The key facts
- The TRACE method is described in the journal Science; 0.5% to 1% of every person's genome comes from an unknown ancient population that mixed with ancestors in Africa.
- The 'ghost' split off about 800,000 years ago, the admixture occurred about 50,000 years ago, so the trace is present in all peoples; linking it to fossils is not yet possible.
- A lineage that split off about 1.8 million years ago left 3–5% of the genome to Denisovans; 'ghost' segments are more often found in immunity and metabolism genes.
An unknown ancestor in everyone's genome
The genome of every living person carries an inheritance from a mysterious 'ghost' species of humans: 0.5% to 1% of DNA came to modern humanity from an unknown ancient population that mixed with our ancestors in Africa. These segments have, for the first time, been found and mapped by geneticists at the University of California, Berkeley led by Priya Moorjani. The method, called TRACE, is described in the journal Science.
How TRACE works
For the past 15 years genetics has been painting a tangled picture of the past: human ancestors interbred with Neanderthals and Denisovans, and roughly 2% of the genome of any modern human is of ancient origin. Suspecting other, nameless 'relatives' was easy, but identifying them without a genome from fossils proved impossible. TRACE builds a genealogy of each DNA segment: as chromosomes are passed to descendants they constantly reshuffle, and segments from distantly diverged relatives show up as branches that split off very early.
Who was the 'ghost'
The 'ghost', which split from human ancestors about 800,000 years ago, contributed its genes to an African population roughly 50,000 years ago — before humanity spread beyond the continent, which is why its trace is found in all peoples of the planet. Who it was remains unclear: in Africa's hot and humid climate ancient DNA is almost never preserved. At that time various groups of human relatives lived on the continent, including Homo naledi in southern Africa, but it is not yet possible to tie the genetic 'ghost' to specific fossils.
A trace 1.8 million years deep
The second finding goes even deeper into history: a lineage that split off about 1.8 million years ago left 3–5% of the genome to the Denisovans — human relatives whose bones were found in Denisova Cave in the Altai. Around that era, the first members of the genus Homo were leaving Africa. Since peoples of Oceania carry up to 4% Denisovan DNA, crumbs of this ultra-ancient inheritance ultimately reached people living today.
Evolutionary significance and caveats
'We are used to thinking of human evolution as a branching tree,' Moorjani reflects. 'The new picture is more like the braided channels of a river: branches merged again and again.' The inheritance appears to have been evolutionarily significant: 'ghost' segments are found more often than usual in genes for immunity and metabolism, meaning natural selection favored them. The same fate befell Neanderthal DNA, which helped modern humans adapt to infections, cold and high altitudes. The authors warn that the method relies on statistical reconstruction, so the dates and proportions of ancient admixture are determined with a margin of error, and debates about the past of African populations are not yet settled.
