IE-speaking West Europeans are West Asian-admixed relative to Non-IE speaking Basques

Previous ADMIXTURE experiments have shown that the Basques differ from the Indo-European speaking Europeans primarily due to a lack of a "West Asian" genetic component most strongly represented on the highlands of West Asia, from Anatolia and the Caucasus through Iran to Baluchistan. The same component is "missing" from ancient European DNA prior to 5kya, making it a good candidate for an element present in the elusive Proto-Indo-Europeans.

I wanted to test the admixture of IE-speaking populations formally, so I used threepop as implemented in TreeMix which performs a formal f3 test of admixture. According to Patterson et al. (2012):

An important feature of this test is that it definitively shows that the history of mixture occurred in population C; a complex history for A or B cannot produce negative F3(C; A,B).

A negative Z-score of the f3 test is unambiguous evidence of admixture, but a zero or positive one does not exclude it.

I report f3 statistics of the following form:

f3(A; B, West_Asian)

where West_Asian consists of 50 random individuals drawn from the K7b West_Asian component.

The full list of populations used in this experiment can be seen below. They include two sources of Basques (from the HGDP and 1000Genomes Project, from France and Spain), as well as 22 Indo-European speaking populations from Western Europe

I set A as each of the 24 populations, and calculate f3-statistics of the form f3(A; B, West_Asian) where B is any one of the remaining 23 populations. Thus, there are 24*23 = 552 f3-statistics in total, of which  2*22 = 44 are of the form f3(IE; non-IE, West_Asian).

If my conjecture is correct, then I expect:

1. the IE-speaking Europeans to show significantly negative f3(IE; non-IE, West_Asian) statistics
2. the non-IE speaking Basques to show non-negative f3(non-IE; IE, West_Asian) statistics
3. the remaining f3(IE1; IE2, West_Asian) statistics to be either negative or not, depending on different levels of West_Asian-related admixture in different IE populations associated with either the Indo-Europeans or other, later, population movements emanating from West Asia.

My expectation is confirmed by the evidence. You can see all f3 statistics in the spreadsheet. I note that:

(1) Here is a histogram of the 44 f3(IE; non-IE, West_Asian) comparisons:

42 of 44 Z-scores are negative and significant, suggesting that most  IE-speaking West European populations are West Asian-admixed relative to non-IE Basques. The two that are not, involve A='Orkney_1KG', which is a drifted island population. According to Patterson et al. (2012):

As mentioned earlier, the only case where the f3-statistic for a population that is truly admixed fails to be negative is when the population has experienced a high degree of population-specific genetic drift after the admixture occurred.

(2) All f3(non-IE; IE, West_Asian) statistics are positive. With the caveat about drift in mind, there does not seem to be any evidence that Basques are more West Asian-admixed than any other population.

(3) Here is a histogram of the 462 f3(IE1; IE2, West_Asian) statistics:

This shows evidence in differences in West_Asian admixture in some but not other IE populations. 55 of the 462 comparisons show significant evidence of admixture. These mostly involve German, French, and Italian populations vs. Iberian and British Isles ones. As mentioned above, this may reflect either the diminution of Indo-European-related West Asian ancestry across Europe, or it may be due to post-IE population movements.

Discussion

It is becoming increasingly apparent that modern Europeans are the descendants of both early Neolithic farmers, presumably from the Levant or Anatolia, as well as the indigenous Mesolithic hunter-gatherers. Neolithic ancestry has persisted most strongly in southern Europe, and in Sardinia above all. Mesolithic ancestry has persisted most strongly in northern Europe, and especially in the Baltic area; however, it is everywhere in the minority, as evidenced by the ~10-fold diminution of mtDNA haplogroup U related lineages from near 100% in the earliest samples until today.

In all probability there do not exist unmixed descendants of either early Neolithic or Mesolithic Euroeans. Intriguingly, one population that may be most strongly descended from the Mesolithic Europeans are the Saami, who possess very high levels of mtDNA haplogroup U5b. But even in their case, there is evidence of more recent influences, such as Y-haplogroup N1c.

The Saami have always been somewhat of a puzzle for prehistorians, with some attributing their physical appearance to survival of cold-adapted Paleolithic northern Europeans, while others attributing it to more recent movements from Siberia. As it is so often the case, both may have been partially right: it is now revealed that the Saami are not unique in possessing affinities with northeast Asians and Amerindians, so they are descended both from the Mesolithic northern European substratum (as evidenced by mtDNA haplogroup U5b) and from more recent Siberian peoples, and are thus positioned between east and west for more than one reason.

In the rest of Europe things were not any simpler. Both analysis of modern populations, as well as the mounting ancient DNA evidence ought to have convinced us by now that "there's something about Sardinians." It does seem to appear that this island population represents has preserved most faithfully the early Neolithic European gene pool, which, as it turns out, took its time mixing with the indigenous Mesolithic populations, since it is still evident down to the Iron Age. But, all things come to an end, and so did the domination of ancient Europe by Sardinian-like people.

In continental, and especially, northern Europe, the Neolithic inhabitants, resembling modern southern Europeans, eventually admixed with the Mesolithic foragers. A legacy of this event, as well as, possibly further incursions from the east, combined to give modern northern Europeans a greater affiliation with the east of Eurasia. But, it turns out, things were not much simpler in southern and western Europe.

The modern Basques share the East Eurasian-like admixture of continental Europeans, albeit to a smaller degree than people living in the north. They, like other Europeans are a mix of Mesolithic and Neolithic peoples. But, one thing stands out in their case: their language is not Indo-European and they live surrounded by Romance Indo-European speakers. In older times, their neighbors were Indo-European Celts, some of which have survived in places like Ireland. Further away, live Germanic peoples, some of which ventured into Iberia, without much affecting the local population. One thing is certain: the Basques can no longer be seen as unmixed descendants of Cro-Magnon man. But, if they have not continued as living fossils of Paleolithic man, then, what is to account for their linguistic peculiarity?

In the current post I make one such suggestion in the framework of my theory on the Indo-Europeanization of Europe. I showed that Basques differ from all their Romance, Celtic, and Germanic fellow West Europeans in lacking a "West_Asian" influence. I have previously investigated segments of such influence in two northern Europeans. In the future, with new instruments, such as ADMIXTOOLS, we may be able to figure out exactly when other European populations were affected by this influence. For peoples living close to West Asia (e.g., Greeks or Italians), the pattern may be obscured by recent historical contacts. But, the same will probably not be true for populations living in far Western Europe (e.g., Iberians or Irish).

If my theory is correct, then this signal will postdate the 5kya mark. By how much? It is not clear how long the Indo-Europeans of western Europe maintained themselves separately, perhaps as I have speculated, as a trading/military elite centered around metallurgy and its products. Ancient DNA research has the potential of resolving this issue by first identifying the earliest arrival of the West Asian influence, and, subsequently, detecting the first emergence of something akin to the modern population. One way or another, the cat is out of the bag, and in a the coming years many of these issues will be resolved.