Neanderthals and humans interbred in Europe for 5,400 years

We report genome-wide data from a modern human mandible, Oase 1, found in 2002 in the Pes¸tera cu Oase, Romania. The age of this specimen has been estimated to be ,37,000–42,000 years by direct radiocarbon dating2,17,18. Oase 1 is therefore one of the earliest modern humans in Europe. Its morphology is generally modern but some aspects are consistent with Neanderthal ancestry19–21. Subsequent excavations uncovered a cranium from another, probably contemporaneous individual, Oase 2, which also carries morphological traits that could reflect admixture with Neanderthals17,19


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

The mtDNA sequence based on all fragments clusters with present-day Europeans (Extended Data Fig. 1) (Supplementary Note 1). In contrast, the mtDNA sequence based on deaminated fragments is related to a large group of present-day Eurasian mtDNAs (haplogroup N) but diverges from these before they diverged from each other. This Oase 1 mtDNA carries a few private mutations on the basis of which its age can be estimated to be 36,330 years before present (14,520–56,450; 95% confidence interval). Using six positions at which the mtDNA sequence differs from at least 99% of 311 present-day humans, we estimate the contamination among all mtDNA fragments to be 67% (95% confidence interval 65–69%). When we restrict to mtDNA fragments that carry terminal C-to-T substitutions, the contamination estimate is s 4% (95% confidence interval of 2–9%) (Supplementary Note 1).

To isolate nuclear DNA from Oase 1, we used three sets of oligonucleotide probes that cover about two million sites that are single nucleotide polymorphisms (SNPs) in present-day humans and captured DNA molecules from the five libraries. Of the SNPs targeted, 51% (n 5 1,038,619) were covered by at least one DNA fragment, and 13% (n 5 271,326) were covered by at least one fragment with a terminal C-to-T substitution. To estimate nuclear DNA contamination, we tested whether Oase 1 DNA fragments with or without evidence of deamination share more alleles with present-day Europeans or with East Asians. We found that Europeans share significantly fewer alleles with Oase 1 fragments that are deaminated than with Oase 1 fragments that are not, consistent with European contamination of 17–30% (Supplementary Note 1). On the basis of these findings and those from mtDNA, we restricted all subsequent analyses to DNA fragments that carry terminal C-to-T substitutions. After doing this, we found that we captured targeted SNPs from the X and Y chromosomes at a similar rate, indicating that Oase 1 carried both an X and a Y chromosome and thus that he was male. The Y chromosome alleles belong to the F haplogroup, which is carried by most males in Eurasia today (Supplementary Note 2).



We find that Oase 1 shared more alleles with present-day East Asians and Native Americans than with present-day Europeans, counter to what might naively be expected for an ancient individual from Europe (Fig. 1). However, it has been suggested that Europeans after the introduction of agriculture derive a part of their ancestry from a ‘basal Eurasian’ population that separated from the initial settlers of Europe and Asia before they split from each other28. Therefore, we replaced present-day Europeans with Palaeolithic and Mesolithic European individuals in these analyses. We then find that the Oase 1 individual shares equally many alleles with these early Europeans as with present-day East Asians and Native Americans (Fig. 1). Restricting this analysis to transversion polymorphisms, which are not susceptible to errors induced by cytosine deamination, does not influence this result (Extended Data Table 2 and Supplementary Note 3). This suggests that the Oase 1 individual belonged to a population that did not contribute much, or not at all, to later Europeans. This contrasts, for example, with the ,36,000–39,000-year-old Kostenki 14 individual from western Russia, who was more closely related to later Europeans than to East Asians.

We also observe more Neanderthal-like alleles in the Oase 1 individual when we compare
him to four early modern humans: an 8,000-year-old individual from Luxembourg, and three individuals from Russia who vary in age between 24,000 and 45,000 years. Thus, the Oase 1 individual appears to have carried more Neanderthal-like DNA than any other modern human analysed to date. This observation cannot be explained by residual present-day human contamination among the DNA fragments that carry terminal C-to-T substitutions, because all modern humans studied to date carry less Neanderthal ancestry than the Oase 1 genome, and thus contamination would lower, rather than increase, the apparent Neanderthal ancestry.


