Archaeological evidence suggests that agrarian societies emerged in Western Asia around 11,000 years before present (YBP) 
and rapidly spread reaching South Eastern Europe by approximately 9,000 YBP 
. The transition from pre-Neolithic hunter-gatherer societies to Neolithic farming and cattle breeding is often called the Neolithic revolution and marks one of the most pronounced cultural changes in European prehistory 
that can be observed in the archaeological record all over Europe 
. By around 5,000 YBP almost all populations in mainland Europe practiced agriculture. There are two main hypotheses for how Neolithic cultures spread across Europe. The first, suggests cultural transmission as the main factor, i.e. that the new technologies and subsistence strategies were learned from neighbouring groups 
. The second hypothesis suggests an expansion of farmer populations from the Near East into Europe, replacing most of the pre-Neolithic hunter-gatherer populations. This population replacement model, termed demic diffusion, is conceived as population spread and expansion, with limited admixture with resident populations.
Recently, mitochondrial DNA (mtDNA) from skeletal remains of European early farmers and late hunter-gatherers has been retrieved 
. The frequency of mtDNA haplogroups, defined by substitutions shared by related mtDNA types (Phylotree.org-mtDNA tree build 12), in early farmers across Europe 
was found to be overall similar to those in modern Europeans (, Figure S4
, Figure S5
), while pre-Neolithic hunter-gatherers appear to be quite distinct (). 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 (Figure S4
) 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 genetic contribution of pre-Neolithic hunter-gatherers to later Neolithic populations is furthermore supported by a similar frequency of U subhaplogroups (U5, U4, K and U2) that were found in pre-Neolithic hunter-gatherers (Figure S3
) and are still the most common U-subhaplogroups in modern Central Europeans (Figure S5
Haplogroup frequencies of hunter-gatherer and early farmer populations based on short segments of the mtDNA (A); Haplogroup frequencies of three contemporary European complete mtDNA datasets (B).
The mtDNA sequences determined from early farmers and hunter-gatherers are however less than 400 bp in length and their number is quite small (105 and 21, respectively), limiting the information that can be gained about population sizes and putative population expansions in the past. Here, we use a total of 1,151 complete mtDNAs from present-day populations in Europe, along with 38 mtDNAs which we determined from a modern population in Croatia, to estimate the frequency of the haplogroup U, putatively typical of hunter-gatherers, and mtDNAs of the haplogroup H, putatively typical of the early farming cultures. We then use these data to study potential differences in signatures of demographic history of hunter-gatherers and farmers in Europe that are discernable in present-day European mtDNAs.