UC Berkeley-led study identifies DNA from two unknown archaic human groups in living people

The ghost ancestor interbred with modern humans in Africa more than 50,000 years ago, before the most recent major migration of Homo sapiens out of Africa, the researchers report. DNA inherited from this lineage makes up approximately 1% of the modern human genome, an amount the researchers describe as comparable to the Neanderthal contribution.

How the DNA was traced

The Berkeley team developed a technique called TRACE, for TRacking Archaic Contributions via ARG Estimation. It analyzes hundreds of complete genomes from present-day humans around the world and reconstructs an ancestral recombination graph, a map of how DNA segments are related through shared ancestry over time. The method identifies regions whose ancestry extends unusually far back, allowing the team to locate DNA from extinct populations even without ancient DNA from them. Earlier studies had found hints of such interbreeding but had not mapped where the traces sat. “Genealogies preserve a record of our evolutionary past,” said Priya Moorjani, a Berkeley associate professor of molecular and cell biology. “TRACE reconstructs those histories across the genome. By identifying regions whose ancestry extends unusually far back in time, we can uncover genetic contributions from extinct human populations, even in the absence of ancient DNA.”

The analysis points to interbreeding between modern humans and at least four archaic human relatives, among them Neanderthals and Denisovans.

The ghost ancestor in Africa

The ghost lineage split from the modern human line around 800,000 years ago, close to when Neanderthals and Denisovans diverged from each other. The interbreeding happened before 50,000 years ago, earlier than the Neanderthal and Denisovan encounters outside Africa.

Most people outside Africa carry about 1 to 2% Neanderthal DNA.

“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,” said Yulin Zhang, a Berkeley graduate student and one of two first authors.

The super-archaic ancestor

The second group is older still. The researchers describe a super-archaic ancestor whose lineage dates back about 1.8 million years. It probably interbred with Denisovans in Eurasia more than 200,000 years ago. Denisovans later mixed with Homo sapiens, which is how a small slice of that older DNA reached modern genomes. “The super-archaic finding is particularly exciting because it reveals genetic contributions from a human lineage that lived over a million years ago, despite the absence of any sequenced DNA from that population,” said Arjun Biddanda, a postdoctoral researcher at Johns Hopkins University and a co-first author.

What the dates line up with

The inferred divergence dates overlap with the existence of Middle Pleistocene Homo groups in Africa around 800,000 years ago and Homo erectus populations in Eurasia around 1.8 million years ago, the researchers said.

Priya Moorjani, an associate professor of molecular and cell biology at Berkeley, said in a university release that mixture among human populations has been pervasive across time. “We often think of human evolution as a branching tree, but new genomic data and analytical methods reveal a much more interconnected history - more like a complex web of populations connected by repeated episodes of migration and mixing,” she said.

The authors argue that early Homo sapiens lived alongside numerous related hominin groups in Africa and Eurasia over the past million years. They were close enough genetically to interbreed with many of them.

What is still open

The study does not identify the two populations, and neither has been tied to a sequenced genome. The inferred dates overlap with known groups, but that overlap does not establish identity. Without DNA from either population, the identities remain unresolved.