Figure 2 | Spatial distribution of alleles matching Neanderthals in modern humans. Coloured vertical lines indicate alleles shared with Neanderthals and no colour indicates alleles shared with the great majority of West Africans. D, Dinka; F, French; H, Han; K, Kostenki 14; O, Oase 1; U, Ust’-Ishim. The seven grey bars indicate segments of putative recent Neanderthal ancestry. This analysis is based on 78,055 sites. Numbers refer to chromosomes.

We plotted the positions of Neanderthal-like alleles across the Oase 1 genome (Fig. 2). We detect three segments that are over 50 centimorgans (cM) in size, suggesting that the Neanderthal contribution to the Oase 1 individual occurred so recently in his family tree that chromosomal segments of Neanderthal origin had little time to break up due to recombination. To estimate the date of the most recent Neanderthal contribution to the Oase 1 genome, we studied the size spans of seven segments of the genome that appeared to be recently derived from Neanderthals. Their genetic lengths suggest that the Oase 1 individual had a Neanderthal ancestor as a fourth-, fifth- or sixth-degree relative (Supplementary Note 5). This would predict that an average of 1.6% to 6.3% of the Oase 1 genome derived from this recent Neanderthal ancestor. Visual inspection of the Oase 1 genome suggests that in addition to these seven segments, other smaller segments also carry Neanderthal-like alleles (Fig. 2). When we remove the seven longest segments, the estimate of Neanderthal ancestry in Oase 1 drops from 7.3% to 4.8%, which is still around twice the 2.0–2.9% estimated for the French, Han, Kostenki and Ust’-Ishim individuals in this remaining part of the genome.

This additional Neanderthal ancestry could reflect an older Neanderthal admixture into the ancestors of Oase 1, or that we failed to find all segments of recent Neanderthal ancestry. The Oase 1 genome shows that mixture between modern humans and Neanderthals was not limited to the first ancestors of present-day people to leave Africa, or to people in the Near East; it occurred later as well and probably in Europe. The fact that the Oase 1 individual had a Neanderthal ancestor removed by only four to six generations allows this Neanderthal admixture to be dated to less than 200 years before the time he lived.

"An early modern human from Romania with a recent Neanderthal ancestor." Nature (2015) DOI: 10.1038/nature14558

Neanderthals (Homo neanderthalensis) were widespread across Europe and Western Asia for a long time, starting about 400,000 years ago. But things began to change when populations of Homo sapiens (earlier members of our own species) migrated from Africa to Europe at about 45,000 years ago. Five thousand years later not a single Neanderthal remained. What happened? To find out, Smithsonian Science News posed a seemingly simple question to Briana Pobiner, paleoanthropologist at the Smithsonian’s National Museum of Natural History.



Q: So, why exactly did Neanderthals go extinct?
Pobiner: It is hard to know exactly why many species are on the verge of extinction now, let alone species in the deep past that are already gone. However, we can assume some of the same basic ecological processes driving animals to extinction today are part of the puzzle. In the case of Neanderthals, we think competition and changes to their habitat due to climate change were two of the main factors. Neanderthals were fairly specialized to hunt large, Ice Age animals. But sometimes being specialized isn’t such a good strategy. When climates changed and some of those animals went extinct, the Neanderthals may have been more vulnerable to starvation.



We also think Homo sapiens had a competitive edge over Neanderthals. There is evidence that early Homo sapiens had long-distance trade networks, possibly buffering them against times of climate change when their preferred foods were not available; Neanderthals did not. Neanderthals had physical features that helped them survive cold climates, like large noses to humidify and warm dry, cold air and short, stout bodies to conserve heat, but early Homo sapiens had technology that Neanderthals didn’t, including sewing needles to make clothing, important during the colder periods of the Ice Ages. Homo sapiens also had innovative tools like bows and arrows and seemed to have a more diverse diet than Neanderthals. We don’t have evidence of direct combat between the two species, but we know they interacted, because they interbred. Some would say Neanderthals didn’t go extinct, because everyone alive today whose ancestry is from outside of Africa (where Neanderthals never lived) carries a little bit of Neanderthal DNA in their genes.