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Early humans and Neanderthals: The original family feud

New sequencing studies show Europe’s first humans had Neanderthal ancestors
Early humans and Neanderthals: The original family feud hero image

The Takeaway: A growing body of evidence shows that modern humans regularly mated with Neanderthals and other now-extinct relatives.


Between 45,000 and 35,000 years ago, anatomically modern humans spread across Europe, while the Neanderthals, who had been present in Europe for some 300,000 years, disappeared. How this turnover happened has been debated for years. Although Neanderthals disappeared from Europe approximately 39,000–41,000 years ago, they contribute 1–3% of the DNA of present-day people in Eurasia.

The most recent piece to fit into this puzzle comes from the sequencing of the oldest Homo sapiens DNA on record — genetic material more than 45,000 years old found in caves in Bulgaria and Czech.

While ancient DNA sequencing studies have shown that different species of humans mixed, this most recent study shows that many of Europe’s first humans had Neanderthals in their lineage, although they are not related to later Europeans.

DNA from a human in a cave in Bulgaria adds to evidence of Neanderthal ancestry

In the past, researchers have sequenced DNA from Neanderthals and other extinct humans dating as far back as 430,000 years ago, but there is little genetic information from the period between about 47,000 and 40,000 years ago, and no Homo sapiens DNA from before that time period.

According to a recent study in Nature, modern humans appeared in Europe at least 45,000 years ago while current evidence shows that Neanderthals disappeared relatively shortly before that, around  40,000 years ago. In the study, researchers presented genome-wide data from three individuals dated to between 45,930 and 42,580 years ago from a cave in Bulgaria called Bacho Kiro Cave, which may help researchers fill in gaps in evolution and migration.

“Unlike two previously studied individuals of similar ages from Romania and Siberia who did not contribute detectably to later populations, these individuals are more closely related to present-day and ancient populations in East Asia and the Americas than to later west Eurasian populations,” the authors wrote. “This indicates that they belonged to a modern human migration into Europe that was not previously known from the genetic record, and provides evidence that there was at least some continuity between the earliest modern humans in Europe and later people in Eurasia.”

The DNA extract from the cave in Bulgaria also had another secret to divulge: All three individuals had Neanderthal ancestors a few generations back in their family history, confirming that the first European modern humans mixed with Neanderthals and suggesting that such mixing could have been common.

“The Bacho Kiro Cave genomes show that several distinct modern human populations existed during the early Upper Paleolithic in Eurasia,” the study noted. “Some of these populations … show no detectable affinities to later populations, whereas [other] groups … contributed to later populations with Asian ancestry as well as some western Eurasian humans.”

This evidence suggests that mixing between Neanderthals and the first modern humans who arrived in Europe was perhaps more common than is often assumed.

A sequenced genome from a 45,000-year-old skull found in Czech

In a separate Nature study, also published in 2021, a group of researchers analyzed a genome generated from the skull of a female individual from Zlatý kůň in Czech Republic. The researchers found that the person belonged to a population that appears to have contributed genetically neither to later Europeans nor to Asians.

The skull was found alongside other “skeletal elements” in 1950 inside a cave called Koněprusy, not far from the capital of present-day Czech, Prague. Zlatý kůň, the name researchers gave to the person the skull came from – who they refer to as a “she” – is also the name of a hill atop the cave.

“Her genome carries ~3% Neanderthal ancestry, similar to those of other Upper Paleolithic hunter-gatherers,” the researchers wrote. “However, the lengths of the Neanderthal 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.”

DNA were extracted from about 15 mg of bone powder from the temporal bone. The mitochondrial genome was sequenced, with about 4% of the mtDNA stemming from human contamination. The reconstructed DNA, the researchers found, belong to rare haplogroup N and is branch length is similar to those of the current oldest sequenced modern human mtDNA genomes, including that from the Bacho Kiro cave in Bulgaria.

While the Zlatý kůň individual fills an important gap in DNA evidence about early humans, it is also a bit of an outlier. The person shares more alleles with Asians than Europeans, which matches with evidence from other Upper Paleolithic and Mesolithic European hunter-gatherers when compared to present-day Europeans.

“This suggests that Zlatý kůň falls basal to the split of the European and Asian populations,” the authors wrote.

Of course, it’s important to realize there is still much left to learn: as the study notes, of the thousands of individuals who lived in this era, only two ancient Eurasian genomes have been produced from individuals like the one found in Zlatý kůň, appear to come before the split of Europeans and Asians.

“Most of the Neanderthal ancestry in present-day and ancient humans probably originates from a common admixture event with a group of Neanderthals who were more closely related to European Neanderthals than to a Neanderthal from the Altai Mountains” of Mongolia, the authors noted. Neanderthal ancestry in Zlatý kůň, they added, shows the same relationship.