A substantial prehistoric European ancestry amongst Ashkenazi maternal lineages

The origins of Ashkenazi Jews remain highly controversial. Like Judaism, mitochondrial DNA is passed along the maternal line. Its variation in the Ashkenazim is highly distinctive, with four major and numerous minor founders. However, due to their rarity in the general population, these founders have been difficult to trace to a source. Here we show that all four major founders, ~40% of Ashkenazi mtDNA variation, have ancestry in prehistoric Europe, rather than the Near East or Caucasus. Furthermore, most of the remaining minor founders share a similar deep European ancestry. Thus the great majority of Ashkenazi maternal lineages were not brought from the Levant, as commonly supposed, nor recruited in the Caucasus, as sometimes suggested, but assimilated within Europe. These results point to a significant role for the conversion of women in the formation of Ashkenazi communities, and provide the foundation for a detailed reconstruction of Ashkenazi genealogical history.


Supplementary
. Phylogenetic tree of Ashkenazi founders within haplogroups H26 and H40. A Neolithic European lineage is shown with a red circle 29 . Time scale (ka) based on ML estimations for mitogenome sequences.

Phylogeography of haplogroup U8: context of the Ashkenazi haplogroup K founders
Here we present the context for the Ashkenazi haplogroup K lineages, providing the detailed phylogeographic evidence supporting a deep ancestry for the Ashkenazi founder clades within Europe.
Haplogroup K is by far the largest subclade within haplogroup U8. The The estimates are broadly similar (allowing for the greater imprecision of the synonymous estimates), although those from BEAST tend to be rather lower. It is worth noting that the Bayesian estimates are completely independent from those using ρ and ML, using a wholly different approach to both calibration and estimation. However, they were necessarily carried out with only a subset of the data (398 sequences) due to the limitations of the software, and given the necessary assumptions of the Bayesian approach (and, conversely the lack of any mutation model for the ρ estimates) we regard the ML values as the most reliable.  Fig. S2). Given the timing of the appearance of haplogroup K, just prior to the global climatic downturn, an origin in the Near Eastwhich acted as a major reservoir for mtDNA variation during the glacial period 30,52might also more plausibly account for its survival than an origin in Europe.
None of these arguments is compelling, however, and on the other hand, the majority of the major subclades within haplogroup K appear to have arisen within Europe (see below), with K1a the only likely exception, which points to a European origin for haplogroup K (Fig. 1) Late Glacial origin in the Near East. Its major subclade, K1a1b1 (Fig. 2), however, appears to be exclusively European/North African, with a geographical focus on the western Mediterranean, and dates to 11.7 ka. K1a1 therefore most likely dispersed to Europe during the Late Glacial, sometime between the age of the common ancestor, ~18 ka, and 12 ka. The much more recent Ashkenazi founder clade K1a1b1a therefore has a very deep European ancestry, in sharp contrast to HV1b2, for example (Fig. 5). The question arises as to why an assimilation founder event might draw in several lineages from a single haplogroup (K) from a presumably diverse source population in Europe. However, we would caution against assuming that the source must have been enriched for haplogroup K. We have now shown that N1b2 underwent a similar process (main text; Fig. 6; Table S5), and numerous minor lineages may have been assimilated at the same time (with some lost later by drift). Moreover, whereas K1a1b1a and K1a9 were most likely assimilated in Mediterranean/Western Europe, the third major K founder, K2a2a1, with its slightly younger age estimate and its nesting within a German lineage, may have been assimilated in central Europe slightly later, again along with numerous minor lineages (such as many of those from haplogroup H; see below). The survival of three distinct haplogroup K founder lineages through the early bottleneck may simply have been due to chance.

Southern Russian mtDNA lineages and the "Khazar hypothesis"
There is no evidence in the mtDNA pool to support the contention that lineages might have been recruited on a large scale from the North Caucasus and/or Chuvashia regions of southern Russia, as would be predicted by the "Khazar hypothesis" 16 . Not only are the subclades of haplogroup K that gave rise to the three major Ashkenazi founders absent, and N1b virtually so, but there is little evidence for any assimilation of the more minor Ashkenazi lineages either, most of which comprise mtDNAs found primarily in Europe. Extant southern Russians from these regions carry either distinct subclades of haplogroups from those found in the Ashkenazim (for example, amongst the more common west Eurasian clades such as haplogroups H, J and T lineages) or they lack the other haplogroups found in the Ashkenazim altogether.
There are 208 sequences from the North Caucasus in the HVS-I database (excluding Kalmyks who arrived from China in the seventeenth century AD), of which eight belong to haplogroup K 23 . We fully sequenced seven of these and partially sequenced the eighth, in order to resolve their haplogroup status. All belonged to Near Eastern subclades, and none belonged to one of the three Ashkenazi founder clades.
There are several subclades within H5 ( Supplementary Fig. S5), which again nest with west European lineages; and in H7 ( Supplementary Fig. S6), which also