Contemporary Jews comprise an aggregate of ethno-religious communities whose worldwide members identify with each other through various shared religious, historical and cultural traditions1,2. Historical evidence suggests common origins in the Middle East, followed by migrations leading to the establishment of communities of Jews in Europe, Africa and Asia, in what is termed the Jewish Diaspora3,4,5. This complex demographic history imposes special challenges in attempting to address the genetic structure of the Jewish people6. Although many genetic studies have shed light on Jewish origins and on diseases prevalent among Jewish communities, including studies focusing on uniparentally and biparentally inherited markers7,8,9,10,11,12,13,14,15,16, genome-wide patterns of variation across the vast geographic span of Jewish Diaspora communities and their respective neighbours have yet to be addressed. Here we use high-density bead arrays to genotype individuals from 14 Jewish Diaspora communities and compare these patterns of genome-wide diversity with those from 69 Old World non-Jewish populations, of which 25 have not previously been reported. These samples were carefully chosen to provide comprehensive comparisons between Jewish and non-Jewish populations in the Diaspora, as well as with non-Jewish populations from the Middle East and north Africa. Principal component and structure-like analyses identify previously unrecognized genetic substructure within the Middle East. Most Jewish samples form a remarkably tight subcluster that overlies Druze and Cypriot samples but not samples from other Levantine populations or paired Diaspora host populations. In contrast, Ethiopian Jews (Beta Israel) and Indian Jews (Bene Israel and Cochini) cluster with neighbouring autochthonous populations in Ethiopia and western India, respectively, despite a clear paternal link between the Bene Israel and the Levant. These results cast light on the variegated genetic architecture of the Middle East, and trace the origins of most Jewish Diaspora communities to the Levant.
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Gene Expression Omnibus
The array data described in this paper are deposited in the Gene Expression Omnibus under accession number GSE21478.
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.
This file contains Supplementary Notes 1-6, References and Supplementary Tables 1-5.
This file contains Supplementary Figures 1 and 3-6 and legends for Supplementary Figures 1-6 (see separate file for 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.
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Pharmaceutical Research (2018)