Genomic Data Reveal a Complex Making of Humans

Figure 1

The Ashkenazi Levite phylogenetic branch
All R1a-M582 Y chromosomes sampled from Ashkenazi Levites, non-Ashkenazi Levites, Ashkenazi non-Levites, and non-Jews with known or suspected Ashkenazi origin established a well-defined phylogenetic branch nested within haplogroup R1a-M582 and demonstrated a star-like expansion pattern (Fig. 2 and Supplemental Figure S1). The root of this branch is defined by a total of six polymorphic sites and designated according to one of the positions, R1a-Y2619 (g.6733896A>G) coalescing 1,743 (1,334–2,200) ybp (Table 1). The five non-Ashkenazi Levites and the single Iraqi Jew did not establish a distinct phylogenetic cluster but scattered within the Ashkenazi Levite samples. The sister clades of R1a-Y2619 within R1a-M582, coalescing ~3,143 (2,620–3,682) ybp, were sampled in Iranian Azeris, a Kerman, a Yazidi and one sample from Iberia. Further, the phylogeny demonstrates a rich diversity of R1a samples distributed throughout the Middle East, Anatolia, Caucasus and the Indian sub-continent, whereas East European branches represent an early split within R1a.

We then explored the allocation of the Horowitz Levite samples included in the phylogeny. First, the six tested Horowitz Levites were grouped into the Y chromosome haplogroup R1a-Y2619, allowing a unique glimpse into medieval Europe (Fig. 3a). The genealogic records for three of the individuals with the Horowitz surname converged to a common male ancestor born at 1615 CE or 402 ybp (Fig. 3b). The observed sequence variation between these three samples is consistent with this proposed genealogy (Fig. 3c), and accordingly, their genealogical claim could not be refuted. This prompted us to use this node as an internal calibration point. The two additional individuals affiliating with the Horowitz dynasty formed the closest paraphyletic clade R1a-YP268 to the described three sample cluster, coalescing with them 691 (555–852) ybp (Fig. 3c). The sixth sample carrying the Horowitz surname but claiming no ancestral relations with the Horowitz dynasty did not cluster with these five samples (Supplemental Figure S1).


Figure 2

The proposed Middle Eastern origin of the Ashkenazi Levite lineage based on what was previously a relatively limited number of reported samples20, can now be considered firmly validated. While the highest frequencies of haplogroup R1a are found in Eastern Europe18,28, our data revealed a rich variation of haplogroup R1a outside of Europe which is phylogenetically separate from the typically European R1a branches. Evidently, R1a-Y2619 is well nested within a plethora of phylogenetically close Middle Eastern sister-clades, sampled in Iranian Azeris, a Kerman, a Yazidi and one man from Iberia. This provides the needed evidence for its origin (Fig. 2 and Supplemental Figure S1). However, the exact migration pathway of R1a-Y2619 to Europe remains elusive. Most historical records suggest two major routes of Jewish migration to Europe (Fig. 1)29,30. Ashkenazi Jewry is considered to have been founded as the result of Jewish migration via Italy to the Rhine Valley, and then Poland. Sephardic (Spanish) Jews are considered to have migrated along with the gradual Islamic expansion to North Africa and then Spain14. Because R1a-Y2619 is of Middle Eastern origin, it is possible that its introduction to Europe was by either, or both, of these routes. Naturally, the strong founding event for R1a-Y2619 among Ashkenazi Jews, coupled with the presence of all known branches of R1a-Y2619 in Ashkenazi Jews, tempts to infer that its migration route from the Levant was directly related to the Ashkenazi founders. However, these facts might merely reflect an expansion within Ashkenazi Jews rather than a proof of first arrival of the R1a-Y2619 with or into the Ashkenazi population. More confusing is the fact that genealogical records of the Horowitz rabbinical dynasty, now shown to carry the R1a-Y2619 Y chromosome, suggest their presence in the Iberian Peninsula in the 15th century and probably earlier (Fig. 3)17. In fact, repeated Jewish migrations that might have carried R1a-Y2619 Y chromosomes to Catalonia are documented since the 4th century and during the Muslim expansion to Iberia31.

Additionally, because Catalonia was again Christian territory since 800 CE, proto-Horowitz R1a-Y2619 ancestors could also represent migration of Ashkenazi Jews to Iberia. Accordingly, the presence of R1a-Y2619 in Spain in the 15th century could not establish proof for the first arrival of the R1a-Y2619 lineage to the Iberian Peninsula, as this could simply reflect repeated and unrecorded movements of Jews back and forth between Eastern and Western Europe and the Iberian Peninsula. Previous evidences from mtDNA and autosomal markers have already suggested a likely gene flow between Ashkenazi and Sephardic Jews within Europe32,33,34. Taken together, our results tend to favor a single route of entry to Europe as part of the Ashkenazi migration and expansion in Europe. Because the coalescence time of all contemporary R1a-Y2619 Levites is ~1,743 ybp, well within the time of the Roman exile Diaspora, and each of the branches of R1a-Y2619 is found in Ashkenazi Jews, our results are inconsistent with a scenario of rapid expansion in the Levant followed by a spread via multiple routes to Europe. The results from the non-Ashkenazi R1a-Y2619 Levite samples also suggest single expansion route. Had the R1a-Y2619 Levite lineage already been as widely prevalent in the Levant, the non-Ashkenazi Levites would have been expected to split from the Ashkenazi Levite samples prior to the time of the Diaspora and to form a different cluster. However, the results show that the non-Ashkenazi Levites fall within multiple relatively recently coalescing sub-branches of R1a-Y2619 (Fig. 2 and Supplemental Figure S1). This pattern is more compatible with continuous gene flow from the Ashkenazi population to the non-Ashkenazi population during the Diaspora, rather than multiple routes of entrance for haplogroup R1a-Y2619 to Europe from the Levant.