Modern humans arrived in Europe ~45,000 years ago, but little is known about their genetic composition before the start of farming ~8,500 years ago. Here we analyse genome-wide data from 51 Eurasians from ~45,000–7,000 years ago. Over this time, the proportion of Neanderthal DNA decreased from 3–6% to around 2%, consistent with natural selection against Neanderthal variants in modern humans. Whereas there is no evidence of the earliest modern humans in Europe contributing to the genetic composition of present-day Europeans, all individuals between ~37,000 and ~14,000 years ago descended from a single founder population which forms part of the ancestry of present-day Europeans. An ~35,000-year-old individual from northwest Europe represents an early branch of this founder population which was then displaced across a broad region, before reappearing in southwest Europe at the height of the last Ice Age ~19,000 years ago. During the major warming period after ~14,000 years ago, a genetic component related to present-day Near Easterners became widespread in Europe. These results document how population turnover and migration have been recurring themes of European prehistory.
European Nucleotide Archive
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Extended data figures and tables
Extended Data Figures
- Extended Data Figure 1: A decrease in Neanderthal ancestry in the last 45,000 years. (127 KB)
This is similar to Fig. 2, except we use ancestry estimates from rates of alleles matching to Neanderthal rather than f4-ratios, as described in Supplementary Information section 3. The least-squares fit excludes Oase1 (as an outlier with recent Neanderthal ancestry) and Europeans (known to have reduced Neanderthal ancestry). The regression slope is significantly negative (P = 0.00004, Extended Data Table 3).
- Extended Data Figure 2: Heat matrix of pairwise f3(X, Y; Mbuti) for selected ancient individuals. (332 KB)
Only individuals with at least 30,000 SNPs covered at least once are analysed.
- Extended Data Figure 3: Studying how the relatedness of non-European populations to pairs of European hunter-gatherers changes over time. (525 KB)
Statistics were examined of the form D(W, X; Y, Mbuti), with the Z-score given on the y axis, where W is an early European hunter-gatherer, X is another European hunter-gatherer (in chronological order on the x axis), and Y is a non-European population (see legend). a, W = Kostenki14. b, W = GoyetQ116-1. c, W = Vestonice16. d, W = ElMiron. |Z| > 3 scores are considered statistically significant (horizontal line). The similar Fig. 4b gives absolute D-statistic values rather than Z-scores (for W = Kostenki14) and uses pooled regions rather than individual populations Y.
- Extended Data Figure 4: Three admixture graph models that fit the data for Satsurblia, an Upper Palaeolithic individual from the Caucasus. (127 KB)
These models use 127,057 SNPs covered in all populations. Estimated genetic drifts are given along the solid lines in units of f2-distance (parts per thousand), and estimated mixture proportions are given along the dotted lines. All three models provide a fit to the allele frequency correlation data among Mbuti, Ust’-Ishim, Kostenki14, Vestonice16, Malta1, ElMiron and Satsurblia to within the limits of our resolution, in the sense that all empirical f2-, f3- and f4-statistics relating the individuals are within three standard errors of the expectation of the model. Models in which Satsurblia is treated as unadmixed cannot be fit.
Extended Data Tables
- Supplementary Information (7.8 MB)
This file contains Supplementary Text and Data, Supplementary Tables, Supplementary Figures and additional references (see Contents for more details).