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Document Type

Article

Authors

Doron M. Behar, Molecular Medicine Laboratory, Rambam Health Care Campus, Haifa, IsraelFollow
Mait Metspalu, Estonian Biocentre, Evolutionary Biology Group, Tartu, EstoniaFollow
Yael Baran, Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, IsraelFollow
Naama M. Kopelman, Porter School of Environmental Studies, Department of Zoology, Tel-Aviv University, Tel-Aviv, IsraelFollow
Bayazit Yunusbayev, Estonian Biocentre, Evolutionary Biology Group, Tartu, Estonia.Follow
Ariella Gladstein, ARL Division of Biotechnology, University of Arizona, Tucson, AZFollow
Shay Tzur, Molecular Medicine Laboratory, Rambam Health Care Campus, Haifa, IsraelFollow
Hovhannes Sahakyan, Estonian Biocentre, Evolutionary Biology Group, Tartu, Estonia.Follow
Ardeshir Bahmanimehr, Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences, Yerevan, ArmeniaFollow
Levon Yepiskoposyan, Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences, Yerevan, ArmeniaFollow
Kristiina Tambets, Estonian Biocentre, Evolutionary Biology Group, Tartu, Estonia.Follow
Elza K. Khusnutdinova, Estonian Biocentre, Evolutionary Biology Group, Tartu, Estonia.Follow
Alena Kushniarevich, Estonian Biocentre, Evolutionary Biology Group, Tartu, Estonia.Follow
Oleg Balanovsky, Vavilov Institute for General Genetics, Russian Academy of Sciences, Moscow, RussiaFollow
Elena Balanovsky, Vavilov Institute for General Genetics, Russian Academy of Sciences, Moscow, RussiaFollow
Lejla Kovacevic, Institute for Genetic Engineering and Biotechnology, Sarajevo, Bosnia and HerzegovinaFollow
Damir Marjanovic, Institute for Genetic Engineering and Biotechnology, Sarajevo, Bosnia and HerzegovinaFollow
Evelin Mihailov, Estonian Genome Center, University of Tartu, Tartu, EstoniaFollow
Anastasia Kouvatsi, Department of Genetics, Development and Molecular Biology, Aristotle University of Thessaloniki, Thessaloniki, GreeceFollow
Costas Triantaphyllidis, Department of Genetics, Development and Molecular Biology, Aristotle University of Thessaloniki, Thessaloniki, GreeceFollow
Roy J. King, Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CAFollow
Ornella Semino, Dipartimento di Biologia e Biotecnologie “Lazzaro Spallanzani,” Università di Pavia, Pavia, ItalyFollow
Antonio Torroni, Dipartimento di Biologia e Biotecnologie “Lazzaro Spallanzani,” Università di Pavia, Pavia, ItalyFollow
Michael F. Hammer, ARL Division of Biotechnology, University of Arizona, Tucson, AZFollow
Ene Metspalu, Department of Evolutionary Biology, University of Tartu, Tartu, EstoniaFollow
Karl Skorecki, Molecular Medicine Laboratory, Rambam Health Care Campus, Haifa, IsraelFollow
Saharon Rosset, Department of Statistics and Operations Research, School of Mathematical Sciences, Tel-Aviv University, Tel-Aviv, IsraelFollow
Eran Halperin, Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, IsraelFollow
Richard Villems, Estonian Biocentre, Evolutionary Biology Group, Tartu, Estonia.Follow
Noah A. Rosenberg, Department of Biology, Stanford UniversityFollow

Abstract

The origin and history of the Ashkenazi Jewish population have long been of great interest, and advances in high-throughput genetic analysis have recently provided a new approach for investigating these topics. We and others have argued on the basis of genome-wide data that the Ashkenazi Jewish population derives its ancestry from a combination of sources tracing to both Europe and the Middle East. It has been claimed, however, through a reanalysis of some of our data, that a large part of the ancestry of the Ashkenazi population originates with the Khazars, a Turkic-speaking group that lived to the north of the Caucasus region ~1,000 years ago. Because the Khazar population has left no obvious modern descendants that could enable a clear test for a contribution to Ashkenazi Jewish ancestry, the Khazar hypothesis has been difficult to examine using genetics. Furthermore, because only limited genetic data have been available from the Caucasus region, and because these data have been concentrated in populations that are genetically close to populations from the Middle East, the attribution of any signal of Ashkenazi-Caucasus genetic similarity to Khazar ancestry rather than shared ancestral Middle Eastern ancestry has been problematic. Here, through integration of genotypes on newly collected samples with data from several of our past studies, we have assembled the largest data set available to date for assessment of Ashkenazi Jewish genetic origins. This data set contains genome-wide single-nucleotide polymorphisms in 1,774 samples from 106 Jewish and non-Jewish populations that span the possible regions of potential Ashkenazi ancestry: Europe, the Middle East, and the region historically associated with the Khazar Khaganate. The data set includes 261 samples from 15 populations from the Caucasus region and the region directly to its north, samples that have not previously been included alongside Ashkenazi Jewish samples in genomic studies. Employing a variety of standard techniques for the analysis of population-genetic structure, we find that Ashkenazi Jews share the greatest genetic ancestry with other Jewish populations, and among non-Jewish populations, with groups from Europe and the Middle East. No particular similarity of Ashkenazi Jews with populations from the Caucasus is evident, particularly with the populations that most closely represent the Khazar region. Thus, analysis of Ashkenazi Jews together with a large sample from the region of the Khazar Khaganate corroborates the earlier results that Ashkenazi Jews derive their ancestry primarily from populations of the Middle East and Europe, that they possess considerable shared ancestry with other Jewish populations, and that there is no indication of a significant genetic contribution either from within or from north of the Caucasus region.

Supplemental File 1.xlsx (166 kB)
Samples information

Supplemental Table 1.xlsx (23 kB)
ASD

Supplemental Table 2.xlsx (10 kB)
IBD

Behar Fig2.pdf (2048 kB)
Figure 2: Principal components analysis and spatial ancestry analysis

Behar Fig4.pdf (3298 kB)
Figure 4: Correlation of population-level mean membership proportions

Behar SuppFig1-2.pdf (591 kB)
Supplemental Figures 1-2: Scatter plot of the first, second, and third principal components for all samples included in the study

Behar SuppFig3.pdf (9564 kB)
Supplemental Figure 3: Admixture plots

Behar SuppFig6.pdf (179 kB)
Supplemental Figure 6: Clumpp scores versus log-likelihood (LL) differences

Behar SuppFig7.pdf (1509 kB)
Supplemental Figure 7: Clumpp scores (right y-axis) versus log-likelihood (LL) differences for different values of K

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