Shortly after the first representatives of Homo sapiens came from Africa to Eurasia, they interbred with the Neanderthals living there. Traces of it can still be found in our genome to this day. Using DNA analyzes of modern and prehistoric people, two studies now show that this mixing of the two species began around 50,500 years ago and continued for around 7,000 years. The results also provide new insights into the ancestry of the oldest known settlers in Central Europe.
For thousands of years, Homo sapiens and Neanderthals lived side by side in Eurasia. The two types of people mixed again and again. If the Neanderthal genes brought advantages to the offspring, they were preserved, so that to this day most people outside of Africa carry around one to two percent of Neanderthal genes. But when exactly did the phase of genetic mixing begin and end? And what Neanderthal influences can be seen in the genome of the oldest known representatives of Homo sapiens in Central Europe?
A team led by Leonardo Iasi from the Max Planck Institute for Evolutionary Anthropology in Leipzig has now examined this in more detail. To do this, they analyzed the genomes of 275 modern humans from different parts of the world as well as 59 prehistoric representatives of Homo sapiens who lived between 2,200 and 45,000 years ago. The researchers evaluated the length and number of Neanderthal segments in the genome. The shorter the crossing, the longer contiguous fragments of Neanderthal DNA are found in the genome. As the researchers report, they were able to date the time of mixing more precisely and reliably than before.
Gene variants with advantages and disadvantages
“We found strong evidence for a single, extensive period of Neanderthal gene flow that occurred between 50,500 and 43,500 years ago,” explain Iasi and his team. “This period corresponds well with the archaeological evidence for the temporal overlap between Neanderthals and modern humans in Europe.” According to the researchers, this dating is also important because it shows that Homo sapiens opened up regions outside of Africa 50,500 years ago crossed with Neanderthals in Eurasia. The results also show which gene variants were able to prevail and which were not. Some regions of the genome contain particularly large numbers of Neanderthal sections, which influence, among other things, our immune system, our skin color and our metabolism and probably made it easier to adapt to the climate of Eurasia.
“The fact that we find some of these regions in samples that are 30,000 years old shows that some of them were actually adapted shortly after mixing,” says co-author Manjusha Chintalapati from the University of California at Berkeley. In other parts of the genome, however, there are no traces of Neanderthal DNA – not even in prehistoric individuals. “Neanderthal variants that could have been harmful to modern humans were apparently quickly eliminated through evolutionary processes,” explains Chintalapati.
Genomes of early Europeans analyzed
While the study by Iasi and his team is based on genomes that have already been published, a second team led by Iasi’s colleague Arev Sümer has reanalyzed the genomes of some of the oldest known prehistoric Europeans. For the first time, they sequenced the DNA of six individuals from the Ilsenhöhle in Ranis, Thuringia, who lived around 45,000 years ago. In addition, they re-sequenced the genome of the “wife of Zlaty kun” from the Czech Republic, who lived around the same time. “The genomes contain Neanderthal segments that date back to a single mixing event that we date to around 45,000 to 49,000 years ago,” the research team reports in Nature. The analysis thus confirms the results of the “Science” study.
In addition, the researchers revealed the family relationships of the early Europeans. Accordingly, the people from Ranis belonged to one family. Among other things, the team identified a mother-daughter pair. But that’s not all: “To our great surprise, we discovered a fifth or sixth degree genetic relationship between the woman from Zlaty kun and two individuals from Ranis,” reports Sümer. However, the family from Ranis has left no trace in the genome of today’s Europeans. The population thus represents the earliest known split from the population of modern humans, which later spread throughout Eurasia. The fact that their genome still contains some of the same Neanderthal sequences as that of today’s humans shows that the mixing must have begun before the split.
Sources: Leonardo Iasi (Max Planck Institute for Evolutionary Anthropology, Leipzig) et al., Science, doi: 10.1126/science.adq3010
Arev Sümer (Max Planck Institute for Evolutionary Anthropology, Leipzig) et al., Nature, doi: 10.1038/s41586-024-08420-x