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

It is a well-established fact that human ancestors interbred: Homo sapiens with Neanderthals, Neanderthals with Denisovans, and Denisovans with Homo sapiens. Recent findings suggest another ancient interbreeding event between Denisovans and Homo erectus. This conclusion arises from the analysis of ancient proteins extracted from the teeth of six H. erectus individuals who lived in China 400,000 years ago. This research, published in Nature today, presents the first genetic evidence of this interbreeding.

Homo erectus was significant in human evolution. This species existed from 1.9 million to 100,000 years ago, an era when Neanderthals, Denisovans, and early modern humans also inhabited the Earth. Homo erectus was the pioneer among human relatives to migrate out of Africa, reaching Eurasia and even the Indonesian island of Java in Southeast Asia.

Genetic information has been retrieved from only one H. erectus specimen from Georgia, dating back 1.8 million years. However, researchers could not identify any distinct genetic markers to differentiate H. erectus from other human ancestors.

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In China, scientists have discovered H. erectus remains of different ages at over a dozen locations, offering a valuable opportunity to gather genetic information about the species. In this new study, Qiaomei Fu, a palaeogeneticist at the Institute of Vertebrate Paleontology and Paleoanthropology in Beijing, and her team focused on teeth from three sites. These sites include the Zhoukoudian site in Beijing, known for the discovery of ‘Peking man’ remains in the 1920s, as well as locations in Hexian, southern China, and Sunjiadong, central China. All the analyzed teeth date to the Middle Pleistocene, approximately 400,000 years ago.

East Asian marker

Fu and her team extracted protein from the enamel of six H. erectus teeth — five from male and one from female specimens. Scientists are increasingly turning to ancient proteins in fossil samples, as they can remain in specimens that lack DNA. These protein sequences, like DNA, can help determine relationships among ancient humans.

The researchers sequenced fragments from nine proteins. In one protein, known as ameloblastin, they identified two significant amino-acid sequence variants present in all six H. erectus specimens, distinguishing them from other human relatives.

“It’s challenging to get that kind of data from ancient enamel, so to have a 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 appears in humans and all other human relatives tested so far, including the H. erectus fossil from Georgia. This suggests that the glycine variant might be unique to H. erectus populations in East Asia.

Denisovan trysts

Additionally, the team identified a variant at position 273: a valine instead of methionine. This variant had been previously identified in two Denisovans: a 70,000-year-old specimen from the Denisova cave in Siberia and a specimen from near Taiwan with an unclear age. This finding suggests that the East Asian H. erectus populations, or a closely related group, transferred the variant to Denisovans through interbreeding.

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

This hypothesis is supported by data from older Denisovans who lived closer to the time when interbreeding likely occurred. The researchers extracted enamel proteins from a Denisovan over 150,000 years old from Harbin in northern China and obtained data from a 200,000-year-old Denisovan in Siberia. These Denisovans had both the methionine (M) and valine (V) variants, inherited from each parent.

‘Ghost’ species

The narrative became even more intriguing when Fu and her team examined modern human sequences. The M273V in ameloblastin (AMBN) variant is present in a small portion of the modern human population. Previous genomic studies of the modern human genome have identified contributions from Denisovans and Neanderthals, as well as an unidentified super-archaic ‘ghost’ species. Homo erectus was a likely candidate. The new data bolster this theory.

“We realized maybe this is the super-archaic [species],” says Fu. “So it was really exciting.”

The rare AMBN(M273V) likely entered the early modern human population through interactions with Denisovans, who acquired it from H. erectus.

The issue is far from resolved, notes Hawks. Genetic variants can emerge independently in different populations, leaving open the possibility that the shared variant wasn’t inherited from H. erectus but appeared by chance. Proteins from older fossils attributed to H. erectus in China could help clarify which scenario is more plausible.

Nonetheless, discovering a genetic variant specific to H. erectus that also appears in a fraction of modern human genomes was “a big surprise,” especially given the rarity of super-archaic sequences in the modern human genome and the limited information obtainable from ancient proteins. “It’s like, wow,” says Hawks. “The data just had to line up exactly right for this to happen.”

This article is reproduced with permission and was first published on May 13, 2026.