Denisovans, the extinct human relatives who once roamed Asia, carried DNA from a previously unknown ancient lineage that made up three to five percent of their genome, according to a new study. Researchers say part of that ancient genetic material was later passed down to modern humans, adding a hidden chapter to the long story of human evolution.
The findings were published in the journal Science. The study was led by Yulin Zhang of the University of California, Berkeley, and Arjun Biddanda of Johns Hopkins University, working with Priya Moorjani, a Berkeley associate professor whose lab guided the research.
The team built a computer method called TRACE, short for Tracking Archaic Contributions via Ancestral Recombination Graph Estimation, which can spot traces of extinct human groups hidden inside modern DNA without needing a fossil or an ancient genome sample.
Denisovans’ unknown DNA lineage traced across two ancient encounters
The study found that this unidentified “super-archaic” population split from the human family tree about 1.8 million years ago, a time that overlaps with an early human relative known as Homo erectus, though researchers have not confirmed the group’s identity.
More than 200,000 years ago in Eurasia, descendants of this unknown lineage interbred with Denisovans, leaving a lasting mark inside their DNA. When Denisovans later mixed with modern humans, a small share of that older inheritance passed along again, meaning some people today carry genetic traces from two separate ancient encounters.
Researchers traced this pattern by studying 92 high-quality genomes from Oceania, where people carry unusually high levels of Denisovan ancestry. The old genetic signal turned up mostly inside sections of the genome already linked to Denisovans, not inside sections tied to Neanderthals.
That pattern led the team to conclude the ancient DNA reached modern humans through Denisovans rather than through direct contact with the mystery population.
Scientists react to a more tangled picture of human origins
Biddanda said the discovery was exciting because it points to genetic input from a human lineage that lived more than a million years ago, even though no DNA from that population has ever been recovered.
Moorjani said the results show that human evolution looked less like a simple branching tree and more like a connected web, shaped by repeated waves of mixing between different ancient groups over time.
The finding builds on earlier work. A 2020 study published in Science Advances also suggested that the ancestors of Neanderthals and Denisovans mixed with a very old, separate population, though it placed that split closer to 2 million years ago.
Researchers say more ancient Denisovan genomes and newly recovered protein evidence from older fossils could eventually help reveal who this mysterious ancestor was.
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