What proteins in prehistoric teeth reveal about Stone Age sex between early human species

Researchers have utilized paleoproteomics to establish a molecular link between Homo erectus and later human species, including Homo sapiens, and Denisovans. By analyzing ancient proteins extracted from tooth enamel, scientists have provided new evidence regarding the interbreeding of early human populations and the structure of the human evolutionary tree.

The study, published May 14, 2026, in the journal Nature, was led by Chinese geneticist Fu Qiaomei and her colleagues. The team analyzed proteins from six teeth discovered at three different sites across China. The fossils, which belong to five men and one woman, date back approximately 400,000 years.

The Technical Advantage of Protein Analysis

The use of protein analysis represents a significant technical shift in paleoanthropology, particularly for specimens of extreme age. While DNA is the primary tool for genetic mapping, it is a fragile molecule that degrades relatively easily over time, making it difficult to retrieve from fossils like those of Homo erectus.

Proteins, which are composed of sequences of amino acids, are more robust than DNA and can survive longer in the fossil record. Although proteins provide less detailed information than a full genome, they can still reveal critical data about a specimen’s evolutionary history and biological relationships.

Evidence of Interbreeding

The researchers successfully recovered two proteins from the enamel of the Homo erectus teeth. One of these, a variant of the enamel protein ameloblastin known as M273V, was present in all six analyzed fossils. This specific protein compound had been previously identified in the teeth of Denisovans, who are close relatives of Neanderthals.

The presence of the M273V variant in both species implies that Homo erectus, which originated in Africa, and the Denisovans, who were adapted to Eurasia, encountered one another and produced fertile offspring around 400,000 years ago. This finding suggests that the human evolutionary tree is porous, meaning different human species retained the ability to interbreed despite adapting to different environments.

New Genetic Markers for Homo erectus

Beyond the evidence of interbreeding, the study identified a second dental protein that appears to be unique to Homo erectus. This discovery provides scientists with a new genetic marker that can be used to identify this specific species in future fossil finds.

Homo erectus was the first of human ancestors to leave Africa, roaming the planet for nearly 2 million years. Despite their wide distribution across Africa, Asia, and Europe, the species has remained a mystery due to the scarcity of usable molecular data.

This is a major step forward in tying together the broken branches of our human evolutionary tree. Homo erectus has long been a bit of an enigma.

Ryan McRae, paleoanthropologist at the Smithsonian National Museum of Natural History

The ability to extract informative molecular data from 400,000-year-old enamel allows researchers to move beyond morphological comparisons of bone structure and toward a precise, molecular understanding of how early human species interacted and evolved.