North African Jewish and non-Jewish populations form distinctive, orthogonal clusters

Abstract

North African Jews constitute the second largest Jewish Diaspora group. However, their relatedness to each other; to European, Middle Eastern, and other Jewish Diaspora groups; and to their former North African non-Jewish neighbors has not been well defined. Here, genome-wide analysis of five North African Jewish groups (Moroccan, Algerian, Tunisian, Djerban, and Libyan) and comparison with other Jewish and non-Jewish groups demonstrated distinctive North African Jewish population clusters with proximity to other Jewish populations and variable degrees of Middle Eastern, European, and North African admixture. Two major subgroups were identified by principal component, neighbor joining tree, and identity-by-descent analysis-Moroccan/Algerian and Djerban/Libyan-that varied in their degree of European admixture. These populations showed a high degree of endogamy and were part of a larger Ashkenazi and Sephardic Jewish group. By principal component analysis, these North African groups were orthogonal to contemporary populations from North and South Morocco, Western Sahara, Tunisia, Libya, and Egypt. Thus, this study is compatible with the history of North African Jews-founding during Classical Antiquity with proselytism of local populations, followed by genetic isolation with the rise of Christianity and then Islam, and admixture following the emigration of Sephardic Jews during the Inquisition.

Fig. 1.

Principal component analysis (PCA) of Jewish populations combined with other HGDP groups in global (A) and regional contexts (B and C). Dense regions with many overlapping populations are circled for the purpose of illustration, with a list of the groups adjacent.

Fig. 2.

Neighbor-joining tree showing the relationship of European, Jewish, Middle Eastern, and North African populations, using F_ST as the distance metric. The tree was rooted by using the reference mixed Central and Southern African population as an out-group. Major population groups are labeled at the right, with the red bar within the Jewish group denoting North African Jews. Five hundred bootstrap iterations were tested to assess the robustness of the tree [the labels at the nodes represent the number of iterations (%) in which that configuration was seen]. Populations labeled with an asterisk (*) cluster outside of their expected groups.

Fig. 3.

Genome-wide IBD sharing for the average pair of individuals within (A) and across (B and C) populations. With the exception of non-Jewish Tunisian samples, IBD sharing is higher within Jewish groups, reflecting higher levels of endogamy. Jewish populations exhibit higher sharing with other Jewish populations than with geographically near groups, The average total sharing across Jewish populations is generally higher than the sharing across other population pairs, and pairs of North African Jewish populations (dark to red color bars) share more segments IBD than most other Jewish pairs.

Fig. 4.

STRUCTURE results for Jewish populations combined with Middle Eastern, European, East Asian, and African populations from HGDP. K values of 3–7 are shown; each represents an alignment of 10 independent runs. Vertical bars represent individuals, which are grouped by their known populations and further combined into general regional groups, illustrated by the top bar.

Fig. 5.

Ancestry deconvolution. The genome-wide ancestry of North African Jewish and non-Jewish populations is compared with respect to European (Basque), Maghrebi (Tunisian non-Jewish), and Middle Eastern (Palestinian) origins. Jewish populations exhibit increased European and decreased Maghrebi ancestry compared with corresponding non-Jewish groups. The Middle Eastern component is comparable across all groups.