The Ranis13 and Zlatý kůň genomes represent the oldest high-quality modern human genomes sequenced to date.
They reveal the existence of a small isolated group that recently hybridized with Neanderthals and left no current descendants.
They also shift in time the very first interbreeding of modern humans with Neanderthals, which would ultimately have taken place there around 45,000 to 49,000 years ago, much later than previously thought.
This is work that should mark a milestone in paleogenomics. This December 12, 2024, an article appeared in the prestigious journal Nature informs us that an international team led by researchers from the Max Planck Institute for Evolutionary Anthropology, in Germany, has succeeded in sequencing the oldest genomes of modern human beings, dated around 45,000 years ago. These genomes, belonging to seven individuals, highlight a lineage of Sapiens which diverged most anciently from the group of modern humans who left Africa around 50,000 years ago.
A genome of exceptional quality
The team's results also demonstrate that these first modern humans in Europe hybridized with Neanderthals later than previously thought, between 45,000 and 49,000 years ago, thus moving forward in time the episode of interbreeding common to all non-African populations, the same one which resulted in the presence of approximately 2 to 3% of Neanderthal DNA in the genome of the populations current non-African. These are breathtaking results, firstly because our knowledge of the genetics of early modern humans is still very limited, secondly because the researchers succeeded in obtaining the highest quality genome ever achieved for an individual of more than 10,000 years old. Remember that he has 45,000!
The skull of Zlatý kůň. Credits: Marek Jantač/Petr Velemínský/Department of Anthropology of the National Museum in Prague
This formidable feat could be achieved using bones found on two distinct sites: Zlatý kůň, in the Czech Republic, and the Ilsenhöhle in Ranis, in Germany, both 230 kilometers apart. In 1950, the Zlatý kůň cave yielded a skull. Belonging to a woman, it is suspected of being very old – perhaps 15,000 years old – but in the absence of any archaeological context, it cannot be dated. More than seventy years later, the Max Planck Institute subjected it to a series of genomic analyses. Verdict: much older than we thought, it surprisingly provides the oldest modern human genome, dating back 45,000 years. Also, for three years, Zlatý kůň's wife has been considered the oldest representative of the oldest lineage of modern humans on European territory.
Ranis' family group
Direction Ranis this time. Since the 1930s, this cave has spoiled us with a type of cut stone tools which is associated with a particular culture: that of the Lincombian-Ranisian-Jerzmanowician (LRJ), which is estimated to date back 45,000 years (each culture is often identified by a specific style or technique of making tools from stone, bone, or other materials). The attribution of this culture to Neanderthals or Sapiens has been debated for decades. And for good reason: if a large pile of bones accompanied the tools, it seemed to contain only fauna. But the saying “you should never trust appearances” is also valid in archaeoanthropology. “A few years ago, a biochemical analysis found human proteins in the mix, indicating that we had missed something”says Hélène Rougier, anthropologist and associate professor at California State University, Northridge.
An artist's view of this population of The Golden Horse-Ranis which, around 45,000 years ago, probably traveled across the open landscapes of the steppes of Europe. Credits: Tom Björklund
The expert, who is among the signatories of the article Naturetherefore begins careful sorting work. For their part, archaeologists are returning to excavate in Ranis to be sure not to miss anything. In total, 13 small bone fragments belonging to at least six modern humans and not Neanderthals are identified. Hélène Rougier manages to know that two of these individuals were “immature”when genetics shows that three were women, three were men, and that they were biological parents. Even more impressive, the team deduced from a small piece of phalanx and a fragment of clavicle that the group included a mother (phalanx) and her infant daughter (clavicle).
Genetic links
Among the 13 fragments, one bone – a piece of femur – was particularly well preserved. “It is even the best preserved modern Pleistocene human bone that we have ever had for extracting DNA”affirms, enthusiastically, Hélène Rougier. “It allowed us to obtain a high-quality genome for this male individual called Ranis13.” Even if it is still a bit of a miracle, such quality of preservation is not surprising in northern Europe, and more particularly in a cave where temperature variations are limited. “In areas of Africa that are rich in fossils, it is so dry that almost nothing of the DNA remains.”regrets Hélène Rougier.
But what do the genomes of Ranis and Zlatý kůň tell us? Firstly, they carried variants associated with dark skin color and hair, as well as brown eyes, reflecting their recent African origin. Then that they both had a genetic proximity. “To our great surprise, we discovered a fifth or sixth degree genetic relationship between Zlatý kůň and two Ranis individuals”declared Arev Sümer, lead author of the study, at a press conference. “This means that Zlatý kůň was genetically part of the extended Ranis family and probably also made LRJ-type tools.”
A population apart
This also means that we now have several fossils belonging to the same group: the branch of A wise man elders who separated first. Because if the genome of the Zlatý kůň-Ranis population shows that the latter included Neanderthals among its recent ancestors – the result of the famous episode of interbreeding which can be detected in all current non-Africans – there is no trace of a more recent hybridization could not be detected there. “We can imagine that the Zlatý kůň-Ranis population followed a different route out of Africa, so that they did not occupy the areas where Neanderthals lived as widely as other populations of early modern humans in Europe”explains Hélène Rougier. “We can also consider that Sapiens ultimately arrived later than we thought in Europe.”
For researchers, the population of The Golden Horse-Ranis should be composed at most of a few hundred individuals who could be distributed over a larger territory than that highlighted in the study. However, there is no evidence to date that this small group of early modern humans contributed to later Europeans or any other populations around the world.
A later interbreeding between Sapiens and Neanderthals
Until now, the very first interbreeding between Sapiens and Neanderthals was dated between 50,000 and 60,000 years ago (we also know that the two species coexisted for around 5000 years in Europe). But by analyzing the length of the Neanderthal DNA segments in the genome of Ranis13 and using the radiocarbon dates obtained on this individual, the researchers established that it instead occurred between 45,000 and 49,000 years ago. Given that all current non-African populations share this Neanderthal ancestry with Zlatý kůň and Ranis, it must be understood that approximately 45,000 to 49,000 years ago, a coherent non-African ancestral population must still have existed.
So, “any modern human remains found outside of Africa and dating back more than 50,000 years could not have been part of the ancestral non-African population which hybridized with the Neanderthals and whose descendants are found today in a most of the world”, concludes Johannes Krause, archaeogeneticist at the Max Planck Institute and one of the lead authors of the study.
The genomic study of another international team, including numerous researchers from the Max Planck Institute, appeared at the same time, in a concerted manner, in the journal Science. Covering more than 334 modern human genomes, it demonstrates that the vast majority of Neanderthal gene flow is attributable to a single period of gene flow that probably occurred 50,500 to 43,500 years ago, a result consistent with those obtained from the fossils of Zlatý kůň and Ranis.
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