New research led by the University of California, Berkeley reveals that beyond Neanderthals and Denisovans, humans interbred with two mysterious ‘ghost’ lineages: one in Africa more than 50,000 years ago, another in Eurasia over 1.7 million years ago.
Archaic hominins. Image credit: Ninara / CC BY 2.0.
“The sequencing of the Neanderthal and Denisovan genomes has transformed our understanding of human evolution, revealing evidence for gene flow between modern humans and archaic hominins,” said University of California, Berkeley graduate student Yulin Zhang and colleagues.
“Most non-Africans living today possess 1 to 2% Neanderthal ancestry, and Asians and Oceanians harbor 0.1 to 5% Denisovan ancestry.”
“Archaic ancestry has had a major impact on human adaptation and disease, contributing to a range of traits such as skin pigmentation, high altitude adaptation, and immune function.”
“To date, however, only six high-coverage archaic genomes have been published — four Neanderthals and two Denisovan — all from Eurasia.”
“Thus, our knowledge of the evolutionary history and impact of archaic ancestry outside Eurasia and at deeper timescales remains incomplete.”
To detect the genetic signatures of ancient interbreeding, the authors developed a new computational method called TRACE (TRacking Archaic Contributions via ARG Estimation).
Rather than relying on fossil DNA, the technique reconstructs genealogical relationships buried within hundreds of genomes from living people, allowing scientists to spot DNA segments whose ancestry stretches back further than expected.
Applying the TRACE method, the researchers identified what they call a ghost lineage that mixed with anatomically modern Homo sapiens in Africa more than 50,000 years ago, before the major migration into Europe and Asia.
That lineage split from the human family tree roughly 800,000 years ago — around the same time as the Neanderthal and Denisovan split — and its DNA now makes up about 1% of the genome of every person alive today, regardless of ancestry.
“Previous publications suggested that there might be ghost ancestry — ancestry from unknown archaic lineages in modern humans — but they hadn’t concluded whether this unknown ancestry is present only in Africans or not, and when this introgression event happened,” Zhang said.
“We were actually able to find and map genomic locations in modern humans that are from this ghost lineage and show that this ghost ancestry is in all modern humans, not only in Africans.”
The second, ‘super-archaic’ lineage is even older, tracing back roughly 1.8 million years.
Rather than interbreeding directly with modern humans, this population appears to have mixed with Denisovans in Eurasia.
When Denisovans later interbred with Homo sapiens, some of the super-archaic DNA came along for the ride.
Traces of it show up most strongly in present-day populations from Oceania, which carry unusually high levels of Denisovan ancestry.
“The super-archaic finding is particularly exciting because it reveals genetic contributions from a human lineage that lived over a million years ago, despite the absence of any sequenced DNA from that population,” said Dr. Arjun Biddanda, a postdoctoral researcher at Johns Hopkins University.
Altogether, the two newly identified lineages account for roughly 2% of the modern human genome.
“We discovered that about 2% of the modern human genome is from archaic hominins,” Zhang said.
“In the case of the ghost lineage, modern-day Africans and non-African populations both inherited similar amounts of ghost ancestry.”
“Each individual has about 0.5 to 1% of their genome inherited from this ghost lineage.”
Many of the archaic segments cluster in regions tied to immunity and metabolism, suggesting the genetic material may have helped ancient humans adapt to new environments, pathogens, and food sources.
“This pattern is not entirely surprising,” said Dr. Priya Moorjani, also from the University of California, Berkeley.
“Adaptation to new pathogens and food sources has been one of the strongest selective pressures in human evolution.”
“Interbreeding with other human groups introduced new genetic variation, providing additional raw material for natural selection.”
“Beneficial variants could then be retained and spread over many generations.”
The scientists hope to detect faint signals of additional lineages in human DNA as the world’s genome databases become more diverse, sampling a broader variety of humanity. The discovery of more Denisovan genomes would also help.
Protein sequences recently sequenced from Homo erectus fossils could even help identify who the super-archaic ancestor was.
“I think these new computational methods that allow us to reconstruct genealogical relationships are really the next frontier in this field because they are allowing us to uncover hidden episodes from our past without requiring ancient DNA,” Dr. Moorjani said.
The study was published July 30, 2026 in the journal Science.
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Yulin Zhang et al. Recovering signatures of archaic hominin introgression using ancestral recombination graphs. Science, published online July 30, 2026; doi: 10.1126/science.aef8874
