Hidden inside the genome of every person alive today may be the ghost of a human lineage that no fossil has ever revealed. A team led by computational biologists Yulin Zhang (UC Berkeley) and Arjun Biddanda (Johns Hopkins) has developed a method called TRACE — Tracking Archaic Contributions via ARG Estimation — that reconstructs the thousands of family trees embedded in each person's DNA, using only genomes from living people.

Analyzing 503 complete genomes from populations around the world, the researchers found that about 2% of non-African DNA comes from archaic lineages — roughly half matching sequenced Neanderthals, a sliver matching Denisovans, and the rest matching nothing ever sequenced. That unknown 'ghost' lineage makes up about 0.5% to 1% of the genome, a share comparable to Neanderthal ancestry in many people, and it appeared in every population examined.

The ghost lineage likely split from our branch more than half a million years ago, around the time Neanderthals and Denisovans diverged. Strikingly, it also turned up in stretches of DNA that scientists had considered uniquely modern — including a region around FOXP2, a gene linked to speech. 'We were really surprised,' said co-author Priya Moorjani, a population geneticist at Berkeley.

The team also found a second, far older signal: traces of a 'super-archaic' lineage in Oceanian genomes that diverged about 1.8 million years ago, likely entering modern humans through interbreeding with Denisovans, and possibly originating from Homo erectus. As candidates for the ghost itself, the researchers point to Homo heidelbergensis, which lived in Africa until about 300,000 years ago.

The findings, published in Science, still need independent confirmation — outside experts warn of potential false positives. But if confirmed, they suggest human history is less a branching tree than a web: 'Hybridization is the norm and not the exception,' said Fernando Villanea of the University of Colorado Boulder. Moorjani put it simply: the genomes of living people now let scientists recover hidden history 'without waiting for extraordinary fossil preservation.'

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