My post, Are Turks Armenians Under The Hood?, attracted a little bit of controversy. The main criticism, which was a valid one, is that I did not sample Anatolian Greeks. A reader passed on three Anatolian Greek samples. I also added a Cypriot data set. To my mild surprise, the Anatolian Greeks and Cypriots cluster together, at the end of the Greece cline toward West Asians. Therefore, for further analysis, I pooled the three Greeks with the Cypriots.
Additionally, there are two Balkan Turk samples. Even on the PCA it’s pretty clear that they’re genetically very different from the other Turks (one of them is from what has become Bulgaria), though the shift toward East Asians indicates that Turkification is very rarely a matter purely of religious conversion to Islam and assimilation of the Turkish language (obviously it initially is for many people, but these people then intermarry with those with some East Asian ancestry).
One of the major problems is that the Armenian sample and the Anatolian Greek/Cypriot sample are genetically very close. This is obvious in the Fst distance. This is also totally reasonable since both populations occupy Anatolia, and historically there would have been a lot of gene flow between the two groups through isolation-by-distance dynamics.
The Turk position closer to East Asians is due to their East Asian admixture.
You can see it in the admixture plot too. As we all know there is definitely some northern admixture in the mainland Greeks. I haven’t bothered to check with the Mycenaean paper, but I assume that some of this is due to the migration of Slavs after much of the Balkans was abandoned after the reign of Maurice.
Of course, I ran Treemix too. Again, the closeness of the Anatolian Greeks/Cypriots and the Armenians is an issue in making a definitive conclusion.
In terms of drift the Turks seem about as far from Anatolian Greeks as Armenians. There’s the gene flow you’d expect, there are two from East Asians to Turks. I think that’s due to the East Asian source being somewhat heterogeneous, and the Dai outgroup not modeling the source populations perfectly.
Finally, there’s the f3 statistics. They basically show what I’m saying above: Armenians and Anatolian Greeks are both good model sources for Turks. The likely truth is that there is gene flow from all across Anatolia into these Turkish samples.