A new study on the maternal ancestry of Ashkenazi Jews at Nature Communications argues that at least 80% of Ashkenazi mtDNA lineages were absorbed from European host populations. Here are a few quotes from the paper that caught my attention:
Several [studies] suggest a primarily Levantine ancestry with south/west European admixture3,4, but another concludes that the ancestry is largely Caucasian16, implying a major source from converts in the Khazar kingdom17. An important reason for disagreement is that the Ashkenazim have undergone severe founder effects during their history, drastically altering the frequencies of genetic markers and distorting the relationship with their ancestral populations.
Actually, genome-wide genetic markers place Ashkenazi Jews squarely in the East Mediterranean region, but closer to Southern Europe than to the Near East (note the position of European Jews on my PCA of West Eurasia here). In other words, Ashkenazi Jews are genetically very similar to southern Italians and many Greeks. So as far as I can see, their origins must be by and large in Mediterranean Europe. They do show some minor admixtures from further north in Europe, and even as far away as Sub-Saharan Africa and East Asia. But genome-wide genetic data certainly doesn't suggest in any way a Caucasian, or Khazar, origin for Ashkenazi Jews.
We show that European and Near Eastern lineages largely fall into discrete, ancient clusters, with minor episodes of gene flow, suggesting that haplogroup K diversified separately in Europe and the Near East during the last glacial period.
The high differentiation between European and Near Eastern mtDNA lineages, and not just those belonging to haplogroup K, is supported by the data and very interesting. But dating coalescent times for genetic markers is still far from a precise science, so I'm skeptical that haplgroup K was in Europe during the glacial period. As far as I know, ancient DNA from pre-Neolithic Europe doesn't support such a claim at the moment.
Overall, it seems that at least 80% of Ashkenazi maternal ancestry is due to the assimilation of mtDNAs indigenous to Europe, most likely through conversion. The phylogenetic nesting patterns suggest that the most frequent of the Ashkenazi mtDNA lineages were assimilated in Western Europe, B2 ka or slightly earlier. Some in particular, including N1b2, M1a1b, K1a9 and perhaps even the major K1a1b1, point to a north Mediterranean source.
As might be expected from the autosomal picture, Y-chromosome studies generally show the opposite trend to mtDNA (with a predominantly Near Eastern source) with the exception of the large fraction of European ancestry seen in Ashkenazi Levites22.
It seems they're referring to Y-chromosome haplogroup R1a in that last comment. However, the R1a lineage most commonly found amongst Ashkenazi Levites is both Asian-specific and Ashkenazi-specific, because it's defined by the Z94 and Z2122 mutations, respectively. So it probably can't be considered a signal of European ancestry. Based on what I've seen, R1a-Z2122 might represent Central Asian Jewish introgression into the Ashkenazi Levite gene pool. But it might well be a marker of the enigmatic Khazars. Like I've said before on these blogs, someone should really look into that.
There's also a huge supplementary PDF to go along with this paper (see here), which includes some fascinating comments about haplogroup H, including my own sub-haplogroup H7.
There are several subclades within H5 (Supplementary Fig. S5), which again nest with west European lineages; and in H7 (Supplementary Fig. S6), which also appears to have arisen in Europe (although several distinct subclades have spread subsequently to the Near East).
Powerful independent evidence corroborating a deep European ancestry for these lineages comes from the study of prehistoric remains, recently achieved for a sample of 39 haplogroup H lineages from prehistoric central Europe29. Haplogroup H1, and in particular H1e, along with haplogroups H5 and H26, have been found in early Neolithic remains, H3 and H7 in mid-Neolithic remains, H6 and H13 in the late Neolithic and H2, H4 and H11 in the early Bronze Age.
Indeed, H7 popped up in Baalberge and Unetice culture remains in the Brotherton et al. study. Both of these cultures are generally considered to be derived from the Kurgan archeological sphere. That's interesting because I know an Indian at 23andMe who belongs to H7, as well as R1a. So he's basically my uni-parental twin, although it's likely that the subclades we belong to are very different.
Costa, M.D. et al. A substantial prehistoric European ancestry amongst Ashkenazi maternal lineages. Nat. Commun. 4:2543 doi: 10.1038/ncomms3543 (2013).
Khazar origins of European Jews finally confirmed?