Let me make something explicit: I believe that the model outlined in First Farmers is too simple, and that extant patters of linguistic and genetic variation need to accept the likelihood of multiple population reorganizations across vast swaths of Eurasia within the last 10,000 years. The classic case in point are the Turks. Because of their exotic character vis-a-vis the populations which they displaced and assimilated we can peg rather easily their expansion. Between 0 and 1000 AD they began to make themselves felt across a broad expanse of Eurasia from the eastern fringes of Europe to the western fringes of China, and south toward the world of Islam. Between 1000 and 1800 the Turkic peoples took over much of Eurasia for various periods of time (e.g., the Ottomans, Safavids, and Mughals, were Turkic, while the Golden Horde which imposed the Tatar Yoke were mostly Turkic, not Mongol). It is notable to me that Turkic peoples contributed ~10 percent to the genetic ancestry of modern Anatolians. This is a significant achievement, because Anatolia has been a densely populated seat of agricultural civilization for almost the whole history of agriculture! In Central Asia Turks genetically admixed significantly, to the point of preponderance, with the Iranian substrate.
Why does this matter? Because if it hadn’t happened, and it hadn’t happened in the light of history, I doubt we’d believe it! The Turks were obscure tribes in Central Eurasia 2,000 years ago. There was no anticipating that somehow they would overturn what had been the Iranian world of western Inner Asia, and, that they would break through into the civilized societies of the periphery, to the point of taking them over from above, and assimilating them from below. I do not think the Turks are exceptional in this. It must have happened many times in the past. We just need to open our minds to the possibilities.
In Strange Parallels Victor Lieberman made a reference to “Turkicized Pathans.” The very term has been gnawing at me. To get some sense of the context, Lieberman was sketching out the impact of Islamic civilization upon Indian civilization. Sometimes this “impact” was very literal. The Arab armies had rolled into Sindh in the 8th century, but that influence upon India was militarily marginal. The first real Muslim raider of consequence was Mahmud of Ghazni, a Turkic raider from what is today Afghanistan, who famously plundered the palaces and temples of North India circa ~1000. But even here the the impact is arguably superficial. Mahmud of Ghazni’s raids did not lead to a large Indian domain under his direct rule except in Punjab. Rather, these sallies into India were sources of supplementation to his broader fiscal resources. He was still fundamentally a Central Asian potentate fixated on Central Asian concerns. The real rise of Islamic civilization in India was precipitated by the Delhi Sultanate, a series of short-lived polities beginning circa ~1200 which dominated the Indian subcontinent for centuries, until they were superseded by the far more robust Mughal Empire.
These Indo-Islamic dominions were often dominated by individuals of Turkic identity. By this, I mean that they were from a lineage of Turkic tribes which had filtered into the world of Islam in the centuries before 1000, enslaved or enrolled in the armies of Muslim warlords. But eventually these pawns turned the tables on their erstwhile masters and snatched the keys to the kingdom for themselves. Mahmud of Ghazni’s own family were originally servitors of the Iranian Muslim Samanid dynasty. But just as Rome was enslaved by Greece culturally after its conquest of Hellas, so many Turks freely granted the manifest superiority of the Persian language in the domain of culture. Therefore the irony is that the Persian language spread as the elite cultural vehicle along with the expansion of the Turks west and east, culminating with the rise of the Ottomans and Mughals. Therefore you had a situation in Mughal India where the ruling dynasty, which was of proud Turco-Mongol origin along the paternal lineage, patronized Persian was the language of the court and administration more generally.
But what about the Afghans? They were not invisible. Along with the Turks and Persians, who came with the sword and quill respectively to serve in the courts of India’s Islamic rulers, came auxiliaries of Afghans, mostly Pashtuns. Though a majority of the dynasts seem to claim Turkic antecedents, some are self-consciously Afghan. For example the Lodi dynasty. The influence of these people is evident in India today insofar as upper class Muslims often refer to themselves as “Pathans,” presumably pointing to an origin outside of Indian proper.
To the left you see a zoom in of a PCA which Dienekes produced for a post, Structure in West Asian Indo-European groups. The focus of the post is the peculiar genetic relationship of Kurds, an Iranian-speaking people, with Iranians proper, as well as Armenians (Indo-European) and Turks (not Indo-European). As you can see in some ways the Kurds seem to be the outgroup population, and the correspondence between linguistic and genetic affinity is difficult to interpret. For those of you interested in historical population genetics this shouldn’t be that surprising. West Asia is characterized by of endogamy, language shift, and a great deal of sub and supra-national communal identity (in fact, national identity is often perceived to be weak here). A paper from the mid-2000s already suggested that western and eastern Iran were genetically very distinctive, perhaps due to the simple fact of geography: central Iran is extremely arid and relatively unpopulated in relation to the peripheries.
But this post isn’t about Kurds, rather, observe the very close relationship between Turks and Armenians on the PCA. The _D denotes Dodecad samples, those which Dienekes himself as collected. This affinity could easily be predicted by the basic parameters of physical geography. Armenians and Anatolian Turks were neighbors for nearly 1,000 years. Below is a map which shows the expanse of the ancient kingdom of Armenia:

There’s a new paper out in The European Journal of Human Genetics which is of great interest because it surveys the genetic and linguistic affinities of two dozen ethno-linguistic groups from the three Central Asian nations of Uzbekistan, Kyrgyzstan, and Tajikistan. This is what the Greeks referred to as Transoxiana, and the Persians as Turan. Originally inhabited by peoples with close cultural affinities with those of Persia, indeed, likely the root of the peoples of Persia, by the historical period Turan developed a distinctive identity as a frontier or march. It was in Turan where the Turk met the Iranian (a class which included non-Persian groups, such as the Sogdians), from the pre-Islamic Sassanians down to the present day. It is a region of the world which has a very ancient urban culture, cities such as Merv, as well as peoples that were only recently nomads, forcibly made sedentary by the Soviet regime.
To add another twist to the picture many of the ethno-linguistic groups which we are familiar with today and which serve as the cores of the new Central Asian nations only came into being within the last few centuries, with a particular “push” from Russian Imperial and Soviet ethnologists who were tasked with fleshing out national identities with which the center could negotiate. A “Tajik” is after all simply part of the Persian-speaking residual population of Central Asia, spreading down into Afghanistan. The carving out of an independent Tajikistan out of the Central Asian landscape is as much a creation of the modern age as the state of Israel. The “Uzbek” identity was once simply that of the ruling caste of Transoxiana who came to power after the decline of the Timurids. Today it is an appellation which brackets the settled Turkic speaking peoples of Uzbekistan and beyond.
Into this near Gordian knot of history and ideology walk the naive and well-meaning geneticists. There is no great objection one can make to the genetics within the paper, but the historical framework and some of the assertions are peculiar and tendentious indeed. It’s a problem which starts within the abstract. In the heartland of Eurasia: the multilocus genetic landscape of Central Asian populations: