Evidence hidden in DNA may help solve the mystery of human ancestors who are absent from the fossil record but remain embedded in the genes of people alive today.

Scientists established years ago that our species, Homo sapiens, interbred with extinct human relatives, including Neanderthals and Denisovans. Yet other ancestral groups have remained difficult to identify. Unlike Neanderthals and Denisovans, whose DNA has been extracted from prehistoric remains, these populations are genetic “ghosts,” leaving no ancient DNA that can be directly compared with signals found in modern genomes.

Earlier research detected fragments associated with these ghost populations, but scientists could not establish when interbreeding occurred or determine how long ago the lineages separated from the ancestors of modern humans.

Researchers have now created a new technique for examining contemporary human genomes. By tracing the DNA of living people backward, they reconstructed missing sections of humanity’s family tree and found signs of two previously unidentified ancestral lineages. One appears to have mixed directly with Homo sapiens in Africa more than 50,000 years ago. The other belonged to a much older population that transferred some of its DNA to modern humans indirectly through Denisovans. The findings were published July 30 in the journal Science.

The research offers a fresh window into one of the central mysteries of human evolution.

The scientists’ approach reconstructs genealogies—maps that indicate where individual pieces of DNA originated and how they were inherited—exposing previously hidden branches of our evolutionary history.

“One of the deepest questions people ask is, ‘Why are we here, and where did we come from?’ These genealogies let us examine the past in ways that were not previously possible,” said Priya Moorjani, a study coauthor and associate professor in the Department of Molecular and Cell Biology at the University of California, Berkeley.

Moorjani said the discovery could also support research into why certain hominin populations endured while others vanished. Studying the genetic contributions of different ancestors may help answer that question, while showing how humans adjusted to changing environments and why some diseases affect people today.

Searching for ghost lineages

Modern humans began their major migration out of Africa about 50,000 years ago. As Homo sapiens spread through Eurasia, they interbred with Neanderthals and Denisovans. The newly identified lineages, however, reveal that the story was even more complicated.

One unknown ancestor described in the study probably interbred with humans in Africa before that migration. Researchers estimate that DNA inherited from this population accounts for roughly 0.5% to 1% of the genomes of people living today—nearly matching the proportion of Neanderthal DNA carried by many modern humans.

This genetic legacy provides another indication that encounters among early human populations were widespread during prehistory.

The second lineage is considerably older. Researchers call it a “super-archaic” ancestor because it belongs to a branch of the human family tree that separated about 1.8 million years ago. This population may have interbred with Denisovans in Eurasia more than 200,000 years ago. Some of its DNA then reached modern humans when Homo sapiens later mixed with Denisovans.

To detect these ghost ancestors, the team developed a computer-based method known as TRACE, which searches present-day human genomes for genetic clues left behind by vanished populations.

“Our genomes are mosaics composed of small pieces of DNA inherited from all our ancestors, so different regions of the genome have different family trees,” Moorjani explained. Some branches are relatively recent, while others reach much deeper into history. DNA inherited from ancient relatives such as Neanderthals lies along these older branches. TRACE scans the genome for exceptionally deep lineages that may indicate ancestry from populations not previously identified.

The researchers applied TRACE to more than 500 modern human genomes representing populations in Africa, Europe and Asia. Evidence of the more recent ghost ancestry appeared in every population examined. This pattern suggests that the unknown lineage contributed DNA to the ancestors of modern humans before the major expansion out of Africa.

“When we look beyond humans, movement of genes and mixing between groups are common across many populations, so it is not especially surprising that we carry DNA from several hominin groups,” Moorjani said. “The challenge is that, until recently, recovering and identifying this genetic material from ancient people was not practical.”

The results add another layer to the complex history of contact between modern humans and their extinct relatives.

Identifying mysterious ancestors

The researchers cannot yet determine exactly which hominin populations these lineages represented. However, they have identified possible candidates by estimating when each branch separated from the wider human family tree. The divergence date of the younger lineage matches Middle Pleistocene Homo populations in Africa, meaning it may have been connected to Homo heidelbergensis, the study’s authors suggested.

Homo heidelbergensis inhabited Africa and Europe between approximately 700,000 and 200,000 years ago. The researchers propose that the much older lineage may have been related to Eurasian Homo erectus. No recoverable DNA has yet been obtained from either hominin population.

“The super-archaic result is particularly compelling because it identifies a genetic contribution from a human lineage that existed more than a million years ago, even though no DNA from that population has ever been sequenced,” said Arjun Biddanda, a postdoctoral researcher at Johns Hopkins University and co-first author of the study.

Modern human genomes are overwhelmingly alike, but they vary slightly between individuals. Some of those uncommon yet detectable differences were introduced by ancient ancestral lineages, explained John Hawks, a paleoanthropologist and professor at the University of Wisconsin–Madison who did not participate in the research.

“People today often concentrate on differences that appear substantial but are actually superficial, such as skin tone or facial features,” Hawks said. “Variation among living humans is extremely small compared with the differences among the ancestors from whom we evolved. Those populations still found ways to interact and survive together. That shared inheritance remains deeply important.”

Other archaeological and genetic evidence likewise suggests that extinct hominins and modern humans sometimes exchanged knowledge, genes and aspects of culture.

The identification of the younger ghost population “places the interbreeding event long before contact with Neanderthals and demonstrates that its genetic influence is present in all populations alive today,” Hawks added.

The team hopes TRACE will reveal additional hidden lineages within human history and among other animal species. Still, the researchers agree that the strongest future evidence would come from DNA recovered directly from ancient fossils.

Until such material is found, the genetic traces preserved in living people remain scientists’ closest connection to these missing ancestors.

“Two people from distant parts of the world might, by chance, inherit the same fragment of DNA from an ancestor whose existence was previously unknown,” said co-first author Yulin Zhang, a doctoral student in computational biology at the University of California, Berkeley. “We can now recognize that shared inheritance and understand that this mysterious ancestor connects us in another way.”