An early modern human from Romania with a recent Neanderthal ancestor

Abstract

Neanderthals are thought to have disappeared in Europe approximately 39,000-41,000 years ago but they have contributed 1-3% of the DNA of present-day people in Eurasia. Here we analyse DNA from a 37,000-42,000-year-old modern human from Peştera cu Oase, Romania. Although the specimen contains small amounts of human DNA, we use an enrichment strategy to isolate sites that are informative about its relationship to Neanderthals and present-day humans. We find that on the order of 6-9% of the genome of the Oase individual is derived from Neanderthals, more than any other modern human sequenced to date. Three chromosomal segments of Neanderthal ancestry are over 50 centimorgans in size, indicating that this individual had a Neanderthal ancestor as recently as four to six generations back. However, the Oase individual does not share more alleles with later Europeans than with East Asians, suggesting that the Oase population did not contribute substantially to later humans in Europe.

Extended Data Figure 1. Mitochondrial DNA tree for Oase 1 and other modern humans

The consensus sequences for all Oase 1 fragments and for deaminated fragments are shown. The tree is rooted with a Neanderthal mtDNA (Vindija33.25) as an outgroup.

Figure 1. Allele sharing between the Oase 1 individual and other genomes

Each point indicates the extent to which the Oase 1 genome shares alleles with one or the other of a pair of genomes from different populations indicated above and below (see Extended Data Table 1 for numbers). Z-scores larger and smaller than |2| indicate an excess of allele sharing (grey).

Figure 2. Spatial distribution of alleles matching Neanderthals in modern humans

Colored vertical lines indicate alleles shared with Neanderthals and no color indicates alleles shared with the great majority of West Africans. (O)ase 1, (K)ostenki 14, (U)st’-Ishim, (F)rench, (H)an, and (D)inka. The seven yellow bars indicate segments of putative recent Neanderthal ancestry. This analysis is based on 78,055 sites.