Ancient DNA research from Europe has tended to paint a picture of substantial population discontinuity. In a Neolithic sample from Derenburg, neither of the two major Y-chromosome haplogroups prevalent in Central-Northern Europe, R1 and I were found. The Tyrolean Iceman belongs to haplogroup G2a4, a minor lineage in modern-day Europeans. In a Neolithic site from the French south, Treilles, haplogroups G2 and I2 were found, the major R1 lineage again being absent. Megalithic mtDNA from France complements that from the Linearbandkeramik in suggesting a picture of discontinuity, or, at least, substantial change, in the occupation of Europe since the Neolithic. An upcoming study suggest that mtDNA haplogroup X2 did not arrive in Central Europe with the early LBK Neolithic, but with the later Bell Beaker folk. The picture of discontinuity, at least for the Mesolithic-Neolithic transition is supported from Scandinavia, as well as Luxembourg. To cap it all off, a pair of unexpected results from Hungary and Ukraine stretch the contact zone of West/East Eurasian populations well to the west of what has already been determined by ancient DNA work in the Tarim basin and Siberia.
There is, however, one population that stands as an outlier against the backdrop of discontinuity: Sardinians. Ghirotto et al. inferred population continuity in Sardinian mtDNA at least until the Bronze Age. Stories about the Tyrolean Iceman, confirmed in the NOVA TV documentary suggest that a 5,000-year old denizen of Central Europe was genetically closest to Sardinians. A study of craniofacial variation confirms population continuity in Sardinia since the Neolithic, with the population of peninsular Italy gradually diverging, consistent with the Iceman findings. Substantial frequencies of Y-haplogroups G and I are found in modern Sardinian newborns, the same two haplogroups detected in Neolithic southern France at Treilles. And, a study of European genetic isolates finds Sardinians to be lacking in some European polymorphic sites, suggesting a degree of genetic isolation compared to mainland Europeans; this is consistent with my own finding that Sardinians are maximally "western" along the east-west Eurasian axis.
Two cryptic bits of revealed information suggest that a major event may have happened in Europe. In an ICHG 2011 talk, David Reich revealed that his lab has unpublished work of ancient admixture in Europe and that "Europeans are anciently mixed just like South Asians." A blog post by Ewen Callaway suggests that Zink's Tyrolean Iceman investigators are asking "whether he and his kin died out and were replaced by migrants from elsewhere, such as the Middle East."
In the absence of concrete data, it is difficult to interpret such hints of things to come. But the idea of an episode of admixture in Europe from the East that would leave a South Asian-like cline of diminishing West Asian ancestry is supported by admixture studies of West Eurasians, showing that the Near-East to Atlantic-Baltic vector captures the principal aspect of variation in this region.
Interestingly, a "West Asian" ancestral component centered on the South Caucasus region has an Fst distance of 0.028 with the main European "Atlantic-Baltic" component, and of 0.058 with a "Southern" component present at non-trivial amount in southern populations from both sides of the Mediterranean and the Near East.
The possibility of a major east-west population movement into Europe that left Sardinians least affected is intriguing. At K=7 Sardinians have almost none of the "West Asian" ancestral component and most of the "Southern" one in Europe. This appears to be consistent with a population that was least affected by population movements from the northern parts of West Asia.
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.
In a roundabout manner, the Caucasus and its environs may soon reclaim their position as the fons gentium that Blumenbach, more than two centuries ago, ascribed to them. More than one century ago, Italian anthropologist Giuseppe Sergi, proposed a model of the double origin of Europeans, supposing that the Mediterraneans of southern Europe (a branch of the "Eurafricans") were invaded by peoples from the east, the "Eurasiatics." Naturally, the ideas of Blumenbach and Sergi cannot be adopted today in their entirety, but they do well to remind us that inklings of truth can be found in the most unexpected of places.
And, when one reads this quote from Carleton Coon's classic 1939 synthesis The Races of Europe (section "The western Mediterranean Islands")... "Sardinia and Corsica were peopled at the beginning of the Neolithic by a race of short-statured, dolichocephalic, low-vaulted, brunet Mediterraneans, coming probably from several quarters, including the adjacent European coasts, North Africa, and the eastern Mediterranean. Subsequent immigrations of other Mediterranean peoples have affected the racial composition of these islands but little." ... one is inclined to say "Dr. Coon, you were right!"