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Ancient genomes shed new light on the earliest Europeans and their relationships with Neandertals


Ancient genomes shed new light on the earliest Europeans and their relationships with Neandertals


An international research team has sequenced the genomes of the oldest securely dated modern humans in Europe who lived around 45,000 years ago in Bacho Kiro Cave, Bulgaria. By comparing their genomes to the genomes of people who lived later in Europe and in Asia the researchers from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, show that this early human group in Europe contributed genes to later people, particularly present-day East Asians. The researchers also identified large stretches of Neandertal DNA in the genomes of the Bacho Kiro Cave people, showing that they had Neandertal ancestors about 5-7 generations back in their family histories. This suggests that mixture with Neandertals was the rule rather than the exception when the first modern humans arrived in Europe.


Last year, a research team led by researchers from the National Archaeological Institute with Museum at the Bulgarian Academy of Sciences and the Max Planck Institute for Evolutionary Anthropology, Germany, reported the discovery of modern human remains found in direct association with the Initial Upper Palaeolithic stone tools at the site of Bacho Kiro Cave in Bulgaria. The oldest individuals found in the cave were directly radiocarbon dated to between 43,000 and 46,000 years ago. They are thus the earliest known dispersal of modern humans across the mid-latitudes of Eurasia.


Mateja Hajdinjak and colleagues have now sequenced the genomes of five individuals found at the Bacho Kiro Cave. Four individuals are between 43,000-46,000-years-old and were found together with stone tools belonging to the Initial Upper Palaeolithic, the earliest culture associated with modern humans in Eurasia. An additional individual found in the cave is around 35,000-years-old and found with stone tools of a later type. It was previously thought that bearers of the Initial Upper Palaeolithic died out without contributing genetically to modern humans arriving later. However, the researchers now show that the oldest Bacho Kiro Cave individuals, or groups closely related to them, contributed genes to present-day people. Surprisingly, this contribution is found particularly in East Asia and the Americas rather than in Europe where the Bacho Kiro Cave people lived. These genetic links to Asia mirror the links seen between the Initial Upper Palaeolithic stone tools and personal ornaments found in Bacho Kiro Cave and tools and ancient jewelry found across Eurasia to Mongolia. Importantly, the later ~35,000-year-old individual found in Bacho Kiro Cave belonged to a group that was genetically distinct from the earlier inhabitants of the cave. This shows that the earliest history of modern humans in Europe may have been tumultuous and involved population replacements.


The earliest people at Bacho Kiro Cave lived at a time when Neandertals were still around. The researchers therefore scanned their genomes for fragments of Neandertal DNA.  ”We found that the Bacho Kiro Cave individuals had higher levels of Neandertal ancestry than nearly all other early humans, with the exception of a ~40,000-year-old individual from Romania. Crucially, most of this Neandertal DNA comes in extremely long stretches. This shows that these individuals had Neandertal ancestors some 5 to 7 generations back in their family trees” says Mateja Hajdinjak. Although only a handful of genomes from modern humans who lived at the same time in Eurasia as some of the last Neandertals have been recovered, nearly all of them have recent Neandertal ancestors. “The results suggest that the first modern humans that arrived in Eurasia mixed frequently with Neandertals. They may even have become absorbed into resident Neandertal populations. Only later on did larger modern human groups arrive and replace the Neandertals” says Svante Pääbo, who coordinated the genetic research.

"The paleogenetic results from Bacho Kiro Cave demonstrate that the Balkans are key region for investigating early modern human migrations and interactions with local Neanderthals. These new data also help link these early modern humans in Europe to Initial Upper Paleolithic material culture known from Palaeolithic sites across the mid-latitude of Eurasia as far east as Mongolia.”- says Tsenka Tsanova, one of the excavation leader and specialist in lithic technologies.

