Scientists at UC Berkeley have identified genetic evidence of two previously unknown human populations that interbred with Homo sapiens at different points in evolutionary history. The discovery, published in Science on July 30, adds to existing knowledge about interbreeding with Neanderthals and Denisovans by revealing additional layers of genetic mixing among ancient human groups.
The first unknown population, referred to as a ghost ancestor by researchers, interbred with modern humans in Africa more than 50,000 years ago. This encounter occurred before the major migration of Homo sapiens out of Africa into Europe and Asia. DNA from this lineage comprises approximately 1% of the modern human genome, a proportion comparable to Neanderthal ancestry. The ghost lineage diverged from the ancestors of modern humans around 800,000 years ago, roughly the time when Neanderthals and Denisovans split from one another. Notably, this ghost ancestry is found in both African and non-African populations today.
The second unknown population represents an even more ancient lineage, dating back approximately 1.8 million years, which researchers call a super-archaic ancestor. This hominin appears to have interbred with Denisovans in Eurasia more than 200,000 years ago. When Denisovans later mixed with Homo sapiens, small portions of this super-archaic DNA entered modern human genomes. The super-archaic genetic signal became visible when researchers examined genomes from Oceania and Pacific island populations, where it appears within Denisovan DNA segments.
The UC Berkeley team developed a new computational method called TRACE (TRacking Archaic Contributions via ARG Estimation) to identify these genetic contributions without relying on ancient DNA sequences. Rather than examining fossil remains, TRACE reconstructs ancestral relationships by analyzing complete genomes from present-day populations worldwide. The method successfully identified regions containing archaic genetic material by examining how DNA segments connect through shared ancestry across multiple generations.
Researchers found that archaic DNA segments, including those from the ghost and super-archaic populations, are concentrated in genomic regions associated with immune function and metabolism. This distribution suggests that genes inherited from other hominin populations may have provided adaptive advantages as Homo sapiens migrated into new environments and encountered unfamiliar diseases and food sources. The findings indicate that human evolution involved extensive interbreeding among multiple related populations rather than a simple branching pattern, creating a complex genetic legacy that persists in modern humans.
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