[/B]This is what I was trying to explain in the
thread about the Tripolye mtdna. The reason why mt-haplogroups N1a almost vanished and K1a starkly decreased from the European gene pool from the Chalcolithic and Bronze Age might simply be that the modern admixture between Near Eastern farmers and 'native' Europeans took place in eastern Europe, especially with the 4000-year exchange of populations between the Cucuteni-Tripolye culture and its neighbours, then its increasing contact with Steppe cultures. Once the Indo-Europeans invaded central Europe, they already had the 40% of so of EEF admixture in them, and all the modern mtDNA lineages from Near Eastern farmers. The merger would have happened around modern Romania and western Ukraine, not progressively as they moved west. Of course, some more blending of population would have occurred later too, but the bulk of intermarriages would have happened maybe in the 1500 years from 4500 to 3000 BCE, right before the Corded Ware expansion. After all, Steppe incursions into the Balkans started from c. 4200 BCE. If this theory is correct, it would mean that the vast majority of Neolithic Europeans were wiped out by the PIE invaders or by diseases, or for other reasons - such as climatic change causing a farming collapse, as has been suggested. In that scenario, the majority of EEF genes in northern and central Europeans today would have come from the Cucuteni-Tripolye and adjacent cultures that mixed early with Steppe people, before the major invasion began. After all it took the PIE some 1500 years to leave the region of modern Romania, Moldova and western Ukraine, but it took them only a few centuries to conquer the whole of western Europe once they had reached Germany, Austria and Bohemia c. 2500 BCE. The pace was very different, hinting at an "express" conquest, perhaps also because Europe had become badly depopulated due to the cooling of the climate and failing crops.
That theory would also explain why so many Neolithic Y-DNA lineages disappeared (C1a2, G2a2, H2) while some very specific sub-branches prospered (G2a3b-L141, T1a1a2a, I2a1b-M423). It would be because those few select lineages would have been assimilated early by the PIE before the big westward migration and recolonisation of Europe.