"The recently discovered modern human remains in Bulgaria, in the Bacho Kiro cave near the town of Dryanovo, dating from 43,000 - 46,000 years ago, are undoubtedly one of the most ancient modern people discovered in Europe. They were found together with an archeological assemblage from the Initial Upper Paleolithic, which differs from the Aurignacian culture and definitely precedes its appearance.”- say Nikolay Sirakov and Svoboda Sirakova, leaders from the Bulgarian side of the Bulgarian-German research project of Bacho Kiro Cave.


Original publication:


Title: Initial Upper Palaeolithic humans in Europe had recent Neanderthal ancestry

Authors: Mateja Hajdinjak, Fabrizio Mafessoni, Laurits Skov, Benjamin Vernot, Alexander Hübner, Qiaomei Fu, Elena Essel, Sarah Nagel, Birgit Nickel, Julia Richter, Oana Teodora Moldovan, Silviu Constantin, Elena Endarova, Nikolay Zahariev, Rosen Spasov, Frido Welker, Geoff M. Smith, Virginie Sinet-Mathiot, Lindsey Paskulin, Helen Fewlass, Sahra Talamo, Željko Rezek, Svoboda Sirakova, Nikolay Sirakov, Shannon P. McPherron, Tsenka Tsanova, Jean-Jacques Hublin, Benjamin M. Peter, Matthias Meyer, Pontus Skoglund, Janet Kelso and Svante Pääbo

Journal: Nature

  1. Entrance to the Bacho Kiro Cave (Bulgaria). The excavations are just inside the entrance and to the left. The cave extends over 3 km and is a popular tourist destination (Picture credit: Nikolay Zahаriev, NBU Sofia).

2. The Niche 1 sector (left) and the Main sector (right) during the excavations of Bacho Kiro Cave, Bulgaria in 2016-19. The cement area in the foreground was previously excavated in the 1970s. New excavations picked up where these excavations left off (Picture credit: Nikolay Zahаriev, NBU Sofia).

3. Excavations at Bacho Kiro Cave (Bulgaria). The excavator in the foreground is recording artifacts (each marked with a colored pin) from the Initial Upper Paleolithic Layer I in the Niche sector. The bags with barcodes on them are for individual artifacts once their position has been recorded with a total station. The Main Sector is shown in the background (Picture credit: Željko Režek, MPI-EVA Leipzig).

4. Excavations in Initial Upper Paleolithic Layer I at Bacho Kiro Cave (Bulgaria). Four modern human bones were recovered from this layer along with a rich stone tool assemblage, animal bones, bone tools, and pendants made of cave bear teeth (Picture credit: Tsenka Tsanova, MPI-EVA Leipzig).

5. Second lower molar of a modern human found in Bacho Kiro Cave in the Main sector (ID: F6-620, Layer J- upper part), associated with the Initial Upper Palaeolithic stone tools. Genome-wide data from this individual indicates that he had a Neandertal ancestor less than six generations before he lived. Another human fragment (ID: AA7-738) from the same individual was found in the Layer I in the Niche 1 area of the cave (Picture credit: Rosen Spasov, NBU Sofia).

6. Mateja Hajdinjak in the clean room at the Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. (Picture credit: Alexander Hübner, MPI-EVA Leipzig)

7. Long segments of Neandertal DNA identified in the genome of ~43,000-year-old Initial Upper Palaeolithic individual from Bacho Kiro Cave, Bulgaria. These segments indicate that this individual had a recent Neandertal ancestor in his family tree, less than six generations back (Illustration credit: Mateja Hajdinjak and Petra Korlević, MPI-EVA Leipzig).

8. Part of the research team of the Bulgarian-German project and other participants in front of the monument of Bacho Kiro in the guest house Platex, in Dryanovo, October 2019. From left to right, back row: Naomi Martisius, Mateja Hajdinjak, Ivaylo Krumov, Svoboda Sirakova, Dessislava Filcheva and Violet Fish (bellow), Elka Anastasova (above), Elena Endarova; Foreground from left to right: Vladimir Lafchiiski (host), Nikolay Sirakov, Nikolay Zahariev, Rosen Spasov, Tsenka Tsanova, Pedro Horta and Svante Svante Pääbo (Picture credit: Petar Petrunov).