Ancient DNA from South-East Europe reveals different events during Early and Middle Neolithic influencing the European genetic heritage

The importance of the process of Neolithization for the genetic make-up of European populations has been hotly debated, with shifting hypotheses from a demic diffusion (DD) to a cultural diffusion (CD) model. In this regard, ancient DNA data from the Balkan Peninsula, which is an important source of information to assess the process of Neolithization in Europe, is however missing. In the present study we show genetic information on ancient populations of the South-East of Europe. We assessed mtDNA from ten sites from the current territory of Romania, spanning a time-period from the Early Neolithic to the Late Bronze Age. mtDNA data from Early Neolithic farmers of the Starčevo Criş culture in Romania (Cârcea, Gura Baciului and Negrileşti sites), confirm their genetic relationship with those of the LBK culture (Linienbandkeramik Kultur) in Central Europe, and they show little genetic continuity with modern European populations. On the other hand, populations of the Middle-Late Neolithic (Boian, Zau and Gumelniţa cultures), supposedly a second wave of Neolithic migration from Anatolia, had a much stronger effect on the genetic heritage of the European populations. In contrast, we find a smaller contribution of Late Bronze Age migrations to the genetic composition of Europeans. Based on these findings, we propose that permeation of mtDNA lineages from a second wave of Middle-Late Neolithic migration from North-West Anatolia into the Balkan Peninsula and Central Europe represent an important contribution to the genetic shift between Early and Late Neolithic populations in Europe, and consequently to the genetic make-up of modern European populations

Genome of Pesxtera Muierii skull shows high diversity and low mutational load in pre-glacial Europe

Few complete human genomes from the European Early Upper Palaeolithic (EUP) have been sequenced. Using novel sampling and DNA extraction approaches, we sequenced the genome of a woman from "Pesxtera Muierii,"Romania who lived similar to 34,000 years ago to 13.5x coverage. The genome shows similarities to modern-day Europeans, but she is not a direct ancestor. Although her cranium exhibits both modern human and Neanderthal features, the genome shows similar levels of Neanderthal admixture (similar to 3.1%) to most EUP humans but only half compared to the similar to 40,000-year-old Pesxtera Oase 1. All EUP European hunter-gatherers display high genetic diversity, demonstrating that the severe loss of diversity occurred during and after the Last Glacial Maximum (LGM) rather than just during the out-of-Africa migration. The prevalence of genetic diseases is expected to increase with low diversity; however, pathogenic variant load was relatively constant from EUP to modern times, despite post-LGM hunter-gatherers having the lowest diversity ever observed among Europeans

Geographic location of ten Romanian sites analyzed in the present study.

<p>(The figure has been provided by M. Rotea and T. Károly).</p

Principal Component Analysis (47% of the total variance) performed considering mtDNA haplogroup frequencies of the ancient and present-day European and Near East populations.

<p>In green Neolithic populations, in pink Hunter-Gatherer groups (HG), in yellow ancient and present-day Romania groups, present-day European population in blue and present-day Near East population in orange. Interpretation based on the haplogroup frequency has been written on both PC (Absence of haplogroups D, M, C and N on one side of the first component and absence of haplogroup H on the top of the second component). PC1 represents 30% of variance and PC2 represents 17% of variance.</p

Multidimensional Scaling Analysis performed by haplogroup frequencies of the ancient and present-day European and Near East populations.

<p>In green Neolithic populations, in pink hunter-gatherer groups and in yellow ancient and present-day Romanian groups, present-day European population in blue and present-day Near East population in orange. Stress: 0.07553 and RSQ: 0.99071.</p

Haplotype (ht) and haplogroup (hg) mtDNA distribution resulting of the analysis of 62 ancient individuals from Romania.

<p>Haplotype (ht) and haplogroup (hg) mtDNA distribution resulting of the analysis of 62 ancient individuals from Romania.</p

Prehistoric samples from Romania analysed in the present study: Chronology, Cultural stages (also in Supporting Information S1 Table), Archaeological sites and Sample size (I.D.: Identification name; N analysed: Number of individuals analysed; N rep: number of individuals with reproducibility results).

<p>Prehistoric samples from Romania analysed in the present study: Chronology, Cultural stages (also in Supporting Information <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0128810#pone.0128810.s009" target="_blank">S1 Table</a>), Archaeological sites and Sample size (I.D.: Identification name; N analysed: Number of individuals analysed; N rep: number of individuals with reproducibility results).</p