Abraham's children in the genome era: major Jewish diaspora populations comprise distinct genetic clusters with shared Middle Eastern Ancestry

Abstract

For more than a century, Jews and non-Jews alike have tried to define the relatedness of contemporary Jewish people. Previous genetic studies of blood group and serum markers suggested that Jewish groups had Middle Eastern origin with greater genetic similarity between paired Jewish populations. However, these and successor studies of monoallelic Y chromosomal and mitochondrial genetic markers did not resolve the issues of within and between-group Jewish genetic identity. Here, genome-wide analysis of seven Jewish groups (Iranian, Iraqi, Syrian, Italian, Turkish, Greek, and Ashkenazi) and comparison with non-Jewish groups demonstrated distinctive Jewish population clusters, each with shared Middle Eastern ancestry, proximity to contemporary Middle Eastern populations, and variable degrees of European and North African admixture. Two major groups were identified by principal component, phylogenetic, and identity by descent (IBD) analysis: Middle Eastern Jews and European/Syrian Jews. The IBD segment sharing and the proximity of European Jews to each other and to southern European populations suggested similar origins for European Jewry and refuted large-scale genetic contributions of Central and Eastern European and Slavic populations to the formation of Ashkenazi Jewry. Rapid decay of IBD in Ashkenazi Jewish genomes was consistent with a severe bottleneck followed by large expansion, such as occurred with the so-called demographic miracle of population expansion from 50,000 people at the beginning of the 15th century to 5,000,000 people at the beginning of the 19th century. Thus, this study demonstrates that European/Syrian and Middle Eastern Jews represent a series of geographical isolates or clusters woven together by shared IBD genetic threads.

Figure 1

Principal Component Analysis of Jewish and Non-Jewish Populations Principal components analysis of Jewish populations in a global (A) and regional context (B, PC1 versus PC2; C, PC1 versus PC3) CNVs (D, PC1 versus PC3). ASH, Ashkenazi Jews; IRN, Iranian Jews; IRQ, Iraqi Jews; SYR, Syrian Jews; ITJ, Italian Jews; GRK, Greek Jews; TUR, Turkey Jews. N. Italian is a combined set comprising Bergamo and Tuscan Italians. In (A), Middle Eastern non-Jewish populations are in blue, Jewish populations are in brown, and European populations are in red.

Figure 2

STRUCTURE and Phylogenetic Analysis of Jewish Populations (A) STRUCTURE results for K = 2 to 6 for Jewish populations combined with selected HGDP worldwide populations. Each individual is represented by a vertical line, partitioned into colored segments that correspond to membership coefficients in the subgroups. The analysis is based on 3904 SNPs with potentially high informativeness in revealing population structure (see Material and Methods). (B) Expanded view of STRUCTURE results for Jewish populations for K = 4 to 6. (C) Neighbor-joining tree of Jewish, European, and Israel non-Jews populations with Central/Southern African population as outgroup. Pairwise Fst distances were used for constructing the tree. Major population groups are indicated by right bracket. 500 bootstrap replications were performed to obtain confidence value for each interior node. Only bootstrap values above 50% are shown.

Figure 3

Analysis of Shared Informative by Descent Segments across Jewish and Non-Jewish Populations (A) Average total sharing across populations. The genome-wide average IBD sharing (y axis) for any two individuals sampled from different Mediterranean and European population pairs (x axis: top 50% sharing pairs, detail on top 15% pairs) was computed. The population pairs have been grouped into Jewish-Jewish (red bars), Jewish-non-Jewish (yellow bars), and non-Jewish-non-Jewish (blue bars). (B) Distribution of segment lengths within each Jewish population. The expected number of IBD segments shared within each Jewish population (y axis) for segments of length 5 cM and 10 cM were computed. (C) Planar embedding of Jewish populations, with their inverse distances corresponding to average IBD between them (see Material and Methods).