Some related analyses of mine:
- fastIBD analysis of Afroasiatic groups (Jews, Arabs, Assyrians, Berbers, Somalis, Amharas, etc.)
- fastIBD analysis of Iberia, France, Italy, Balkans, Anatolia and European Jews
- Admixture proportions for various populations (incl. various Jewish groups)
Below is Fig. 3 from Campbell et al.:
One can see that Jewish groups have high degree of intra-population IBD sharing (A); many of the highest levels of IBD sharing is between Jewish groups (B and C).
This paper definitely shows that Jewish groups differ from non-Jewish North Africans. But, the lack of comparative samples from non-Jewish non-North Africans makes the interpretation of this result difficult. Both the PCA analysis, shown below, and the structure analysis indicates a significant Sub-Saharan component in North African non-Jewish populations.
So, it seems, based on these results, that Jewish groups are differentiated from North Africans due to their general lack of sub-Saharan admixture, and they also show a variable degree of affiliation to European groups; however, by "European" groups we go only as far as north Italy and Sardinia. What of the relationships of different Jewish groups to people from southern Italy, Greece, Anatolia, the Caucasus, or even Iranian speakers of the Near East?
Admixture calculations were carried out using a supervised learning approach in a structure-like analysis. This approach has many advantages over the unsupervised approach that not only traces ancestry to K abstract unmixed populations under the assumption that they evolved independently (Chakravarti 2009; Weiss and Long 2009) but also problematic when applied to study Jewish ancestry, which can be dated as far back as 3,000 years (Figure 2). Admixture was calculated with a reference set of seven populations representing genetically distinct regions: Pygmies (Africa), French Basque (West Europe), Chuvash (East Europe), Han Chinese (Asia), Palestinians (Middle East), Turk-Iranians (Near East), and Armenians (Caucasus) (Figure 5).But, Palestinians too have African admixture, so using them as a parental population conflates two separate issues: their old Near Eastern Semitic ancestors which could be reasonably inferred to be somewhat related to the Semitic ancestors of Jews, and their recent African admixture. Similarly, Turks have east Eurasian admixture, and Iranians have South Asian admixture.
On the other hand, there may be something to the Khazar story (but in the sense of admixture, rather than replacement). High IBD sharing with Caucasians is one such piece of evidence. Another is the presence of Y-haplogroup Q and R-Z93+, both of which could in principle track a Central Asian Turkic influence (although Z93 could also track an Iranian influence). Then, there is the limited but persistent evidence for a little East Eurasian admixture present in Ashkenazi Jews and not in Sephardic Jews, which might also be consistent with a little Turkic influence.
Overall, I am convinced that most modern Jewish groups have some variable old Near Eastern Jewish ancestry, primarily on the basis of the elevated "Southwest Asian" that seems to correlate reasonably well with groups of Semitic speakers. But, it is difficult to say "how much" and to identify all the potential sources of admixture. Jews have been an international people for quite a long time, so I would guess that fragments of different peoples they encountered may remain in their genomes. Perhaps something akin to Ralph and Coop (2012) may give more information about the timing of these admixture events, as well as the date of the common ancestry of different Jewish groups.
PS: I started a small fastIBD analysis of different Jewish and non-Jewish groups with a fairly large assortment of populations, and will probably post it here in the next few days.
PNAS doi: 10.1073/pnas.1204840109
North African Jewish and non-Jewish populations form distinctive, orthogonal clusters
Christopher L. Campbell et al.
North African Jews constitute the second largest Jewish Diaspora group. However, their relatedness to each other; to European, Middle Eastern, and other Jewish Diaspora groups; and to their former North African non-Jewish neighbors has not been well defined. Here, genome-wide analysis of five North African Jewish groups (Moroccan, Algerian, Tunisian, Djerban, and Libyan) and comparison with other Jewish and non-Jewish groups demonstrated distinctive North African Jewish population clusters with proximity to other Jewish populations and variable degrees of Middle Eastern, European, and North African admixture. Two major subgroups were identified by principal component, neighbor joining tree, and identity-by-descent analysis—Moroccan/Algerian and Djerban/Libyan—that varied in their degree of European admixture. These populations showed a high degree of endogamy and were part of a larger Ashkenazi and Sephardic Jewish group. By principal component analysis, these North African groups were orthogonal to contemporary populations from North and South Morocco, Western Sahara, Tunisia, Libya, and Egypt. Thus, this study is compatible with the history of North African Jews—founding during Classical Antiquity with proselytism of local populations, followed by genetic isolation with the rise of Christianity and then Islam, and admixture following the emigration of Sephardic Jews during the Inquisition.
The Missing Link of Jewish European Ancestry: Contrasting the Rhineland and the Khazarian Hypotheses
The question of Jewish ancestry has been the subject of controversy for over two centuries and has yet to be resolved. The "Rhineland Hypothesis" proposes that Eastern European Jews emerged from a small group of German Jews who migrated eastward and expanded rapidly. Alternatively, the "Khazarian Hypothesis" suggests that Eastern European descended from Judean tribes who joined the Khazars, an amalgam of Turkic clans that settled the Caucasus in the early centuries CE and converted to Judaism in the 8th century. The Judaized Empire was continuously reinforced with Mesopotamian and Greco-Roman Jews until the 13th century. Following the collapse of their empire, the Judeo-Khazars fled to Eastern Europe. The rise of European Jewry is therefore explained by the contribution of the Judeo-Khazars. Thus far, however, their contribution has been estimated only empirically; the absence of genome-wide data from Caucasus populations precluded testing the Khazarian Hypothesis. Recent sequencing of modern Caucasus populations prompted us to revisit the Khazarian Hypothesis and compare it with the Rhineland Hypothesis. We applied a wide range of population genetic analyses - including principal component, biogeographical origin, admixture, identity by descent, allele sharing distance, and uniparental analyses - to compare these two hypotheses. Our findings support the Khazarian Hypothesis and portray the European Jewish genome as a mosaic of Caucasus, European, and Semitic ancestries, thereby consolidating previous contradictory reports of Jewish ancestry.