The genetic variation in the R1a clade among the Ashkenazi Levites' Y chromosome

Abstract

Approximately 300,000 men around the globe self-identify as Ashkenazi Levites, of whom two thirds were previously shown to descend from a single male. The paucity of whole Y-chromosome sequences precluded conclusive identification of this ancestor's age, geographic origin and migration patterns. Here, we report the variation of 486 Y-chromosomes within the Ashkenazi and non-Ashkenazi Levite R1a clade, other Ashkenazi Jewish paternal lineages, as well as non-Levite Jewish and non-Jewish R1a samples. Cumulatively, the emerging profile is of a Middle Eastern ancestor, self-affiliating as Levite, and carrying the highly resolved R1a-Y2619 lineage, which was likely a minor haplogroup among the Hebrews. A star-like phylogeny, coalescing similarly to other Ashkenazi paternal lineages, ~1,743 ybp, suggests it to be one of the Ashkenazi paternal founders; to have expanded as part of the overall Ashkenazi demographic expansion, without special relation to the Levite affiliation; and to have subsequently spread to non-Ashkenazi Levites.

Figure 1

Origin and expansion of the Ashkenazi Levite Y chromosome clade. The suggested gradual movement and expansion pattern of the Ashkenazi Levite haplogroup R1a-Y2619 are denoted by ascending numerical labels. An ancestral origin in the Middle East (1) is followed by a migration route (purple arrows) paralleling the dispersal of Ashkenazi Jews to Europe (2). Expansion within the Ashkenazi Jewish population in Europe (3) is followed by a paternal gene flow of R1a-Y2619 Y chromosomes to non-Ashkenazi Jewish communities (4). A second theoretical expansion route of Levites from the Middle East to Europe (5) via the expansion of non-Ashkenazi Jews is shown but not supported by the obtained results. Map data is from ©2017 Google Maps.

Figure 2

The Ashkenazi Levite clade. (a) Haplogroup R1a phylogeny comprising 170 samples is illustrated to nest the refined Ashkenazi Levite clade R1a-Y2619. The phylogeny and coalescence times (Y axis) were calculated using the software package BEAST v.1.7.5. The Ashkenazi Levite R1a-Y2619 clade coalesces 1,743 (1,334–2,200) ybp. Each terminal branch represents one sample (Supplemental Figure S1). The single arrow points to a sample sequenced by both the Complete Genomics and Illumina platforms. Samples highlighted by a blue star are from non-Ashkenazi Levites. The area shaded in blue represents the sub-Ashkenazi Levite clade nesting all the samples self-affiliating as belonging to the Horowitz pedigree (Fig. 3). The area shaded in red is magnified in (b) and details the ancestries of the individuals making the Ashkenazi paraphyletic clades within haplogroup R1a-M582.

Figure 3

The Horowitz Levite pedigree. (a) The presumed migration route of the first named founder of the Horowitz pedigree from Girona to Horovice, circa 1400 CE, is shown. (b) A total of five individuals self-affiliated as descendants of the pedigree. Of these, three individuals supplied detailed written genealogies showing the ancestral relatedness among them. These three individuals are highlighted by the green, yellow and blue colors, and the noted birth years of their ancestors are noted. The node noted by the blue star symbol was used as an internal calibration point for the R1a phylogeny (Fig. 1). (c) The obtained YP268 clade phylogeny including all five Horowitz Y chromosomes is shown to coalesce 690 (555–852) ybp. The respective allocations of the three individuals comprising the written genealogies are noted by the same colors. The digits to the left of the branches denote the number of mutational events observed in each branch (Supplemental File 1). The two additional individuals are noted in red. The dashed double-headed arrow points to the YP268 node and the first named ancestor of Horowitz pedigree. Map data is from ©2017 Google Maps.