Genomic microsatellites identify shared Jewish ancestry intermediate between Middle Eastern and European populations

Abstract

Background: Genetic studies have often produced conflicting results on the question of whether distant Jewish populations in different geographic locations share greater genetic similarity to each other or instead, to nearby non-Jewish populations. We perform a genome-wide population-genetic study of Jewish populations, analyzing 678 autosomal microsatellite loci in 78 individuals from four Jewish groups together with similar data on 321 individuals from 12 non-Jewish Middle Eastern and European populations.

Results: We find that the Jewish populations show a high level of genetic similarity to each other, clustering together in several types of analysis of population structure. Further, Bayesian clustering, neighbor-joining trees, and multidimensional scaling place the Jewish populations as intermediate between the non-Jewish Middle Eastern and European populations.

Conclusion: These results support the view that the Jewish populations largely share a common Middle Eastern ancestry and that over their history they have undergone varying degrees of admixture with non-Jewish populations of European descent.

Figure 1

Variability statistics as functions of the number of sampled chromosomes, for combined samples from European, Jewish, and Middle Eastern populations. (a) The mean number of distinct alleles per locus. (b) The mean number of private alleles per locus.

Figure 2

Population structure for European, Jewish, and Middle Eastern populations, inferred with unsupervised clustering. The number of predefined clusters (K) is indicated to the left of each plot. Each individual is represented by a thin vertical line that is partitioned into K colored components according to the inferred membership in K genetic clusters. For each K, only the major mode is shown (obtained in 39 of 40 replicates for K = 2, 40 of 40 replicates for K = 3, 15 of 40 replicates for K = 4, 40 of 40 replicates for K = 5, and 20 of 40 replicates for K = 6).

Figure 3

Neighbor-joining population trees for European, Jewish, and Middle Eastern populations. (a) Neighbor-joining tree based on the allele-sharing genetic distance. (b) Neighbor-joining tree based on the chord genetic distance. (c) Neighbor-joining tree based on Nei's standard genetic distance. External branches were colored to indicate the groups to which populations belong (blue - European; red - Jewish; green - Middle Eastern). Sequentially, internal branches were then colored if all colored branches to which they connected had the same color. The two remaining branches in black separate the European, Jewish, and Middle Eastern groups. The number on an edge represents the fraction of bootstrap replicates supporting that edge, among 10,000.

Figure 4

Similarity to Jewish populations of linear combinations of pairs of populations. (a) The highest-ranking population pairs for each Jewish population according to the minimal allele-sharing genetic distance between the Jewish population and the most similar linear combination of the population pair. The Y-axis indicates the genetic distance to a Jewish population of each pair, measured using the most similar linear combination for the pair. (b) Genetic similarity to a Jewish population (one minus genetic distance) of a linear combination of two populations, as a function of the coefficients in the linear combination. For each Jewish population, the plot shows only the population pair with the most similar linear combination to the Jewish population. The coefficients of the linear combination that produced the greatest similarity were 0.44 and 0.56 for French and Palestinians as the highest-ranking pair of the Turkish Jews (similarity 0.8359), 0.45 and 0.55 for French and Palestinians as the highest-ranking pair of the Moroccan Jews (similarity 0.8240), 0.50 and 0.50 for French and Turkish Jews as the highest-ranking pair of the Ashkenazi Jews (similarity 0.8233), and 0.42 and 0.58 for Sardinians and Palestinians as the highest-ranking pair of the Tunisian Jews (similarity 0.8070).

Figure 5

Multidimensional scaling (MDS) analysis of population structure. (a) MDS for European, Jewish, and Middle Eastern individuals. (b) MDS for European and Jewish individuals. (c) MDS for Jewish and Middle Eastern individuals, excluding Mozabites. (d) MDS for Palestinian and Jewish individuals.

Figure 6

Jewish population structure. (a) Inference using unsupervised clustering. (b) Multidimensional scaling analysis for Jewish individuals. In the unsupervised clustering analysis, the predefined number of clusters was K = 2. The most frequent mode found by Structure for K = 2 included all 40 replicates. For higher values of K, only modes with small numbers of replicates were found (not shown).