If I had to guess, I would propose that most extant Europeans will be discovered to be a 2-way West Asian/Ancestral European mix, just as most South Asians are a simple West Asian/Ancestral South Indian mix. In both cases, the indigenous component is no longer in existence and the South Asian/Atlantic_Baltic components that emerge in ADMIXTURE analyses represent a composite of the aboriginal component with the introduced West Asian one. And, like in India, some populations will be discovered to be “off-cline” by admixture with different elements: in Europe these will be Paleo-Mediterraneans like the Iceman, an element maximally preserved in modern Sardinians, as well as the East Eurasian-influenced populations at the North-Eastern side of the continent.
This does not seem to be totally implausible on the face of it. But it seems likely that any “West Asian” component is going to be much closer genetically to an “Ancestral European” mix than they were to “Ancestral South Indians,” because the two former elements are probably part of a broader West Eurasian diversification which post-dates the separation of those groups from Southern and Eastern Eurasians. In other words, pulling out the distinct elements in Europeans is likely a more difficult task because the constituents of the mixture resemble each other quite a bit when compared to “Ancestral North Indians” vs. “Ancestral South Indians.”
Seriously, sometimes history matches fiction a lot more than we’d have expected, or wished. In the early 2000s the Oxford geneticist Bryan Sykes observed a pattern of discordance between the spatial distribution of male mediated ancestry on the nonrecombinant Y chromosome (NRY) and female mediated ancestry in the mitochondrial DNA (mtDNA). To explains this he offered a somewhat sensationalist narrative to the press about possible repeated instances of male genocide against lineage groups who lost in conflicts.
Here is a portion of the book of Numbers in the Bible:
15 – And Moses said unto them, Have ye saved all the women alive?
16 – Behold, these caused the children of Israel, through the counsel of Balaam, to commit trespass against the LORD in the matter of Peor, and there was a plague among the congregation of the LORD.
17 – Now therefore kill every male among the little ones, and kill every woman that hath known man by lying with him.
18 – But all the women children, that have not known a man by lying with him, keep alive for yourselves.
Then there is the rape of the Sabine women. The ethnogenesis of the mestizo and mulatto populations of the New World in large part was the union between non-European women and European men. These are hard brutal myths and hard brutal facts. But do they reflect an essential aspect of the dynamics which have shaped our species’ past?
I’m not willing quite yet to add a confident weight upon this possibility, but this seems to be part at least part of the picture. You see a major disjunction on male and female lineages among South Asians for example. A new paper in PNAS adds weight to this possibility, albeit only incrementally. Ancient DNA reveals male diffusion through the Neolithic Mediterranean route: