Scientists Found DNA from an Unknown Ancestor That Bred with Our Line Hundreds of Thousands of Years Before Neanderthals Did

Everyone alive carries DNA from an extinct relative whose bones have never been found. Researchers call it a ghost lineage, and a new study estimates it left about as much of itself in us as Neanderthals did.

The Berkeley-led team, working with Johns Hopkins, built a program called TRACE that reads the genome as thousands of tiny family trees. Ghost DNA gives itself away two ways: its tree runs back much further than the DNA around it, and it comes in longer, less scattered pieces. No ancient bone DNA was used at any point.

They ran it on 503 genomes from people across Europe, East Asia, South Asia and Africa, and found ghost DNA in every single person, from about 0.5 percent of the genome in South Asians to 1.1 percent in West Africans. In West Africans, that unknown ancestor left more than ten times as much detectable DNA as Neanderthals and Denisovans combined.

The line split from ours more than 500,000 years ago, and the mixing happened before humans made the last big migration out of Africa. Deeper still, inside Oceanian genomes, the team found stretches whose family tree runs back roughly 1.77 million years, old enough to be consistent with Homo erectus.

The genes it left behind aren’t random. Many cluster at spots that help the body fight infection or process fats, some of them in regions where Neanderthal and Denisovan DNA gets weeded out entirely. “Interbreeding with other human groups introduced new genetic variation, providing additional raw material for natural selection,” said Priya Moorjani, who leads the lab behind the work.

No one can name the group yet, only its candidates. The best record of these long-lost ancestors may never be dug out of the ground. It’s still being carried, quietly, by the people walking around today.