Skull From Czech Cave May Contain Oldest Modern Human Genome

The Zlatý kůň cranium.

The Zlatý kůň cranium.
Image: Martin Frouz

A genome sequenced from a modern human skull has been dated at approximately 45,000 years old, making it the oldest discovery of its kind. It’s a significant archaeological discovery, but the use of an unconventional dating method leaves the result in doubt. In a related study, scientists also show that intermixing between Neanderthals and humans happened more often than we thought.

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Modern humans, otherwise known as Homo sapiens, emerged some 300,000 years ago in Africa. Skeletal remains of our distant ancestors exist, but the fossil record is poor. Poorer still is the genetic evidence, the oldest of which is the genome from a 45,000-year-old Ust’-Ishim person from western Siberia, described in 2014.

But as new research published today in Nature Ecology & Evolution reveals, scientists may have stumbled upon an even older genome. A team co-led by Kay Prüfer from the Max Planck Institute for the Science of Human History in Germany has uncovered what may very well be the most ancient reconstructed modern human genome in the fossil record. That is, if the dating method used can be considered reliable. The genome, pulled from a skull found in the Czech Republic, appears to be at least 45,000 years old and possibly even older.

A related paper, also out today in Nature Ecology & Evolution, describes the remains of early modern humans found in a Bulgarian cave. Dating back to around the same time period, the DNA of these people suggests interbreeding with Neanderthals was likely more common than previously assumed.

The skull described in the Prüfer paper was pulled from Koněprusy cave back in 1950, and it was found alongside other skeletal remains. This cave is located in Zlatý kůň, which means “golden horse” in Czech, and it’s a short 25-mile (40-km) drive from Prague.

Frontal view of the Zlatý kůň skull.

Frontal view of the Zlatý kůň skull.
Image: Zlatý kůň

Genetic analysis of the mostly intact skull, which belonged to a human female, shows that she carried between 2% and 3% Neanderthal ancestry, which basically matches the amounts found in non-African people living today. That said, no humans living today are directly descended from the Zlatý kůň woman, as she belonged to a population that didn’t pass any DNA down to the subsequent European or Asian populations of early modern humans.

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“As far as we can tell, the population she belonged to did not contribute to present-day populations,” explained Prüfer in an email. “We speculate that her people went extinct alongside Neanderthals, who lived in Europe at that time, and that a large volcanic eruption in Italy that occurred approximately 39,000 years ago may have contributed to their demise.”

Prüfer is referring to the Campanian Ignimbrite volcanic eruption, which severely disrupted the climate in the northern hemisphere, making life difficult for both modern humans and Neanderthals during the last European ice age.

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This is all good and (reasonably) uncontroversial—it’s when we get to the dating of the skull that problems emerge.

Initial radiocarbon dating of the skull yielded a date close to 15,000 years ago. Not believing this to be true (the anatomy of the skull suggested an older date), Prüfer and her colleagues tried again, resulting in a date closer to 27,000 years ago. Following some cleaning treatments, a third radiocarbon date was determined, suggesting the woman lived around 19,000 years ago. It was at this point that the scientists realized they were dealing with highly contaminated specimen.

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“We found evidence of cow DNA contamination in the analyzed bone, which suggests that a bovine-based glue used in the past to [fix] the skull was returning radiocarbon dates younger than the fossil’s true age,” Cosimo Posth, co-lead author of the study and a professor of paleogenetics at the University of Tübingen, explained in a statement. Posth had previously done work as a research group leader at the Max Planck Institute.

With radiocarbon dating ruled out as a useful tool for this specimen, the team turned to a technique in which the length of DNA segments can be used to infer the age of a person. Specifically, the scientists measured the length of Neanderthal segments, as these segments become shorter with each successive generation.

