Origins of modern Armenian genetic profile. How and when.
Unlike main Europe the genetic history of Near East is much more complicated.
In the current stage of our knowledge the Mesolithic Near East had two distinct and quite distant from each other populations after the Late Glacial Maximum. One in the western parts in Levant and Anatolia, the other in eastern. In Iran and parts of Caucasian range. To understand how unusual was this situation You must realize that the genetic distance between Mesolithic Iranian and Levantine pops was comparable to the distance between foragers living in Baikal region and modern England. Obviously a barrier existed in Near East that permitted to such a distant populations to live side by side without mixing. It was the Armenian Highlands in the North, then probably the Mesopotamian deserts and Zagros and finally Persian Gulf was larger in the past.
The attached maps present the genetic legacy of this ancient pops. As You can see the Iran/Zagros Neolithic ancestry today is best preserved in the East in Pakistan, while Anatolian farmers ancestry is best preserved in the South Europe. Sardinia is famous for being the closest to NW Anatolian farmers. Anatolia had another type of farmers in the south from Tepecik Ciftlik. Those farmers were slightly different and their map as expected is different. Their genetics is close to ancient Minoans. You can also notice the Anatolian farmers ancestry in Central Asia and Africa. The first is due to Corded Ware (R1a-M417) expansion while the latter is due to migration to Africa from SW Europe which introduced there the R1b-V88 lineage, which is today prominent in Chadic speakers.
Returning back to Near East You can notice that modern North Near Easterners in general and Armenians in particular do show ancestry from a different type of farmers. Here represented by South Caucasian sample from Neolithic period known as Shulaveri culture. South Caucasian Neolithic recently became famous by its old wine producing site. But they had other interesting features like round houses similar to those found in Halaf culture. While we are waiting aDNA from Halaf, Hassuna and Ubaid there is little doubt that their genetic profile will be the same Centristic type as farmers of ancient Armenia/SC. From anthropologic point of view it is in those cultures that we see the earliest skulls close to Armenoid type.
Do this mean that the typical Armenian ( and not only Armenian) Centristic genetic profile formed as a mixture of Eastern and Western Near Eastern distinct pops. Maybe yes, maybe no. Or both yes and no. We don't know for sure the answer to this question because we don't have ancient DNA from Iraq, Syria, East Turkey/SC old enough to understand this puzzle.
But it is possible that the reality will be even more surprising than we imagined. Many scholars believe that both Iran and Levant Mesolithic foragers descend from a more archaic population labeled as Basal Eurasians. So what if those Basal Eurasians who lived before the LGM turn out the have a Centristic profile? An unpublished ancient DNA from pre LGM yielded a shocking result. There wasn't any CHG in west Georgia (Dzudzuana) 26.000 years ago. It had more alleles with Anatolian farmers than with CHG which lived in the same place after the LGM.
In any case we already know that this Centristic profile existed already 8-10 thousands years ago in Near East and it expanded in various occasions playing an important role in the formation of modern Near Eastern genetics, which is much more homogenous than it was in late Paleolithic.
PS After this introduction to the subject You can better understand this PCA and analysis.