Estimating "Basque" admixture in Balts

As Dienekes pointed out, in the absence of an "unadmixed" parent population an admixed population can appear in an ADMIXTURE analysis as if it was less mixed or "unadmixed" itself. And it can be very complicated to determine a reasonable estimate of suspected admixture proportions...

Assuming a (near-) Complete Replacement model, Balts are an interesting population. Since neighbouring Scandinavia and Northern Poland present archaeological evidence of Megalithic Culture wave colonization, it seems likely that they would present non-zero Western Wave admixture. Additionally Baltic Finns seem to derive their "European" (originally Near Easterner) element much more from Scandinavian-like populations than from Baltic-like populations, suggesting that the Comb Ceramic culture was founded mainly by Neolithic immigrants from the Western Wave and not the Eastern one. The "Siberian"-like element found in low percentages in current Finns would, in this model, be derived from ancient Northeastern European Hunter-Gatherers, and not from any ancient undocumented Siberian expansion.

However it is difficult to ascertain this, since the main parent population of Balts is likely not represented in any currently available collections.
Adyguei and other Caucasian populations were likely modified in ancient times by secondary more advanced waves coming from the Neolithic Core Area further south- the Fertile Crescent (including Egypt). Secondary Neolithic waves apparently are substantially different genetically, with more southern affinities (Egypt? I will explore this later) than the primary waves and an analysis with them renders Balts "Basque-like".

As for intervening populations Russia currently doesn't allow for data collection from it's citizens, and any evidence from steppe populations, unlike agricultural settled ones, presumably suffered much more erosion, since nomadic groups are highly mobile, herds can be stollen and it's much more difficult for conquerors to establish rent-drawing relationships in such environments.

So how can first Western Neolithic Wave ("Basque"-like) admixture in Balts be estimated?
Only by using surrogate populations obeying a set of strict conditions
1 Likely strongly affected by the first Eastern Wave
2 Likely not affected by the Western waves or subsequent Eastern ones
3 Living in environments better suited for agriculture than to pastoralism

Turns out that there is such a population already genotyped: the Chuvash. They're not ideal because they have some significant non-neolithic component ("Siberian") but by running an "unadmixed" Siberian population as a control, reasonable insights may be gained.

I ran an admixture analysis of Europeans with the following populations as poles:
1. Chuvash: I'm using them as an attractor for all Eastern Neolithic influence. Discussible, but just an experiment
2. Basques: representative of possibly little admixed Megalithic culture people? May have been subject to drift effects but Basques may be the closest thing available to a pre-Indo-European population. This pole may also catch some some of the Balkan (Danubian Culture and related) first wave component, since sharing a common origin in Western Anatolia it was likely similar.
3. Yakuts: Siberian. Some superposition with Chuvash, but serves as a control for excess Siberian admixture in analysed populations, allowing better clues for actual Eastern wave affinity between the Chuvash and Northern Europeans.
5. Turks: this pole should draw all secondary wave elements plus a corresponding subsumed part of the primary wave one. It serves as a control for subsequent Southern influence

Here are the results. Bear in mind that even if roughly correct, they are at best indications of actual ancient population admixture percentages. Basques likely have some non-Megalithic admixture, "Turkish" likely consists of a Megalithic substrate superimposed by secondary wave elements; Chuvash partially obfuscates "Yakut". Still these results are the product of a simple set-up, I believe are well based in reasonable assumptions and can be justified by well-grounded arguments.



Fst divergence between estimated populations

"Yakut" "Basque" "Chuvash"
"Basque" 0.124
"Chuvash" 0.087 0.036
"Turkish" 0.101 0.028 0.032

I added my interpretation to the labels.

These results cannot be due to purely geographical clines. Components don't correlate with distance very well.

More speculatively, it seems strange to find some "Yakut" where it shouldn't be. It is most likely noise. However one should expect to find a continuum of hunter-gatherer genotypes across Northern Eurasia (as opposed to just in Northern Europe- the Urals are a poor barrier to gene flow). This region likely was colonized late and most regions from the first one as such populations necessarily has to acquire expensive cultural and genetic adaptations to the cold environment. Also this element is found most significantly in Russians (0.6% likely much subsumed into nearby "Chuvash"), as expected, White Americans (0.4%: Amerindian, less similar so likely underestimated). As for Spaniards and Romenians it is interesting that these are the most mountainous countries whose populations were analysed. In Spain in particular, late surviving hunter gatherer lifestyles are suggested by archaeology.

In the Northern European plains populations, "Basque"+"Chuvash" admixture brings to mind the Kurganized originally Megalithic Corded Ware Culture. I think it's suggestive that the late arriving Eastern Wave achieved such success within an already Western Wave colonized region. This may have something to do with not only with new advanced pastoralist lifestyles and lactose tolerance, but maybe also with the development of Rye, which appears archaeologically in Central Europe around then. East Slavs may then have expanded from Central Europe to the East, absorbing the (Finnic) Comb Ceramic Culture, only after acquiring this cereal.