Modern Human DNA Reveals Traces of Two Previously Unknown ‘Ghost’ Ancestors
Two mysterious branches of the human family tree, neither of which has yielded ancient DNA for scientists to study directly, have been detected through genetic traces still carried by people living today.
Using a new computer-based technique to work backward through modern human genomes, researchers identified evidence of two previously unknown ancestral lineages. One appears to have mixed directly with Homo sapiens in Africa more than 50,000 years ago. The other was far older, contributing DNA to Denisovans hundreds of thousands of years ago before some of that genetic material eventually made its way into modern humans.
The findings, published July 30 in the journal Science, offer a new way of investigating human relatives that have effectively become genetic “ghosts” — populations whose existence can be inferred from genetic evidence even though scientists have not been able to sequence their genomes directly.
“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 of the study, in a statement.
Researchers have known for years that Homo sapiens interbred with extinct relatives, most famously Neanderthals and Denisovans. Ancient DNA recovered from fossils has allowed scientists to identify genetic material those groups contributed to modern humans.
Other ancient populations, however, have been much harder to pin down. Previous research has found hints that humans inherited DNA from unidentified hominins, but scientists could not confidently determine when those groups mixed with human ancestors or how long ago they diverged from other branches of the human evolutionary tree.
The new study attempts to fill in some of those gaps using a method the researchers developed called TRACE. The computer-based technique reconstructs genealogies showing where sections of DNA originated and how those genetic segments were inherited over generations, allowing researchers to search for unusually old branches that could point to previously unknown populations.
“Our genomes are mosaics of little bits of DNA from all our ancestors, and so in different parts of our genome we have a different family tree,” said Priya Moorjani, study coauthor and an associate professor in the department of molecular and cell biology at the University of California, Berkeley.
Some sections of those genetic family trees trace back relatively recently, while others extend much deeper into humanity’s evolutionary history. DNA inherited from Neanderthals, for example, appears on older branches. By comparing these family trees across the genome, TRACE can identify lineages that cannot be explained by populations already known to scientists.
The researchers applied the method to more than 500 modern human genomes representing populations across Africa, Europe and Asia. Their analysis uncovered evidence of the two ghost lineages and allowed the team to estimate when the groups separated from other hominins and when interbreeding took place.
Traces of the younger lineage appeared in every modern population included in the study, indicating that it likely mixed with the ancestors of Homo sapiens in Africa before the major migration that carried modern humans out of the continent.
Modern humans began moving out of Africa around 50,000 years ago, eventually encountering and interbreeding with Neanderthals and Denisovans in Eurasia. The newly detected ancestry suggests Homo sapiens had already exchanged genes with another hominin population before those encounters occurred.
The discovery of the younger ghost lineage “places the time of mixture well before the mixture with Neanderthals, and shows that it affects all populations living today,” said John Hawks, a paleoanthropologist and professor at the University of Wisconsin–Madison who was not involved in the study.
The researchers estimate that DNA inherited from this unidentified lineage now accounts for roughly 0.5% to 1% of modern human genomes. That is close to the proportion of Neanderthal ancestry found in many people alive today.
Based on where the lineage falls on the evolutionary tree, researchers believe it could have belonged to a Middle Pleistocene Homo population in Africa. One possible candidate is Homo heidelbergensis, according to the study.
Homo heidelbergensis lived in Africa and Europe from approximately 700,000 to 200,000 years ago. However, because no DNA sequence is available for the species, the proposed connection remains speculative.
The second ghost lineage reaches considerably further back in human evolution.
Researchers described it as “super-archaic,” estimating that its branch split from other human ancestors approximately 1.8 million years ago. Rather than mixing directly with modern humans, this population appears to have interbred with Denisovans in Eurasia more than 200,000 years ago.
Later, after Homo sapiens encountered Denisovans, portions of that ancient DNA were passed into our own species. In other words, modern humans may carry fragments of genetic material inherited indirectly from a population that lived more than a million years ago.
The researchers suggest the lineage could potentially have been related to Eurasian Homo erectus. That identification, like the possible connection between the younger lineage and Homo heidelbergensis, cannot yet be confirmed.
Exactly which populations the two ghost lineages represent therefore remains uncertain. Researchers can use estimated divergence dates, patterns of inheritance and other genetic clues to narrow down where the groups may fit on the hominin family tree, but those clues cannot establish their identities on their own.
“The most fundamental question that most of us have is, ‘Why are we here? Where do we come from?’ And these genealogies really allow us to look into the past in a way that we have not been able to do before.”
The findings also add to a growing picture of human evolution as a history shaped not simply by one population replacing another, but by repeated encounters and genetic exchanges among different hominin groups.
“If you think about going even beyond humans, gene flow and mixing across groups is pretty pervasive across all populations, and so it’s not very surprising that we harbor DNA from different hominin groups,” Moorjani said. “It’s just that until recently, it’s not been feasible to extract this DNA from people who lived in the past.”
Studying those exchanges may eventually provide clues about why certain hominin populations survived while others vanished. Moorjani said identifying the genetic material different ancestors contributed could also help scientists better understand how modern humans adapted to different environments and why people are susceptible to certain diseases today.
Modern human genomes are overwhelmingly similar to one another, but some of the differences among individuals can be traced to these ancient ancestral branches, Hawks explained.
“Today we have a tendency to focus on differences between people that seem large, but are actually superficial — like skin color or facial appearance,” Hawks told CNN in an email.
“These differences among living people are actually very tiny compared to the ancestors we all evolved from, and those ancestors found ways to interact and survive with each other. That’s our heritage, and it’s one that matters even more than ever.”
Researchers hope TRACE could eventually reveal additional hidden lineages, both within human evolutionary history and among other species.
But computational reconstructions have limits. The strongest evidence for the identities of these ghost populations would ultimately come from recovering and sequencing DNA directly from ancient remains—as scientists have previously done with Neanderthals and Denisovans.
Until fossils containing usable DNA are found, the genetic material inherited by living humans may provide the clearest surviving record of these populations.
“Randomly, two people from the world might inherit the same piece of DNA from an ancestor who we didn’t have an idea of before, but now we actually know,” said the study’s co-first author Yulin Zhang, a doctoral student of computational biology at UC Berkeley. “From this mysterious ancestor, we have something in common from another angle.”
Moumita Basuroychowdhury is a Contributing Reporter at The National Digest. After earning an economics degree at Cornell University, she moved to NYC to pursue her MFA in creative writing. She enjoys reporting on science, business and culture news. You can reach her at moumita.b@thenationaldigest.com.