When we considered continuity between early farmers and modern Europeans, we did identify ancestral population size combinations where
PS>O > 0.05 (black shaded area in
Fig. 2C). Thus, there are demographic conditions under which the observed genetic differences between early European farmers and modern Europeans can be explained by assuming population continuity. Those conditions include assuming
NN < 3000, an effective female population size that may be considered implausibly low and is certainly lower than the current archaeological census estimates of 124,000 (
16). However, we note that (i) ancestral population sizes are notoriously difficult to estimate from archaeological data, and (ii) the relationship between effective and census population size is dependent on unknown factors, including mating systems and population substructure.
Most modern European mtDNA lineages can be assigned to one of the following clades or haplogroups: H, V, U (including K), J, or T, all deriving from clade R; or I, W, or X, the descendants of clade N. Although some subclades, such as U5, are fairly specific to Europe, most are shared with adjacent areas of Asia and North Africa and are of uncertain antiquity in Europe. We are therefore cautious about treating specific clades as markers of particular past population groups or demographic episodes (
17). Nonetheless, it is intriguing to note that 82% of our 22 hunter-gatherer individuals carried clade U (14 U5, 2 U4, and 2 unspecified U types;
Table 1). A high incidence of U types (particularly those belonging to the U5 subclade) in Stone Age Europeans has been inferred from modern mtDNA (
7), but the frequencies found here are surprisingly high. Europeans today have moderate frequencies of U5 types, ranging from about 1 to 5% along the Mediterranean coastline to 5 to 7% in most core European areas, and rising to 10 to 20% in northeastern European Uralic speakers, with a maximum of over 40% in the Scandinavian Saami. U4 types show frequencies between 1 and 5% in most parts of Europe, with Western Europe at the lower end of this range and northeastern Europe and central Asia showing percentages in excess of 7% (
13).
The diversity among the hunter-gatherer U types presented here, together with their continued presence over 11 millennia, and the fact that U5 is rare outside Europe, raises the possibility that U types were common by the time of the post-LGM repopulation of central Europe, which started around 23,000 years ago (3). In a previous study, we showed that the early farmers of central Europe carried mainly N1a, but also H, HV, J, K, T, V, and U3 types (
11,
12). We found no U5 or U4 types in that early farmer sample. Conversely, no N1a or H types were observed in our hunter-gatherer sample, confirming the genetic distinctiveness of these two ancient population samples. This is particularly surprising as there is clear evidence for some continuity in the material culture between the central European Mesolithic and the earliest settlements of the Neolithic Linearbandkeramik culture (LBK) (
18). Thus, it seems that despite the exchange of stone artifacts, genetic exchange between both groups, at least on the female side, was initially limited. The only exception is the site Ostorf (northern Germany), where two individuals carried haplogroup T2, which is also found in our LBK sample. We are cautious about interpreting this as a signature of local admixture (
17), particularly because the hunter-gatherer and early farmer T2 types belong to different sublineages, but it is notable that Ostorf is culturally a Mesolithic enclave surrounded by Neolithic funnel-beaker farmers and is the only hunter-gatherer site where any non-U mtDNA types were observed (
Table 1). Further sampling from such local contexts should shed light on the details of Mesolithic-Neolithic interactions after the arrival of farming. We note that any genetic exchange between hunter-gatherers and early farmers at this site would reduce the overall genetic differentiation between the two groups, so inclusion of this site has, if anything, a conservative effect on our conclusions regarding continuity.
Taken together, our results indicate that the transition to farming in central Europe was accompanied by a substantial influx of people from outside the region who, at least initially, did not mix significantly with the resident female hunter-gatherers. We accept that alternative, more complex demographic scenarios, such as strong local population structure and high group extinction and fission rates, might also explain our data. However, the ubiquity of U types in our hunter-gatherer samples is inconsistent with extensive population structuring and indicates that the demographic processes that shaped the observed patterns of genetic variation extend beyond the local scale.
The extent to which modern Europeans are descended from incoming farmers, their hunter-gatherer forerunners, or later incoming groups remains unresolved. The predominant mtDNA types found in the ancient samples considered in this study are found in modern Europeans, but at considerably lower frequencies, suggesting that the diversity observed today cannot be explained by admixture between hunter-gatherers and early farmers alone. If this is the case, then subsequent dilution through migration and admixture, after the arrival of the first farmers, would need to be invoked, implying multiple episodes of population turnover, which are not necessarily observable in the archaeological record. This, in turn, would mean that the classic model of European ancestry components (contrasting hunter-gatherers with early Neolithic farming pioneers) requires revision.
The geographic origin of the demographic processes that brought the early farmer mtDNA types to central Europe now becomes a major question. On the one hand, all of the early farmer remains analyzed here are associated with the LBK culture of central Europe. Based on ceramic typology, the LBK culture is thought to have originated in present-day western Hungary and southwestern Slovakia, with a possible predecessor in the southeast European Starçevo-Kris culture (
19,
20). These cultural source locations may provide the most plausible origins or routes for the geographic spread of the early farmers, considering that the LBK was the first major farming culture in central and northern Europe and is archaeologically attested to have disseminated over five centuries and covered nearly a million square kilometers. Alternatively, the farmers’ mtDNA types may have an origin closer to the Neolithic core zone in southwestern Asia. Further ancient DNA analysis of early farmer samples from southeastern Europe and Anatolia will be required to resolve this question.