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, 13 (4), e1006644
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The Time and Place of European Admixture in Ashkenazi Jewish History

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The Time and Place of European Admixture in Ashkenazi Jewish History

James Xue et al. PLoS Genet.

Abstract

The Ashkenazi Jewish (AJ) population is important in genetics due to its high rate of Mendelian disorders. AJ appeared in Europe in the 10th century, and their ancestry is thought to comprise European (EU) and Middle-Eastern (ME) components. However, both the time and place of admixture are subject to debate. Here, we attempt to characterize the AJ admixture history using a careful application of new and existing methods on a large AJ sample. Our main approach was based on local ancestry inference, in which we first classified each AJ genomic segment as EU or ME, and then compared allele frequencies along the EU segments to those of different EU populations. The contribution of each EU source was also estimated using GLOBETROTTER and haplotype sharing. The time of admixture was inferred based on multiple statistics, including ME segment lengths, the total EU ancestry per chromosome, and the correlation of ancestries along the chromosome. The major source of EU ancestry in AJ was found to be Southern Europe (≈60-80% of EU ancestry), with the rest being likely Eastern European. The inferred admixture time was ≈30 generations ago, but multiple lines of evidence suggest that it represents an average over two or more events, pre- and post-dating the founder event experienced by AJ in late medieval times. The time of the pre-bottleneck admixture event, which was likely Southern European, was estimated to ≈25-50 generations ago.

Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Simulation results for our localization pipeline.
In each row, admixed genomes were simulated with sources from the Levant (50%) and one European region (50%). Columns correspond to the inferred proportion of the chromosomes classified as each potential source. The source of each chromosome was chosen as the one that maximizes the likelihood of observing the alleles designated by RFMix as European.
Fig 2
Fig 2. Inference of the proportion of Ashkenazi ancestry derived from each European region.
We simulated admixed chromosomes with European and Middle-Eastern ancestries, where the ME ancestry was fixed to the Levant region and to 50% of the overall ancestry. We then varied the sources of the remaining European ancestry to determine which ancestry proportions most closely match the AJ data. In (A), the simulated EU components were Southern and Western EU. For each given proportion of Southern EU ancestry, we used our LAI-based pipeline to compute the proportion of chromosomes classified as Southern European. The best match to the proportion of thus classified chromosomes observed in the real AJ data (red dot) was found when the true simulated Southern EU ancestry was 31% of the total. In (B), the same simulation procedure was repeated, except that the simulated EU components were Southern and Eastern EU. The inferred proportion of Southern EU ancestry in AJ was 37%. (C) We fixed the Southern EU contribution to 34%, the average of its estimates from (A) and (B), and varied the remaining 16% between Western and Eastern EU. The simulations suggest that the closest match to the real results is at roughly equal contribution (8%) from Western and Eastern EU.
Fig 3
Fig 3. Inferring the AJ admixture time using the lengths of admixture segments.
The mean length of RFMix-inferred Middle-Eastern segments is plotted vs the mean simulated length, which is inversely related to the simulated admixture time. The red dot corresponds to the observed mean segment length in the real AJ data.
Fig 4
Fig 4. The Probability Density Function (PDF) of ancestry proportions in AJ and in simulations.
The ancestry proportions in AJ were computed using LAI (RFMix). Simulations are of 1000 genomes with a history of an admixture pulse 32 generations ago between Middle-Eastern, Southern EU, Eastern EU, and Western EU populations. The density was estimated using a normal kernel. The admixture time was estimated by fitting the average standard deviation of the ancestry proportions across all chromosomes to the AJ data, where each chromosome was weighted by the square root of its length in cM. The confidence interval ([31,37] generations) was obtained by resampling AJ individuals, with replacement, 1000 times.
Fig 5
Fig 5. The number of IBD segments shared between Ashkenazi Jews (AJ) and other groups of populations.
IBD segments were detected by Germline and Haploscore, as explained in Methods. The population groups are as in Table 1. Note the different scale of panels (A) and (B) (segments of length between [3,7]cM and >7cM, respectively), and that sharing between AJ and either Southern Europeans or Middle Easterners completely vanishes for the longer (more recent) segments, indicating a relatively older divergence/gene flow. Also note that while sharing with Eastern Europeans is high compared to other groups, it is nevertheless a relatively rare event (≈0.04 segments per pair of individuals), in particular compared to sharing within AJ (≈3.4 segments per pair).
Fig 6
Fig 6. The relationship between the two admixture times in the Ashkenazi history, given bounds on the other admixture parameters.
In the model, two populations (A and B) mixed t1 generations ago (early event; the proportion of ancestry contributed by population A, q, is indicated in the title of each panel). At a more recent time, t2 generations ago (recent event), migrants from A replaced another proportion μ of the admixed population (also in the titles). In each panel, we assumed that q and μ are known, as is the admixture time inferred under the assumption of a pulse admixture model (titles). Under these assumptions, and using Eq (5) in Methods, we plotted the time of the early event (t1) vs the time of the recent event (t2; blue circles). The weighted average (dashed lines) is a simple approximation, in which the time inferred under the pulse model is an average of t1 and t2, weighted by the admixture proportions q and μ, respectively. In the context of the Ashkenazi Jewish admixture history, population A is European and B is Middle-Eastern. Panels (A)-(D) represent the bounds on (i) the admixture time inferred under a pulse model (24–37 generations ago); (ii) the admixture proportions at the early and recent events (34–61% and 15–23%, respectively); and (iii) the time of the recent admixture event (10–20 generations ago). These bounds are justified in the main text. The results demonstrate that (i) the weighted average is a reasonable approximation, though the pulse admixture time is influenced more by the early event, perhaps as it results in more admixture tracts; and (ii) the most extreme values of the early AJ event are 24 and 49 generations ago. The lower bound corresponds to the lowest value of the inferred (single event) admixture time, the highest value of the time of the recent admixture event, and the largest contribution of the early event to the overall admixture proportions, and vice versa for the upper bound.
Fig 7
Fig 7. A proposed model for the recent AJ history.
The proposed intervals for the dates and admixture proportions are based on multiple methods, as described in the main text.

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