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Ancient DNA Study Reveals Early Human Migration and Neanderthal Interbreeding

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New genetic research on ancient human remains, dating back around 45,000 years, has revealed significant insights into early human migrations and the extent of interactions with Neanderthals. The study, which analyzes remains discovered in Bulgaria, offers evidence of a previously unknown migration into Europe and suggests that intermixing between modern humans and Neanderthals was more common than previously thought. These findings shift our understanding of human prehistory and the complex patterns of migration and population replacement in early Europe.

The remains, which include a tooth and bone fragments, were uncovered in the Bacho Kiro cave in Bulgaria in 2021. Genetic sequencing of these remains shows that the individuals were genetically closer to populations in East Asia and the Americas than to modern European populations. This surprising discovery indicates that these humans were part of a migration into Europe that had not been recognized in earlier genetic studies.

“This suggests that these individuals were part of a modern human migration into Europe that had previously been unknown,” said the research, which was published in Nature. The findings also imply that there was continuity between the earliest modern humans in Europe and later populations in Eurasia, providing new insight into the complex history of human settlement in Europe.

The study was led by Mateja Hajdinjak, an associate researcher at the Max Planck Institute for Evolutionary Anthropology. She explained that the research shifts our previous understanding of human migration into Europe. “It shows how even the earliest history of modern Europeans in Europe may have been tumultuous and involved population replacements,” Hajdinjak said. She also suggested that the study points to a process in which early human groups may have dispersed across Eurasia but were later replaced by other groups, even though they continued to contribute ancestry to populations in East Eurasia.

The Niche 1 sector (left) and the Main sector (right) during the excavations of Bacho Kiro Cave, Bulgaria, in 2016. The cement area in the foreground was previously excavated in the 1970s. New excavations picked up where these excavations left off. Credit: MPI-EVA/ Nikolay Zaheriev

The discovery of these remains also sheds new light on the history of human-Neanderthal interactions. The Bacho Kiro individuals had Neanderthal ancestors in the five to seven generations prior to their lives, indicating that admixture between modern humans and Neanderthals was far more common than previously assumed. Before this study, evidence of such interbreeding had been limited to a single individual, known as Oase 1, found in Romania and dating to about 40,000 years ago. While Oase 1 provided initial evidence of Neanderthal-modern human mixing, there had been doubts about whether this was a rare occurrence or part of a broader trend. The new findings suggest that interbreeding was likely widespread.

“Until now, we could not exclude it being a chance find,” Hajdinjak explained. “Our study suggests… it must have been common.” This implies that the mixing between Neanderthals and modern humans may have been a regular occurrence, rather than an isolated event, contributing to the genetic complexity of early human populations.

Alongside the Bacho Kiro findings, a separate study published in Nature Ecology and Evolution analyzed the genome of a skull discovered in the Zlaty kun area of the Czech Republic in 1950. While previous dating efforts had yielded conflicting results, with estimates ranging from 15,000 to 30,000 years old, the new genetic analysis has resolved the issue, confirming that the skull dates back at least 45,000 years. This skull, belonging to a woman, represents one of the earliest known human remains from Europe.

Second lower molar of a modern human found in Bacho Kiro Cave in the Main sector 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 from the same individual was found in the Layer I in the Niche 1 area of the cave. Credit: MPI-EVA/ Rosen Spasov

Kay Prufer, a researcher from the Max Planck Institute’s department of archaeogenetics, led the analysis of the Zlaty kun skull. By examining Neanderthal genetic markers in the woman’s genome, Prufer and his team were able to confidently date the remains and compare them to those from other early human sites, such as the Ust’-Ishim man from Siberia. The Zlaty kun genome revealed longer Neanderthal DNA blocks than those found in the Ust’-Ishim man, suggesting that the woman lived during the same period, or even earlier.

Despite dating from the same time as the Bacho Kiro remains, the Zlaty kun skull does not share genetic links to either modern Asian or European populations. This highlights the possibility that the early human populations that occupied Europe were diverse and that the connections between these groups were more complex than previously understood.

Prufer expressed a desire to further study how the populations represented by these two sets of remains were related. “We do not know who the first Europeans were that ventured into an unknown land,” he said. “By analyzing their genomes, we are figuring out a part of our own history that has been lost in time.”

These findings are significant not only for their revelations about early human migrations and the extent of Neanderthal admixture but also for their potential to reshape our understanding of human evolution. By combining genetic analysis with archaeological discoveries, researchers are uncovering a more detailed and nuanced picture of our ancient past, one that challenges previous assumptions and highlights the complexity of human history in Europe. These discoveries may help answer fundamental questions about the origins of modern humans and the paths they took as they spread across the globe.

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