This was a really tough one. Below are the results of three supervised ADMIXTURE runs, with three very different results. They're different because I slightly changed the reference sets in each one. In the first run the Ashkenazim come out mostly Southern European, in the second they largely look Armenian, while in the third they appear mostly Cypriot. This is because the program looks for a best fit option, even when the ideal reference set isn't available. None of the results are wrong, but then again, it's likely that none of them are really saying anything precise about the origins of the Ashkenazim. All they're showing is that this group has allele frequencies that are largely at home in the Mediterranean zone of Europe and nearby West Asia. By the way, I have no idea why the Sephardi Jews are scoring such high "Italian". Speculations welcome...
Key: Red = Armenian + Georgian (Eastern Anatolian + Caucasus), Yellow = South and Central Italian + Greek (Southern European), Green = Scandinavian + Irish + Lithuanian + Estonian (Northern European), Aqua = Jordanian + selected Palestinian + selected Druze (Middle Eastern), Blue = Mozabite (North African), Pink = Chuvash (Volga Ural). See spreadsheet for details.
Key: Red = Armenian (Eastern Anatolian), Yellow = South and Central Italian + Greek (Southern European), Green = Scandinavian + Irish + Lithuanian + Estonian (Northern European), Aqua = Jordanian + selected Palestinian + selected Druze (Middle Eastern), Blue = Mozabite (North African), Pink = Chuvash (Volga Ural). See spreadsheet for details.
Key: Red = Armenian (Eastern Anatolian), Yellow = South and Central Italian + Greek (Southern European), Green = Scandinavian + Irish + Lithuanian + Estonian (Northern European), Aqua = Jordanian + selected Palestinian + selected Druze (Middle Eastern), Light Blue = Mozabite (North African), Purple = Chuvash (Volga Ural), Pink = Cypriot (Eastern Mediterranean). See spreadsheet for details.
To add further confusion to the issue of Ashkenazim origins, here's a datasheet for an interactive plot (for details on how to compile the plot, see here and here). When you put it together, you'll see that the Ashkenazim don't appear to be a straight up mix of Europeans and Middle Easterners, because they don't cluster between the two. However, I think this is just founder effect and genetic drift playing a bit of havoc with the MDS analysis. Actually, for those who can't be bothered compiling the interactive MDS, here's a screen cap.
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