Two Unknown 'Ghost' Hominins Are Hiding in Modern Human DNA

Using a new computational method called TRACE, researchers at UC Berkeley found DNA from two previously unknown archaic human lineages in modern genomes: a 'ghost' lineage that mixed with Homo sapiens in Africa more than 50,000 years ago, and a far older 'super-archaic' lineage that entered our ancestry via Denisovans. Together they make up about 2% of the modern human genome.

Key Takeaways

Using a new computational method called TRACE, researchers at UC Berkeley found DNA from two previously unknown archaic human lineages in modern genomes: a 'ghost' lineage that mixed with Homo sapiens in Africa more than 50,000 years ago, and a far older 'super-archaic' lineage that entered our ancestry via Denisovans.
Together they make up about 2% of the modern human genome.

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Modern humans carry DNA from at least two mysterious 'ghost' hominin lineages that no fossil has ever been found for — and a new study published in Science shows both are hiding in our genomes today.

Researchers led by the University of California, Berkeley developed a computational method called TRACE (TRacking Archaic Contributions via ARG Estimation) that reconstructs the family trees hidden inside hundreds of genomes from living people, without needing ancient DNA. The approach spots stretches of DNA whose ancestry reaches further back than expected.

The first lineage the team identified is an African ghost population that interbred with anatomically modern Homo sapiens more than 50,000 years ago, before the great migration out of Africa. That lineage split from the human family tree roughly 800,000 years ago — around the same time as the Neanderthal–Denisovan split — and its DNA now makes up about 1 percent of the genome of every person alive today, regardless of ancestry.

The second, 'super-archaic' lineage is far older, tracing back roughly 1.8 million years. Rather than mixing directly with modern humans, this population appears to have interbred with Denisovans in Eurasia; when Denisovans later mixed with Homo sapiens, some of that ancient DNA came along for the ride. Its traces are strongest in present-day populations from Oceania, which carry unusually high levels of Denisovan ancestry.

Altogether, the two newly identified lineages account for roughly 2 percent of the modern human genome, with each individual carrying about 0.5 to 1 percent of the ghost lineage alone. Many of the archaic segments cluster in regions tied to immunity and metabolism — a pattern consistent with the idea that interbreeding supplied raw material for natural selection as humans faced new pathogens and food sources.

'Previous publications suggested that there might be ghost ancestry 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,' said lead author Yulin Zhang, a graduate student at UC Berkeley. '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.'