UC Berkeley scientists used a new method called TRACE to detect "super‑archaic" DNA in modern humans and found evidence for at least two previously unidentified hominin lineages. One ghost lineage contributes roughly 1% of the genome and likely introgressed about 300,000 years ago, affecting all present‑day populations. Older, deeply divergent lineages also appear within Denisovan ancestry in Oceania. Additional ancient genomes from Africa and Asia will be needed to identify the sources and functional impacts of these ghost genes.
Scientists Find DNA From At Least Two ‘Ghost’ Hominin Lineages Hidden in Modern Humans
Two 'Ghost Species' Lurk in Human DNAIlya Lukichev - Getty Images
Researchers at UC Berkeley have developed a new analytical framework that reveals modern humans carry genetic traces not only from Neanderthals and Denisovans but also from at least two previously unidentified archaic hominin lineages. These deeply divergent "ghost" sequences account for measurable portions of the human genome and likely entered our ancestors’ gene pool through interbreeding events hundreds of thousands of years ago.
New Method: TRACE
The team created TRACE (TRacking Archaic Contributions via ARG Estimation), a method that reconstructs ancestral recombination graphs to locate genomic segments that derive from very ancient branches of the human family tree. TRACE is especially powerful at detecting "super‑archaic" DNA: stretches that are too divergent to be explained by known Neanderthal or Denisovan introgression alone.
What They Found
Using TRACE, the researchers identified a ghost lineage that appears to have diverged around the same time as the split between the ancestors of modern humans and Neanderthals. That lineage likely contributed roughly 1% of the genome — about the same order of magnitude as the average Neanderthal contribution — and probably introgressed into our ancestors around 300,000 years ago. Importantly, the signal from this event appears across present‑day human populations, not only in West Africans.
TRACE also detected additional, even older lineages embedded within the Denisovan ancestry of Oceanian populations, indicating multiple introgression events from deeply divergent hominins. These extra layers of archaic DNA could have entered modern humans directly, or indirectly via Neanderthal and Denisovan ancestors who themselves carried super‑archaic sequences.
"We find evidence for at least one ghost introgression predating the [out of Africa] expansion that contributed ancestry to all present‑day populations," Biddanda and Zhang write in their Science paper. "This finding ... extends that model by showing that the event affected all modern human populations rather than being localized to West Africans."
Uncertainties and Implications
Although archaic hominin DNA makes up roughly 2% of the average Homo sapiens genome, the exact identities of these ghost contributors remain unknown. The authors propose plausible candidates such as Homo erectus or Homo heidelbergensis, but they emphasize other, currently undocumented hominin species might also be involved.
When and where these introgression events occurred cannot yet be precisely determined. The researchers stress that sequencing additional ancient genomes—especially from Africa and Asia—and expanding population sampling will be critical to pinpoint sources, timing, and the evolutionary impact of these ghost sequences.
Why It Matters
Beyond reconstructing our species’ tangled history, uncovering these ghost contributions may reveal functional effects on immunity, metabolism, or other traits that shaped human adaptation. As more ancient DNA reference genomes become available, scientists expect to clarify the origins of these sequences and their role in human biology.
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