In particular, 83% (19 out of 23) of hunter-gatherers analyzed to date carry mtDNAs belonging to haplogroup U and none of the hunter-gatherers fall in haplogroup H. In contrast, haplogroup U has been found in only 13 of 105 (around 12%) individuals from early farming cultures of Europe and it occurs in less than 21% of modern Europeans, while haplogroup H comprises between 25% and 37% of mtDNAs retrieved from early farming cultures and is in about 30% of contemporary Europeans. The mtDNA data thus suggest that the pre-Neolithic populations in Europe were largely replaced by in-coming Neolithic farming groups, with a maximum mtDNA contribution of around 20% from pre-Neolithic hunter-gatherers. . . . The high frequency of H-type mtDNAs in European Neolithic populations and its complete absence in pre-Neolithic hunter-gatherers suggests that H-type mtDNAs arrived with early farmers in Europe.
Estimates of the time frame in which a founding member of an mtDNA haplogroup that is survived by existing matrilines in Europe is calculated by making empirically estimated assumptions about how fast mtDNA mutation and counting back the number of mutations necessary to reeach a shared ancestor for a group of related mtDNA lineages. This dating methodology isn't perfect, but has performed much better, for a variety of technical reasons, than similar efforts to generate mutation rate dates from patrlineal Y-DNA.
The estimates of the genetic ages of related mtDNA lineages confirms the conclusion of the ancient DNA samples that mtDNA haplogroup H arrived in Europe with its first wave of farmers.
The population size increase observed between 9,000 and 5,000 YBP likely represents the population expansion that accompanied the Neolithic revolution. . .the H-type mtDNA population size seems to experience an exponential increase around 7,000 YBP, suggesting that both populations are not yet fused.
The more interesting contributions of the new paper are twofold.
First, it suggests that genetic diversity of Europe's hunter-gather populations dates only to the repopulation of Europe, following the Last Glacial Maximum, from refugia at lower latitudes in Europe, rather than having sustained the full range of genetic diversity dating from the pre-Last Glacial Maximum hunters and gathers of Europe in the Upper Paleolithic (ca. 40,000 years ago to 20,000 years ago, including the entire period of time when modern humans and Neanderthals co-existed in Europe), which was also a mtDNA haplogroup U dominated population so far as the small number of samples available to us can discern.
Second, the genetic and archaeological evidence coroborate each other in suggesting that between about 5000 BCE, when the first farmers arrived in a population that was largely from Europe's hunters and gatherers, and about 2000 BCE, when there ceased to be distinct hunter-gatherer populations in Europe, that the 20%-25% of the matrilineal gene pool of Europe that is there today had fully assimilated into to the gene pools of European farmers. For the most part, this fusion took place in the early Neolithic and Copper Ages of Europe, and predated Europe's Bronze Age.
In contrast, U-type mtDNAs show an increase in population size around 15,000 to 10,000 YBP, which coincides with the end of the last glacial maximum in Europe and a northwards expansion of hunter-gatherer populations. The data suggests that this population remained rather constant after 10,000 YBP until the onset of the Neolithic revolution. . . . After 4,000 YBP, no archaeological remains of hunter-gatherers were found in central Europe. From approximately that time on, both H- and U-type mtDNAs expand in a similar way. This may reflect fusion of the two populations where these mtDNAs were prevalent.
While I would argue that the data quoted above arguably support a pre-Neolithic hunter-gatherer contribution to the modern European genome of as much as 25% of Europe's gene pool, rather than 20%, the bottom line is that 75%-80% of Europe's matrilineal ancestors made their way into Europe either with its first farmers, or with later waves of migration.
Caveats and Implications
These conclusions come with some important caveats and implications.
1. Matrilineal ancestors are only a tiny percentage of any given person's ancestry. At a time depth of 2,500 years, someone has up to 2^100 ancestors, with many, in practice tracing multiple lines of descent to each individual alive today in the gene pool. But, there is no particular good reason to think that the statistical make up of all of the female ancestors in a population differs materially from the statistical make up of the matrilineal ancestory of a population.
2. The fact that particular individual has one mtDNA haplogroup or non-recombining Y-DNA haplogroup does not, standing alone, make that individual any more indigenous to Europe than someone else. You might fairly conclude that a whole group of genetically distinctive people who have high concentration of pre-Neolithic haplogroups will have a genetic makeup overall that is more similar to pre-Neolithic peoples of Europe. But, in populations that have even very modest genetic interaction with each other, over time, all genes without selective effects in the interacting populations will tend towards fixation, with each individual in the population tending over time to have particular genes from given source populations for the combined population that has reached genetic fixation of all of its genes similar to the relative genetic contributions of those source populations to the overall community at the start.
In other words, if 25% of maternal European ancestry is traceable to pre-Neolithic peoples of Europe, and 5% of paternal European ancestry is traceable to pre-Neolithic peoples of Europe, the odds are good that any particular European will trace 15% of the genes in their personal genome in a single one of their cells to the pre-Neolithic peoples of Europe, and that percentage is likely to vary to a surprisingly small degree within people in regions as large and larger than major regions within a modern European country.
Moreover, in general, the older a contribution to a gene pool is, the more likely that contribution is to have reached fixation and to have become simply one of random part of the mix that makes up some later gene pool into which the older contributing population to the gene pool has fused.
3. Generally speaking, matrilineal ancestry in a given place is more conservative than patrlineal ancestry in a given place. Mostly, this is because there is a recurring historical pattern of incoming men migrating into an area and having children with local women, in a way that increases their descendant's share of the gene pool relative to the descendants of local men. This implies that our default hypothesis, unless and until we have evidence to the contrary, is that less than 25% of the European paternal contribution to the modern European gene pool, possibly quite a bit less, is traceable to pre-Neolithic European hunters and gatherers.
4. While the literature isn't quite as well developed on this point, I think it is also plausible to suspect that admixture of small porportions of maternal ancestry may be more prone to gender asymmetry of genetic contributions than admixture of large proportions of maternal ancestry. This flows from the assumption that small percentages may arise from isolated instances of newcomers marrying local women, which is much less likely to happen to local men in ethnographically documented examples comparable to the situation of the first farmers of Europe. In contrast, large percentages are more likely to arise from wholesale assimilation of entire communities, which are more demographically balanced, into the society of the newcomers.
5. All other things being equal, a best first order estimate of the total pre-Neolithic European hunter and gatherer contribution to the European gene pool is roughly the average of the matriline and patriline contributions of pre-Neolithic European hunter-gatherers to Europe's modern gene pool.
6. The relative stablity of the matrline gene pool relative to the patriline gene pool, in historical examples, favors the hypothesis that R1b, the most common Y-DNA haplogroup in "Atlantic Europe" arrived with, or after, Europe's first farmers, and not before them.
Moreover, since Y-DNA haplogroup R1b is almost absence from ancient DNA from Europe's first farmers, the most plausible prediction is that it arrived on the European scene at high frequencies in the Copper Age or later, sometime in the last six thousand years or so. But, this is not a hypothesis that is easily tested with direct evidence from ancient DNA, because it is much harder to extract Y-DNA sample good enough to classify by haplogroup from the ancient DNA sources (particularly the interior parts of skeletal teeth) than it is to do the same with mtDNA.