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This analysis suggests the Zlatý kůň woman lived at least 2,000 years after the last interbreeding event involving her modern human and Neanderthal ancestors (approximately 63 to 78 generations). The “lengths of the Neandertal segments are longer than those observed in the currently oldest modern human genome of the ~45,000-year-old Ust’-Ishim individual from Siberia, suggesting that this individual from Zlatý kůň is one of the earliest Eurasian inhabitants following the expansion out of Africa,” wrote the authors in their study. The Ust’-Ishim person was separated from Neanderthals by around 84 to 94 generations, according to the paper.

Working under the assumption of a single interbreeding event, the new results mean that Zlatý kůň is basically the same age as the roughly 45,000-year-old Ust’-Ishim specimen, or possibly “up to a few hundred years older,” according to the paper. But if a second Neanderthal interbreeding event transpired along the Ust’-Ishim lineage after this common Neanderthal intermixing, then “Zlatý kůň could be even several thousands of years older than Ust’-Ishim,” wrote the authors, adding that they haven’t found support for a second Neanderthal admixture.

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This is all very intriguing, but a firmer date obviously needs to be established, hopefully through the use of other methods.

The authors “really don’t know how old the skull is, and the range given is wide,” Israel Hershkovitz, an archaeologist at Tel Aviv University and an expert on early modern humans, said in an email. That said, Hershkovitz said the data used for determining the skull’s age—mitochondrial DNA and the pattern of Neanderthal gene segments—is “interesting,” but he’s not entirely sure about its efficacy as a dating technique.

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If these results are accurate, however, the Zlatý kůň specimen now represents the oldest modern human genome in the fossil record. What’s more, the new paper provides a rare glimpse into the genetic makeup of early modern European humans dating back to this time period.

The group that the Zlatý kůň woman belonged to didn’t survive, which is also interesting. It suggests multiple waves of migrations into Europe from Africa, and/or some complex population replacement scenarios, in which some groups survived and some didn’t. That this specimen belonged to “a population prior to the division between European and Asian populations” is significant, said Hershkovitz, provided that their first claim, “that the skull is very old, is correct.”

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That modern humans were living in Europe so long ago isn’t a major stretch. Evidence from 2020 suggests modern humans were present in southeastern Europe between 47,000 and 43,000 years ago, while evidence from 2019 suggests some modern humans had reached Europe, specifically Greece, as long as 210,000 years ago.

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The second paper, led by Mateja Hajdinjak from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, describes the remains of early modern humans found in Bacho Kiro Cave in Bulgaria. These remains were initially described in the aforementioned paper from 2020, but the new analysis dives into their DNA.

Neanderthals and humans interbred at some point between 55,000 and 60,000 years ago. Up until now, however, archaeologists had only one person, a 40,000-year-old Oase1 fossil from Romania, who exhibited recent Neanderthal ancestry, in a finding that suggests modern humans and Neanderthals bred on multiple occasions.

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“However, we could not exclude this was just a chance find,” explained Hajdinjak in an email. “Now in this study, we have all three approximately 45,000-year-old individuals from Bacho Kiro Cave with Neanderthal ancestors very close in their family history, just like Oase1,” she said, meaning that the “mixing was more common than what we previously thought.”

Indeed, the oldest three individuals found in Bacho Kiro carried between 3% and 3.8% Neanderthal DNA, which is slightly more than present-day populations. Incredibly, these people had Neanderthal ancestors as few as six—or even fewer—generations back, in what is a truly astonishing finding.

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“Unlike what might be expected for ancient individuals in Europe, Bacho Kiro individuals are more closely related to human groups that contributed their genetic material to East Asians rather than West Eurasians,” said Hajdinjak. “Crucially, all older Bacho Kiro Cave individuals have Neanderthal ancestors very closely in their family trees, suggesting that the mixing between these first humans in Europe and Neandertals was common.”

Paleogenetics is revealing some remarkable things about our past, especially when it works in conjunction with both skeletal and archaeological artifacts. Our history is increasingly coming into focus, and the view is only getting more intriguing.

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