Razib Khan has an extended meditation on the genetic origins of the Eurasians.
Some key points:
(1) Culturally driven punctuated change has been the norm for much of the history of humanity.
(2) One factor driving this population replacement trend has been the fragility of the economic subsistence basis of the conquered people. Often they have been so fragile and with so little excess that exacting tribute from them and exploiting them as a ruling class has been impossible and instead they were replaced.
(3) The Y-DNA R1a and R1b branches have seen the explosion of the modern sublineages since ca. 3000 BCE, which correspond with the sweeping expansions of these patrilineages into Europe and South Asia, and to a less extent, into the Middle East.
(4) The Neolithic revolution and the subsequent explosion of steppe DNA beyond the steppe has resulted in the integration of populations that were more or less isolated from each other for tens of thousands years created a new homogenized blended population genetic community that had never existed until then.
Put more bluntly, European hunter-gatherers had an extremely different phenotype from the earliest farmers of Europe. In other words, they were of very distinct races, at least as distinct as Chinese people are from French people today.
One major blending of these two populations gave rise to Early European Farmers to produce a mix much like modern day Sardinians.
Another major blending happened when population genetics from the steppe made its way to Europe sometime in the time frame of the late Copper Age to the early Iron Age to create more or less the modern European phenotype which didn't exist until then. These steppe people were about half Early European farmer (itself a blend of hunter-gatherers and "basal European farmers", with additional contributions of Ancestral Northern European and Eastern Hunter-Gatherer). Admixture percentages from substrate populations varied quite a bit in a systemic fashion with more admixture where the food production package brought be the conquering people was less well suited to local conditions.
(5) Y-DNA lineages have a tendency to extend beyond the tightly knit human communities that drive their initial expansions, and also show strong tendencies towards replacement in excess of that seen in autosomal and mitochondrial DNA.
(6) Selective fitness based selection has been ongoing into the modern era.
(7) Razib feels as it most of the puzzle pieces are in place already. In contrast, I feel as if we have lots of the puzzle pieces together and a good understanding of some regions, but still do not understand the links between the genetic shifts and the historical events that caused them, nearly so well in Western Europe as we do in Eastern Europe and some other areas.