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.

Analysis of DNA from a 37,000–42,000-year-old modern human from Romania reveals that 6–9% of the genome is derived from Neanderthals, with the individual having a Neanderthal ancestor as recently as four to six generations back. This paper presents an analysis of the DNA from a modern human individual from Peştera cu Oase in Romania who lived 37,000–42,000 years ago. This individual male carries 6–9% Neanderthal DNA — compared to just 1–3% reported in other modern Eurasian humans — and given the size of the segments of Neanderthal ancestry in his genome, the authors conclude that he had a Neanderthal among his ancestors four to six generations back in his family tree. This shows that interbreeding between modern humans and Neanderthals was not limited to the Africa and the Near East, but that it occurred in Europe as well. But the population to which the Oase individual belonged did not make a substantial genetic contribution to later humans in Europe. This provides evidence for an early initial migration of modern humans who mixed with Neanderthals but did not contribute to present-day Europeans. 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 Eurasia1. Here we analyse DNA from a 37,000–42,000-year-old2 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.

Modern humans appeared in Europe by at least 45,000 years ago^1–5, but the extent of their interactions with Neanderthals, who disappeared by about 40,000 years ago⁶, and their relationship to the broader expansion of modern humans outside Africa are poorly understood. Here we present genome-wide data from three individuals dated to between 45,930 and 42,580 years ago from Bacho Kiro Cave, Bulgaria^1,2. They are the earliest Late Pleistocene modern humans known to have been recovered in Europe so far, and were found in association with an Initial Upper Palaeolithic artefact assemblage. Unlike two previously studied individuals of similar ages from Romania⁷ and Siberia⁸ who did not contribute detectably to later populations, these individuals are more closely related to present-day and ancient populations in East Asia and the Americas than to later west Eurasian populations. This indicates that they belonged to a modern human migration into Europe that was not previously known from the genetic record, and provides evidence that there was at least some continuity between the earliest modern humans in Europe and later people in Eurasia. Moreover, we find that all three individuals had Neanderthal ancestors a few generations back in their family history, confirming that the first European modern humans mixed with Neanderthals and suggesting that such mixing could have been common.

Previous bone collagen carbon and nitrogen isotopic studies of Late Pleistocene European cave bears ( Ursus spelaeus ) have shown that these bears frequently had low nitrogen isotope values, similar to those of herbivores and indicating either unusual physiology related to hibernation or a herbivorous diet. Isotopic analysis of animal bone from the Peştera cu Oase (Cave with Bones), Romania, shows that most of its cave bears had higher nitrogen isotope values than the associated herbivores and were, therefore, omnivorous. The Oase bears are securely identified as cave bears by both their morphology and DNA sequences. Although many cave bear populations may have behaved like herbivores, the Oase isotopic data demonstrate that cave bears were capable of altering their diets to become omnivores or even carnivores. These data therefore broaden the dietary profile of U. spelaeus and raise questions about the nature of the carnivore guild in Pleistocene Europe.