A team of researchers has wrung fresh insights from the hardest of tissues: the enamel of fossilized teeth. By extracting and analyzing ancient proteins from the dental remains of six Homo erectus individuals, scientists have uncovered molecular evidence that the long-lived human ancestor interbred with Denisovans — a now-extinct group known primarily from a few bone fragments and a trove of DNA recovered from a cave in Siberia.
The study, published this week, focused on teeth roughly 400,000 years old unearthed at several sites across China. Because DNA degrades quickly in warm, humid climates, the H. erectus fossils have resisted genetic sequencing. So lead author Qiaomei Fu of the Institute of Vertebrate Paleontology and Paleoanthropology in Beijing and her colleagues turned to proteins — specifically, a protein called amelogenin that is a major component of tooth enamel — to read the species’ evolutionary history.
The analysis revealed two key mutations in the amelogenin protein. One of the mutations had never been seen before and may be a diagnostic marker of the East Asian branch of Homo erectus, a species that originated in Africa about 2 million years ago and later spread as far as Indonesia and possibly Europe. The second mutation, however, was far more surprising: it matches a variant already documented in the genomes of Denisovans and in a small fraction of living humans.
The pattern points to a series of ancient encounters. The most straightforward interpretation, according to the researchers, is that H. erectus interbred with Denisovans somewhere in eastern Eurasia, passing the genetic variant to them. Later, when Denisovans met and mated with anatomically modern Homo sapiens, the variant was transferred a second time, eventually landing in the DNA of some present-day people.
“Esto nos permite rastrear quiénes somos ahora hasta nuestros antepasados de una manera realmente fascinante y emocionante, utilizando nuevos métodos” (This allows us to trace who we are now back to our ancestors in a really fascinating and exciting way, using new methods), said paleoanthropologist Ryan McRae of the Smithsonian’s National Museum of Natural History, who was not involved in the research.
McRae cautioned that the exact branching order on the human family tree is still far from settled. It is possible, he noted, that Homo erectus gave rise to the Denisovans directly, rather than interbreeding with a separate Denisovan lineage. In that scenario, the shared gene variant would be a simple inheritance rather than evidence of a cross-species liaison.
Fu agreed that the picture remains incomplete. “Realmente necesitamos obtener más ADN,” she said, and added that the field needs more fossil fragments of H. erectus to determine how this predecessor “se relaciona exactamente con otros humanos” (relates exactly to other humans). The fossil record for Homo erectus is relatively rich compared with that of Denisovans, whose known remains could fit in a shoebox, but the chemistry of ancient bones has been a formidable obstacle. The new protein-based approach, Fu said, offers a way forward while the search for suitable DNA continues.
The work underscores the growing power of paleoproteomics — the study of ancient proteins — to reconstruct evolutionary histories in the absence of DNA. As techniques improve, researchers hope to move beyond enamel to other preserved tissues, potentially filling in the many gaps that remain in the story of human origins.
The Associated Press contributed reporting.