Scientists Find a Mysterious 'Ghost Lineage' In the DNA of West Africans

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A mysterious extinct "ghost" human lineage that was an even more distant relation than Neanderthals may have interbred with the ancestors of modern West Africans, significantly contributing to their gene pool, a new study finds.

Although modern humans are now the only surviving lineage of humanity, others once lived on Earth. Some made their way out of Africa before we did, including the familiar Neanderthals in Eurasia and the newfound Denisovan lineages in Asia and Oceania. It isn't completely clear whether these lineages would be considered species or subspecies, but the groups had identifiable genetic differences. Prior work estimated the ancestors of modern humans split about 700,000 years ago from the lineage that gave rise to Neanderthals and Denisovans, and the ancestors of Neanderthals and Denisovans diverged from one another about 400,000 years ago.

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The story is a bit more tangled than the timeline suggests, as genetic analysis of fossils of these extinct lineages has revealed they once interbred with modern humans, unions that may have endowed our lineage with helpful mutations as we began expanding across the world about 194,000 years ago. Neanderthal DNA makes up roughly 1.8% to 2.6% of the genomes of modern humans from outside Africa, whereas Denisovan DNA makes up 4% to 6% of modern Melanesians.

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Any number of now-extinct human lineages that once existed within Africa may have hybridized with modern humans there as well. However, the sparse nature of the ancient human fossil record in Africa makes it difficult to identify DNA from such "ghost lineages" in modern humans.

Instead of hunting for ancient human fossils across Africa, the scientists looked for genetic traces of ghost lineages in modern Africans. They compared 405 genomes from modern people from West Africa with ones from fossils of Neanderthals and Denisovans, focusing on DNA that stood out from the West African genomes roughly as much as Neanderthal and Denisovan DNA did from modern human genomes overall.

The researchers detected statistical anomalies they suggested were best explained by interbreeding between West Africans and an unknown ancient human lineage whose ancestors diverged from those of modern humans before the split between Neanderthals and modern humans. Four West African groups -- Yoruba in southwestern Nigeria, Esan in southern Nigeria, Gambians in western Gambia, and Mende in Sierra Leone -- may derive 2% to 19% of their DNA from a ghost lineage, the researchers said.

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