Human evolution is proving far more tangled than a simple family tree. A team at the University of California, Berkeley, has uncovered stretches of DNA in modern humans that come from at least two previously unknown extinct hominin groups. These so-called “ghost ancestors” left no fossils or sequenced genomes, yet their genetic signatures persist in people alive today.
Homo sapiens is now the only human species, but for most of our history we shared the planet with other hominins. Earlier research established that modern humans interbred with Neanderthals and Denisovans, and many people still carry those genetic echoes. The new study, published by Berkeley researchers, suggests the list of our ancestral partners is longer than thought.
Two mysterious lineages
The first ghost lineage interbred with the ancestors of modern humans in Africa more than 50,000 years ago, before the major migration of Homo sapiens into Europe and Asia. That genetic contribution now accounts for roughly 1% of the DNA of all living humans—comparable to the Neanderthal share in non-Africans. According to the researchers’ calculations, this lineage split from the line leading to modern humans around 800,000 years ago, about the same time Neanderthals and Denisovans diverged from each other.
“Earlier studies had already hypothesised that there is a so-called ghost lineage, meaning genetic traces of unknown extinct human lineages in the genomes of modern humans,” said Yulin Zhang, a doctoral student at Berkeley and lead author of the study. “However, it was previously unclear whether this unknown lineage occurs only in Africans and when this admixture happened. We have now been able to identify and map the relevant DNA segments in the genomes of modern humans and show that this ghost lineage is found in all people living today, not just in Africans.”
The second ancestor is even more enigmatic. Dubbed a “super-archaic ancestor,” this lineage branched off from other hominins around 1.8 million years ago. More than 200,000 years ago, it interbred with Denisovans in Eurasia, and through that detour its ancient DNA eventually entered the modern human genome.
“The evidence for this super-archaic ancestor is particularly exciting because it reveals genetic contributions from a human lineage that lived more than a million years ago, even though no DNA from this population has yet been decoded,” said Arjun Biddanda, a postdoctoral researcher at Johns Hopkins University and co-lead author.
Human evolution as a network
The findings reinforce a growing consensus that human evolution resembles less a branching tree and more a complex web. “Thanks to ancient DNA from Neanderthals and Denisovans and new genealogical methods, we are increasingly realising that human populations have repeatedly mixed with one another in the course of evolution,” said Priya Moorjani, professor of molecular and cell biology at Berkeley. “Human evolution therefore resembles less a branching family tree and more a complex network in which different populations were linked by repeated migrations and admixture.”
Most people outside Africa carry 1–2% Neanderthal DNA, a legacy of interbreeding around 50,000–60,000 years ago. Those segments still influence traits like immunity, skin and hair, and can affect disease risk. In Asia and Oceania, Denisovan DNA is also present. The Max Planck Institute for Evolutionary Anthropology in Leipzig and the Mongolian Academy of Sciences previously sequenced the oldest human fossil from Mongolia—a 34,000-year-old woman from the Salkhit Valley—and found both West Eurasian and Denisovan ancestry.
Neanderthals and Denisovans also interbred with each other. A fossil from Denisova Cave in the Altai Mountains belonged to a woman with a Neanderthal mother and a Denisovan father, direct evidence of mixed offspring.
Exactly who these ghost ancestors were remains unclear, but the timing offers clues. The ghost lineage could belong to Middle Pleistocene Homo groups in Africa around 800,000 years ago. The super-archaic ancestor might be Homo erectus, which spread across Eurasia as early as 1.8 million years ago. As genetic tools improve, more chapters of this hidden history are likely to emerge.
