There are only a few genomes that have been sequenced from early modern humans, who first came to Europe while Neanderthals were already living there. A global team, led by researchers from the Max Planck Institute for Evolutionary Anthropology, has sequenced the earliest known genomes of modern humans. These genomes were extracted from seven individuals who lived in what is now Germany and Czechia between 42,000 and 49,000 years ago. These individuals belonged to a small, closely-knit group of humans that diverged from the population that left Africa approximately 50,000 years ago, later spreading across the rest of the world. Although this group separated early, the Neanderthal DNA found in their genomes reflects a blending event common to all individuals outside Africa, which researchers estimate took place around 45,000-49,000 years ago, significantly later than previously believed.
After modern humans migrated from Africa, they interbred with Neanderthals, resulting in two to three percent Neanderthal DNA that exists in the genomes of all people outside Africa today. However, the genetic makeup of these early settlers in Europe and the timing of their interbreeding with Neanderthals remains largely unknown.
Zlatý kůň in Czechia is a key location where a complete skull from an individual who lived about 45,000 years ago was unearthed and analyzed genetically. Unfortunately, without proper archaeological context, linking this individual to any established group was impossible. A nearby site in Ranis, Germany, about 230 km away, is recognized for its unique archaeological culture known as the Lincombian-Ranisian-Jerzmanowician (LRJ), which dates back to around 45,000 years ago. There has been ongoing debate about whether this culture was created by Neanderthals or early modern humans. Most remains found at Ranis are small bone fragments, but a previous study successfully analyzed mitochondrial DNA from thirteen of these remains, identifying them as belonging to modern humans rather than Neanderthals. However, since mitochondrial sequences provide only a tiny fraction of genetic information, the connections to other modern humans remained unclear.
Connecting Zlatý kůň and Ranis
A recent study published in Nature examined the nuclear genomes of the thirteen specimens from Ranis and determined they represented at least six individuals. Their bone sizes suggested that two were infants, and genetically, there were three males and three females. Notably, among these were a mother and her daughter, along with other distant relatives. Additionally, the team sequenced more DNA from the female skull found at Zlatý kůň, producing a high-quality genome for this individual. “We were surprised to find a fifth- or sixth-degree genetic relationship between Zlatý kůň and two individuals from Ranis,” remarks Arev Sümer, the study’s lead author. “This suggests that Zlatý kůň was genetically part of the extended family in Ranis and likely contributed to the production of LRJ tools.”
Among the six individuals from Ranis, one bone stood out as exceptionally well preserved – it is the best-preserved modern human bone from the Pleistocene for DNA extraction. This enabled the team to obtain a high-quality genome from this male individual, referred to as Ranis13. Together, the genomes from Ranis13 and Zlatý kůň represent the oldest high-quality modern human genomes sequenced thus far. Upon analyzing various genetic traits, they found that individuals from Ranis and Zlatý kůň both carried genetic variants linked to dark skin, hair color, and brown eyes, reflecting their recent African ancestry.
By examining shared genetic segments between the Ranis and Zlatý kůň genomes, the researchers estimate that their population consisted of a few hundred individuals potentially spread over a vast region. The authors found no evidence that this small group of early modern humans contributed genetically to later populations in Europe or elsewhere.
A more precise timeframe for shared Neanderthal admixture
The Zlatý kůň/Ranis population coexisted with Neanderthals in Europe, which raises the possibility that some of their recent ancestors may have interbred with Neanderthals upon arriving in Europe. While prior studies on modern humans dating back over 40,000 years indicated evidence of such admixture, no signs of recent Neanderthal interbreeding were found in the genomes of the Zlatý kůň/Ranis individuals. “The difference between modern human groups, which might have arrived in Europe later and carry Neanderthal ancestry, and the earlier Zlatý kůň/Ranis lineage, which does not, could imply that the latter entered Europe via a different path or did not extensively overlap with Neanderthal habitats,” speculates Kay Prüfer, co-supervisor of the study.
The Zlatý kůň/Ranis population represents the earliest known divergence from the group of modern humans that left Africa and later dispersed across Eurasia. Despite their early separation, the Neanderthal ancestry in Zlatý kůň and Ranis originates from the same ancient interbreeding event still evident in all non-African populations today. By analyzing the lengths of Neanderthal segments in the well-preserved Ranis13 genome and using direct radiocarbon dating on the individual, the study dated this shared Neanderthal mixture to between 45,000 and 49,000 years ago. Since all current non-African populations share this Neanderthal ancestry, it indicates that a cohesive ancestral non-African population must still have existed during that period.
“These findings enhance our understanding of the earliest settlers in Europe,” states Johannes Krause, the senior author of the study. “They also suggest that any modern human remains found outside Africa older than 50,000 years could not have been part of the common non-African population that interbred with Neanderthals, which is now widespread globally.”