The Ashkenazi Jewish (AJ) population is important in medical genetics due to its high rate of Mendelian disorders and other unique genetic characteristics. Ashkenazi Jews have appeared in Europe in the 10th century, and their ancestry is thought to involve an admixture of European (EU) and Middle-Eastern (ME) groups. However, both the time and place of admixture in Europe are obscure and subject to intense debate. Here, we attempt to characterize the Ashkenazi admixture history using a large Ashkenazi sample and careful application of new and existing methods. Our main approach is based on local ancestry inference, assigning each Ashkenazi genomic segment as EU or ME, and comparing allele frequencies across EU segments to those of different EU populations. The contribution of each EU source was also evaluated using GLOBETROTTER and analysis of IBD sharing. The time of admixture was inferred using multiple tools, relying on statistics such as the distributions of segment lengths and the total EU ancestry per chromosome and the correlation of ancestries along the chromosome. Our simulations demonstrated that distinguishing EU vs ME ancestry is subject to considerable noise at the single segment level, but nevertheless, conclusions could be drawn based on chromosome-wide statistics. The predominant source of EU ancestry in AJ was found to be Southern European (≈60-80%), with the rest being likely Eastern European. The inferred admixture time was ≈35 generations ago, but multiple lines of evidence suggests that it represents an average over two or more admixture events, pre- and post-dating the founder event experienced by AJ in late medieval times. The time of the pre-bottleneck admixture event was bounded to 25-55 generations ago.
I think this preprint is coming close to the answer. Why does a small ethno-religious minority in Europe matter? Well, that’s a matter of historical contingency.
In any case, there were some good papers on Ashkenazi Jewish genetics which came out in the spring of 2010. They really moved the ball forward from the uniparental work. But they suffered from two major problems. First, the putative “parent” populations of Ashkenazi Jews are not that genetically distinct. Second, the hypothesized parental populations were often implausible; e.g., Northern Europeans and modern Levantines.
The likely parental populations of Ashkenazi Jews are Roman period peoples of the eastern Mediterranean, particularly the swath of territory from Alexandria up to Anatolia, and, the peoples of the western Mediterranean. That is, Levantines and Iberians & Italians. These two groups are distinct, but they’re not that distinct.
Additionally, the more and more we learn about the Middle East, the more likely it seems that Muslim populations, who are often modeled as a parental group, are highly cosmopolitan compared to ancient groups. Recall that Neolithic farmers from the Levant resemble Sardinians more than they do locals, because of later migration from further east in Eurasia, as well as later African gene flow. Using imperfect reference populations will probably skew the results appropriately.
The major change in the past few years is the usage of more genetic information than common genotypes. This paper for example looks at haplotype information. Sequences of variants across the genome. This preserves more recent genetic variation. In other cases you can look at whole genome sequences, and focus on low frequency variants which are extremely informative of recent population differentiation.
Ultimately the only reason I’d suggest that this paper is lacking is the imperfection of Middle Eastern source populations. That’s probably increasing the European and decreasing the Middle Eastern fraction somewhat on the margins. The contemporary populations of the Near East have changed a fair amount over the past 2,000 years, though there is still some continuity.