Ancient tooth proteins reveal Denisovan‑Homo erectus interbreeding

Scientists have long known that modern humans inherited DNA from Neanderthals and Denisovans after leaving Africa. Older genomes hinted that Denisovans themselves mixed with an even earlier Eurasian group, but the identity of that group remained unclear. Because DNA degrades beyond about 500,000 years, researchers turned to tougher molecules like tooth enamel proteins to reach further back.

The researchers first cleaned the tooth surfaces to remove contaminants, then dissolved the enamel in a weak acid to release protein fragments. They used liquid chromatography coupled with tandem mass spectrometry to separate and identify the amino acid sequences. By comparing the patterns to known protein databases, they confirmed the fragments belonged to enamel‑specific proteins such as amelogenin. This workflow allowed them to detect even short, degraded peptides that survive hundreds of millennia.

The study, published in Nature Ecology & Evolution, a team from the Chinese Academy of Sciences’ Institute of Vertebrate Paleontology and Paleoanthropology examined enamel from five Homo erectus teeth dated to roughly 400,000 years ago, recovered from three sites in China. Using mass spectrometry, they isolated between six and eleven distinct protein fragments per specimen. The Harbin Denisovan molar, processed with the same protocol, yielded a comparable number of fragments, indicating similar preservation quality. The overlapping protein patterns point to gene flow between Denisovans and Homo erectus, meaning some Homo erectus sequences could have entered the Denisovan genome and later been passed to modern humans.

If Denisovans carried Homo erectus DNA, then the small archaic contributions detected in present‑day Asian populations might trace back to a species that left Africa over a million years ago. This protein‑based approach pushes the direct study of hominin ancestry beyond the limits of ancient DNA, opening a window onto populations that lived half a million years earlier. Researchers will now look for additional enamel samples from older Homo erectus sites and from other archaic groups to refine the timing and extent of these interbreeding events.