Did Homo erectus and Denisovans mate? Tooth proteins hint at ancient trysts

It is well known that human parents interbred: Homo sapiens with Neanderthals, Neanderthals with Denisovans, Denisovans with Homo sapiens. There is now evidence of another ancient romantic tryst, between the Denisovans and Homo erectus. This is what an analysis of ancient proteins extracted from the teeth of six H. erectus individuals who lived in China 400,000 years ago. The work, published in Nature today, this is the first genetic evidence of the pairing.

Homo erectus played a central role in the history of humanity. The species lived from 1.9 million to just 100,000 years ago, a time when Neanderthals, their relatives the Denisovans, and early modern humans all roamed the Earth. Homo erectus was also the first human relative to venture out of Africa and into Eurasia, and as far away as the Indonesian island of Java in Southeast Asia.

Genetic data was obtained from a single H. erectus specimen from Georgia, dating from 1.8 million years ago. But researchers haven’t been able to identify any unique genetic variants that could distinguish H. erectus other human relatives.

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In China, researchers discovered H. erectus remains of varying ages at more than a dozen sites, creating a potential treasure trove for uncovering genetic data on the species. For this new work, Qiaomei Fu, a paleogeneticist at the Beijing Institute of Vertebrate Paleontology and Paleoanthropology, and colleagues focused on teeth from three of these sites. These include the Zhoukoudian site in Beijing, where the remains of the famous “Beijing Man” were discovered in the 1920s, as well as sites in Hexian, in southern China, and Sunjiadong, in central China. All the teeth analyzed date from a similar period, to the Middle Pleistocene, around 400,000 years ago.

East Asian marker

Fu and colleagues extracted proteins from the enamel of six H. erectus teeth – five from male specimens and one from female specimens. Scientists are increasingly looking for ancient proteins in fossil samples because they have been found in specimens that no longer contain DNA. Like DNA, protein sequences can be used to infer relationships between ancient humans.

The team sequenced protein fragments belonging to nine proteins. In one of the proteins – an enamel matrix protein called ameloblastin – the team identified two important amino acid sequence variants shared by all six H. erectus specimens that distinguish them from other human relatives.

“It’s hard to get this kind of data on old enamel, so having consistency of results across six teeth was very cool,” says John Hawks, an anthropologist at the University of Wisconsin-Madison.

At position 253, the six H. erectus teeth contain the amino acid glycine instead of alanine, which is present in humans and all other human relatives tested so far, including the H. erectus fossil from Georgia. This suggests that the glycine variant could be specific to H. erectus populations of East Asia.

Denisovan’s date

The team also identified a variant at position 273: a valine instead of methionine. Researchers have already identified this variant in two Denisovans: a 70,000-year-old specimen from Denisova Cave in Siberia and a specimen from near Taiwan, the age of which is unclear. This indicates that East Asia H. erectus populations, or a closely related group, transmitted the variant to Denisovans through interbreeding.

“Given that the two groups were close in space and time, this is a reasonable suggestion,” says Tanya Smith, an evolutionary biologist at Griffith University in Southport, Australia.

This scenario is supported by data from older Denisovans who lived closer to the time when interbreeding likely occurred. The team extracted proteins from the enamel of a more than 150,000-year-old Denisovan from Harbin, northern China, and obtained data from a 200,000-year-old Denisovan from Siberia. These Denisovans had both methionine (M) and valine (V) variants, inherited from each of their parents.

“Ghost” species

The story became even more compelling when Fu and his team examined modern human footage. The M273V variant of ameloblastin (AMBN) is found in a small fraction of the modern human population. Genomic studies of the modern human genome have already identified contributions from Denisovans and Neanderthals, as well as an unknown super-archaic “ghost” species. Homo erectus was a likely candidate. The new data adds weight to this theory.

“We realized it might be the super-archaic [species]”, Fu said. “So that was really exciting.”

The rare AMBN (M273V) likely made its way into the modern human population following rendezvous with the Denisovans, who retrieved it from H. erectus.

The matter is far from settled, Hawks said. Genetic variants can arise independently in different populations, he says, leaving open the possibility that the shared variant was not inherited from H. erectusbut appeared by chance. Proteins from older fossils attributed to H. erectus in China could help clarify which scenario is more likely.

However, finding a genetic variant specific to H. erectus which also exists in a fraction of modern human genomes was “a big surprise”, given how rare super-archaic sequences are in the modern human genome and how little information can be gleaned from ancient proteins. “It’s like, wow,” Hawks says. “All it took was for the data to be perfectly aligned for this to happen. »

This article is reproduced with permission and has been published for the first time May 13, 2026.