The data is, of course, incomplete. It isn't entirely clear how true this is of European hunter-gatherers in Southwest Europe, for example. But, the fact that all of the half a dozen Mesolithic European hunter-gatherers from the two sites for which data is available have Y-DNA haplogroup I is quite powerful evidence (none of the samples exclude I2, but not all are that specific).
Today, Y-DNA haplogroup I accounts for a little less than 20% of Europeans with a much higher percentage of Scandinavians (among the last population of Europe to adopt farming) and in the Balkans. I1 which is not present in the ancient samples currently more common than I2. I1 appears to have expanded much later, perhaps around the time of the Nordic Bronze Age or maybe even a later phase of the Nordic Bronze Age. Thus, less than 10% of European men are in the I2 Y-DNA clade. Its mtDNA counterpart, mtDNA haplogroup U, is found in about 11% of Europeans (the non-U5 clades are mostly outside of Europe or rare). These estimates aren't perfect since some clades of each haplogroup may have been late arrivals, and there may be other haplogroups in ancient DNA of that period which has not yet been discovered.
But, it is a fair guess that the Paleolithic European hunter-gatherer population in which both Y-DNA I and mtDNA U were predominant is the source of something on the order of one-ninth or one-tenth of the modern European gene pool. Likewise, it is fair to say that modern Uralic and Nordic European populations in far Northern Europe in modern Europe, which have high concentrations of both haplogroups, are probably closest to these ancestral populations within Europe. The corollary of this observation is that the contribution of this Paleolithic hunter-gatherer population in other parts of Europe may be even more shallow.
Y-DNA haplogroup R1 is the dominant Y-DNA haplogroup in almost all of the rest of Europe (with more R1b in the West and more R1a in the East, generally speaking); similarly mtDNA haplogroup H is dominant in the modern European gene pool.
The Eurogenes blog recaps a lot of the key figures relating to overall autosomal data from the recent paper. Sardinians, unsurprisingly, are one of the closest matches to Early European Farmers. Early European Farmers are supposed by the authors to about about 44 +/- 10% "basal European" farmer stock and a remainder assimilated indigenous European foragers. But, Sardinians exceptionally low level of Ancient Northeast Eurasian (ANE) admixture could actually reflect a higher percentage of this basal European component, as almost all other Europeans are in a much narrower ANE admixture band that is very low across the board. Thus, while a "three component" mixture (Western Hunter Gatherer, Ancient Northeast Eurasian, and Early European Farmer with a possible additional Scandinavian Hunter Gatherer component) is proposed, for most Europeans a simple two component (Western Hunter Gatherer-Early European Farmer) admixture does a good job of explaining the European autosomal data.
Archaeology and modern population genetics tends to support a Mesolithic expansion of a maritime hunter-gatherer population associated with mtDNA haplogroup V, possibly from a Franco-Cantabrian refugium, whose impact stretched from Northwest Africa to Arctic Scandinavia in coastal areas along the Atlantic Ocean and Baltic Sea coast as a minor contributing population to the more dominant mtDNA U haplogroup population that was present in Europe before the Last Glacial Maximum ca. 20,000 years ago, retreated to European refugia as Northern Europe was completely depopulated at that time, and then repopulated Europe as soon as the glaciers retreated.
We don't know what Y-DNA haplogroups were present together with mtDNA haplogroup V peoples. The ancient DNA from Mal'ta boy and the location of modern Y-DNA R1, R1a and R2 bearers all support the notion that R1b had origins far to the East of its current distribution. But when, given the unreliability of mutation rate dating for Y-DNA?
Eurogenes also notes that the Ancient Northeast Eurasian component appears to be a relatively recent arrival admixing just 5,500 to 4,000 years ago - a match strong suggestive of the expansion of the Uralic languages (such as Finnish, Estonian and Hungarian). The following observation is particularly notable:
Nevertheless, if not for the ANE, we'd simply have a two-way mixture model between indigenous European foragers and migrant Near Eastern farmers, at least for most Europeans anyway. Moreover, the seemingly late arrival of ANE in much of Europe is fascinating, because it's yet another smoking gun for a major genetic upheaval across the continent during the Copper Age (aka. Late Neolithic/Early Bronze Age). Interestingly, archeological data suggest that this was also the period which saw the introduction of new social organization and perhaps Indo-European languages across most of the continent. None of this was lost on the authors of the paper, but it appears they'd rather be cautious pending more ancient genomic data, because they chose not to explicitly mention the Indo-Europeans.He then quotes the study itself (from which I've omitted end note citations for easier reading):
The absence of Y-haplogroup R1b in our two sample locations is striking given that it is, at present, the major west European lineage. Importantly, however, it has not yet been found in ancient European contexts prior to a Bell Beaker burial from Germany (2,800-2,000BC), while the related R1a lineage has a first known occurrence in a Corded Ware burial also from Germany (2,600BC). This casts doubt on early suggestions associating these haplogroups with Paleolithic Europeans, and is more consistent with their Neolithic entry into Europe at least in the case of R1b. More research is needed to document the time and place of their earliest occurrence in Europe.Interestingly, the Mal’ta boy belonged to haplogroup R* and we tentatively suggest that some haplogroup R bearers may be responsible for the wider dissemination of Ancient North Eurasian ancestry into Europe, as their haplogroup Q relatives may have plausibly done into the Americas.Regular readers of this blog know that my working hypothesis, although not an established fact, is that R1b does expand in Europe via the Bell Beaker culture and its successors, while Indo-Europeans exemplified by the Corded Ware culture were probably the source of R1a in Europe. Further, my working hypothesis is that the Bell Beaker culture was Vasconic (i.e. Basque-esque) rather than Indo-European linguistically, although it and its successor cultures were a technological and military peer of the Corded Ware Indo-Europeans for about a thousand years or so (basically until Bronze Age collapse ca. 1200 BCE). Eurogenes has a post largely in accord with this hypothesis. See also here and here and here and here and here.
My working hypothesis is that Bell Beaker culture has origins geographically near that of some early Indo-European culture (somewhere east of France) and absorbed many of the key technological innovations associated with the Indo-Europeans, but retained their own language and culture and then rapidly expanded in population genetic terms in parallel to the Indo-Europeans. Thus, when Indo-European Urnfield and Celtic peoples arrive in Western Europe on the eve of and after Bronze Age collapse, the already technologically advanced Western Europeans adopt the language and much of the culture of the conquering Indo-Europeans, but don't have a huge demographic impact when they arrive.
This working hypothesis is not without its flaws. There is not strong archaeological evidence for substantial population replacement in the Bell Beaker evidence. But, R1b is present at very high levels in the Basque whom all agree were pre-Indo-European in Western Europe, and it is absent in European hunter-gatherer ancient DNA to date and in all available early Neolithic ancient Y-DNA from Europe. There aren't a lot of other good candidates to bring about this change in the right time and place.
Of course, it looks likely that a flood a new early and middle Neolithic ancient DNA is likely to be analyzed in the next several years and this may resolve the question of the source of R1a and R1b in Europe more definitively. If my working hypothesis is correct, there will be little or no R1b in Southwest Europe prior to the arrival of the Bell Beaker culture there ca. 3000 BCE, with earlier Neolithic ancient Y-DNA in Southwestern Europe being mostly Y-DNA haplogroup G2 and other early Neolithic Y-DNA clades, and R1b would also be absent from Mesolithic (aka Epipaleolithic) ancient Y-DNA in Southwest Europe.