fastIBD analysis of Italy/Balkans/Anatolia

I have included the new Turkish data from Hodoğlugil & Mahley (2012) in this analysis. Additionally, there are now 5 participants in the Serb_D and Turkish_Cypriot_D sub-populations, as well as a Bosnian Muslim. There are now project participants from many Balkan countries, although Albania, the fYROM, and Croatia remain as "black holes" in the map.

Still, I am hopeful that there will be more project participants from currently under-represented populations. I have already started processing the same dataset with ChromoPainter (which takes much longer), and hopefully that analysis will be posted at the end of this week or the beginning of the next one.

First, the heatmap of inter-population IBD:

Remember that the tree groups similar populations together, and for each row in the matrix, the red end of the spectrum indicates lots of IBD sharing, and the blue end low IBD sharing. Additionally, I have now calculated the median IBD sharing, which is more resistant in the presence of potential relatives in the data.

The results appear fairly reasonable, with the Balkan, Anatolian, and Italian populations of the title forming separate branches, and the mainland Greek sample joining with Central/South Italians and Sicilians.

The Clusters Galore can be seen below; 28 clusters were inferred with 21 dimensions:

Results for Project participants can be found in the spreadsheet, and include the probabilities that each ID is assigned to each of the 28 clusters, as well as the Z-scores comparing each individual against all populations with 5+ individuals. The Z-score should be read as follows: for each row, high values indicate a high degree of IBD sharing, while low values indicate a low degree of IBD sharing.

Of course, I encourage Project participants to leave a message in the Information about Project samples thread.

Analysis of Greeks, Italians, Cypriots, and European Jews

Here are the first two dimensions of a multidimensional scaling in which the following are included:

• Behar et al. (2010) Cypriots, and Ashkenazi/Sephardi Jews
• HGDP-CEPH North Italians and Tuscans
• Dodecad Project Greeks and Part-Greeks (N=7)
• Dodecad Project Italians (N=14)
• Dodecad Project Ashkenazi Jews (N=2)

The following color coding is used: Greeks: blue; Italians: green; Cypriots: magenta; Sephardic Jews: grey; Ashkenazi Jews: red.

The Jewish/non-Jewish groups can be distinguished by the first axis, with value greater than 0 including almost all Jews and less than 0 including almost all non-Jews. A group of Sephardic Jews, while still distinguishable, nonetheless approaches the non-Jewish individuals. According to Behar et al. (2010):

Samples from the Bulgarian and Turkish communities were combined in the analysis and are referred to as Sephardi Jews.

The separability of Ashkenazi Jews from non-Jewish Europeans had been previously reported, e.g., by Tian et al. (2008), from which the figure on the left is presented.

The current post adds Sephardic Jews into the picture; these are also distinguishable from non-Jewish Europeans, but appear to be somewhat closer to them -- at least in the first 2 dimensions of an MDS plot.

While the MDS plot gives a nice overview of this distinctiveness, to assess the possible admixture between these various groups, we must turn to ADMIXTURE.

Indeed, there are two groups: dark blue (European Jews), and light blue (Cypriots, Italians, Greeks). I don't want to put too much emphasis on this, as there are obviously many factors at play, e.g., (i) admixture with other elements, not represented in this study (e.g., Spaniards or Anatolians for Sephardi Jews / North-Central Europeans for Ashkenazi Jews / Syrians, or Phoenicians, or Arabs for Southern Europeans), or (ii) inability to detect admixture accurately among closely related groups (the two clusters are at an Fst=0.029); previously I had seen some residual admixture among Tuscans and White Americans

Nonetheless, the ADMIXTURE analysis confirms that (i) non-Jewish Greeks (including Cypriots) and Italians are distinguishable from European Jews, and (ii) Sephardi Jews are closer to these Europeans than Ashkenazi are.

PS: Idea for this post by recent Italianthro post.