunusbayev and Mait Metspalu: These authors contributed equally to this work.

Authors and Affiliations

1. Molecular Medicine Laboratory, Rambam Health Care Campus, Haifa 31096, Israel
   Doron M. Behar, Guennady Yudkovsky & Karl Skorecki
2. Estonian Biocentre and Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia
   Doron M. Behar, Bayazit Yunusbayev, Mait Metspalu, Ene Metspalu, Jüri Parik, Siiri Rootsi, Gyaneshwer Chaubey, Ildus Kutuev & Richard Villems
3. Institute of Biochemistry and Genetics, Ufa Research Center, Russian Academy of Sciences, Ufa 450054, Russia
   Bayazit Yunusbayev, Ildus Kutuev & Elza K. Khusnutdinova
4. Department of Statistics and Operations Research, School of Mathematical Sciences, Tel Aviv University, Tel Aviv 69978, Israel
   Saharon Rosset
5. Rappaport Faculty of Medicine and Research Institute, Technion – Israel Institute of Technology, Haifa 31096, Israel
   Guennady Yudkovsky & Karl Skorecki
6. Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moscow 115478, Russia
   Oleg Balanovsky
7. Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia 27100, Italy
   Ornella Semino
8. Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto 4200-465, Portugal
   Luisa Pereira
9. Faculdade de Medicina, Universidade do Porto, Porto 4200-319, Portugal
   Luisa Pereira
10. Institute of Evolutionary Biology (CSIC-UPF), CEXS-UPF-PRBB and CIBER de Epidemiología y Salud Pública, Barcelona 08003, Spain
    David Comas
11. Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
    David Gurwitz & Batsheva Bonne-Tamir
12. Department of the Languages and Cultures of the Near and Middle East, Faculty of Languages and Cultures, School of Oriental and African Studies (SOAS), University of London, London WC1H 0XG, UK
    Tudor Parfitt
13. ARL Division of Biotechnology, University of Arizona, Tucson, Arizona 85721, USA,
    Michael F. Hammer

Authors

1. Doron M. Behar
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2. Bayazit Yunusbayev
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3. Mait Metspalu
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4. Ene Metspalu
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5. Saharon Rosset
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6. Jüri Parik
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7. Siiri Rootsi
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8. Gyaneshwer Chaubey
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9. Ildus Kutuev
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10. Guennady Yudkovsky
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11. Elza K. Khusnutdinova
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12. Oleg Balanovsky
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13. Ornella Semino
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14. Luisa Pereira
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15. David Comas
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16. David Gurwitz
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17. Batsheva Bonne-Tamir
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18. Tudor Parfitt
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19. Michael F. Hammer
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20. Karl Skorecki
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21. Richard Villems
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Contributions

D.M.B. and R.V. conceived and designed the study. B.B.T., D.C., D.G., D.M.B., E.K.K., G.C., I.K., L.P., M.F.H., O.B., O.S., T.P. and R.V. provided DNA samples to this study. E.M., J.P. and G.Y. screened and prepared the samples for the autosomal genotyping. D.M.B., E.M., G.C., M.F.H. and Si.R. generated and summarized the database for the uniparental analysis. B.Y., M.M. and Sa.R. designed and applied the modelling methodology and statistical analysis. T.P. provided expert input regarding the relevant historical aspects. B.Y., D.M.B., K.S., M.F.H., M.M., R.V. and Sa.R. wrote the paper. B.Y., D.M.B. and M.M. contributed equally to the paper. All authors discussed the results and commented on the manuscript.

Corresponding authors

Correspondence toDoron M. Behar, Karl Skorecki or Richard Villems.

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Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Notes 1-6, References and Supplementary Tables 1-5. (PDF 1143 kb)

Supplementary Figures

This file contains Supplementary Figures 1 and 3-6 and legends for Supplementary Figures 1-6 (see separate file for Supplementary Figure 2) (PDF 6701 kb)

Supplementary Figure 2

This file shows the Principal Component Analysis of the Old World High-Density Array Data. a, Scatter plot of Old World individuals, showing the first two principal components. Here, the first PC (4.2% of variation, vertical axis) captures primarily differences between sub-Saharan Africans and the rest of the Old World. The second PC (3.4% of variation, horizontal axis) differentiates West Eurasians from South and East Asians. Axes of variation were scaled according to eigenvalues. Each letter code (Supplementary Table 1) corresponds to one individual and the colour indicates population origin. b, Scatter plot of Old World individuals, showing PC1 and PC3. c, Scatter plot of Old World individuals, showing PC1 and PC4. Note that eigenvalues for PC3 and PC4 are ~8 times smaller than for PC1 and 2. (PDF 1892 kb)

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Behar, D., Yunusbayev, B., Metspalu, M. et al. The genome-wide structure of the Jewish people.Nature 466, 238–242 (2010). https://doi.org/10.1038/nature09103

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• Received: 09 December 2009
• Accepted: 21 April 2010
• Published: 09 June 2010
• Issue Date: 08 July 2010
• DOI: https://doi.org/10.1038/nature09103