Two ‘Ghost’ Ancestors Left Their DNA in Every Living Human
Buried inside every living person’s genome are traces of relatives science has never directly seen. No bones, no teeth, no fossil DNA, just faint genetic echoes of two extinct human lineages that vanished long before anyone thought to look for them.
Finding Relatives Without Any Fossils
Two mysterious human relatives left their genetic footprints in the modern human genome alongside the DNA of Neanderthals and Denisovans, underscoring the fact that our ancestors interbred with many groups of hominins they encountered over millions of years of evolution. While previous research had already found hints that modern humans interbred with ancient hominins beyond Neanderthals and Denisovans, a new study by researchers at UC Berkeley pinpoints exactly where in the genome that inherited material sits, and establishes a timeline for when the interbreeding happened.
The findings, led by Berkeley associate professor Priya Moorjani along with graduate student Yulin Zhang and Johns Hopkins postdoctoral researcher Arjun Biddanda as co-first authors, were published July 30 in the journal Science.
A Method That Doesn’t Need Ancient Bones
Piecing together human ancestry has traditionally depended on sequencing DNA extracted directly from ancient fossils, which is exactly how scientists first confirmed that modern humans interbred with Neanderthals and Denisovans after early Homo sapiens left Africa roughly 50,000 years ago. But for older or rarer hominin lineages, no fossil DNA has ever been recovered, leaving their genetic contribution effectively invisible using older methods.
Moorjani’s team developed a new technique called TRACE, short for TRacking Archaic Contributions via ARG Estimation, that sidesteps that problem entirely. By analyzing complete genomes from present-day humans around the world, the method reconstructs an ancestral recombination graph, essentially a detailed map of how different segments of DNA are related to one another through shared ancestry over time. “Genealogies preserve a record of our evolutionary past,” Moorjani said. “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.”
As a check on the method’s accuracy, the team first confirmed it could correctly identify already-known Neanderthal and Denisovan DNA segments within modern genomes. It passed that test, which gave researchers confidence in what it found next: DNA that matched neither Neanderthal nor Denisovan genomes at all.
A Ghost Lineage Present in Every Human Alive
The team determined that this leftover ancient DNA came from two genetically distinct lineages, each with its own separate history of interbreeding with modern humans. The first, which researchers call a ghost ancestor, interbred with modern humans in Africa more than 50,000 years ago, before the most recent wave of Homo sapiens migration out of Africa into Europe and Asia.
This ghost lineage split off from the modern human family tree at roughly the same time Neanderthals and Denisovans diverged, around 800,000 years ago, though the actual interbreeding with modern humans happened considerably later. “Previous publications suggested that there might be ghost ancestry, ancestry from unknown archaic lineages in modern humans, but they hadn’t concluded whether this unknown ancestry is present only in Africans or not, and when this introgression event happened,” said Zhang. “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.”
That’s a significant detail. Finding the same ghost DNA in both African and non-African populations in similar amounts indicates the interbreeding took place before modern humans spread out of Africa, meaning every person alive today, regardless of ancestry, carries a small piece of this same unknown relative. Each individual carries roughly 0.5 to 1 percent of their genome from this ghost lineage, comparable to the amount of Neanderthal DNA most non-African populations carry.
An Even Older ‘Super-Archaic’ Relative
The second lineage the researchers identified is older still. Dubbed a super-archaic ancestor, it descended from a hominin lineage that split off roughly 1.8 million years ago, making it far more ancient than either Neanderthals or Denisovans. Rather than interbreeding directly with modern humans, this lineage appears to have interbred with Denisovans in Eurasia more than 200,000 years ago. Denisovans then passed a portion of that inherited super-archaic DNA on to modern humans through their own later interbreeding with Homo sapiens.
“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,” Biddanda said. Because Denisovans themselves carry between 3 and 5 percent super-archaic DNA, only a small fraction of that ultimately made it into the modern human genome through this indirect route.
Researchers recovered this super-archaic signal specifically by analyzing genomes from populations in Oceania, since people from this region carry unusually high proportions of Denisovan ancestry, sometimes reaching as much as 4 percent, making the fainter super-archaic signal easier to detect against that background. “TRACE allowed us to contextualize how the ancestry segments from these previously uncharacterized hominins are distributed throughout the human genome,” Biddanda added. “We found that these contributions are widespread throughout the genome, and ghost ancestry is detected even in regions previously thought to be intolerant of Neanderthal and Denisovan ancestry.”
Roughly 2 Percent of the Genome, From Relatives We’ve Never Seen
Altogether, the researchers estimate that about 2 percent of the modern human genome traces back to these archaic hominins, a genuinely significant chunk of ancestry hiding in plain sight, invisible to previous methods simply because no fossil DNA from either lineage has ever been recovered.
Exactly who these ghost and super-archaic populations actually were remains unknown, since there are no fossils to examine directly. Based on the inferred divergence times, researchers note the ghost lineage overlaps with the known existence of Middle Pleistocene Homo groups living in Africa around 800,000 years ago, while the super-archaic lineage’s timing aligns with Homo erectus populations in Eurasia roughly 1.8 million years ago. Those overlaps are suggestive rather than confirmed identifications.
A Genealogy More Tangled Than a Simple Tree
The findings reinforce a broader shift already underway in how scientists think about human origins. “With ancient DNA from Neanderthals and Denisovans and with these new genealogical methods, we are learning that mixture among human populations has been very pervasive across time, and that this is also likely to be true at ancient time scales,” Moorjani said. “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.”
The study also found that many of these ancient archaic DNA segments cluster in regions of the genome associated with immunity and metabolic function. “This pattern is not entirely surprising,” Moorjani explained. “Adaptation to new pathogens and food sources has been one of the strongest selective pressures in human evolution. Interbreeding with other human groups introduced new genetic variation, providing additional raw material for natural selection. Beneficial variants could then be retained and spread over many generations.”
What Might Come Next
Moorjani hopes that as global genome databases grow more diverse, sampling a broader range of human populations, researchers will be able to detect even fainter signals of additional, still-unidentified lineages. Recovering more Denisovan genomes, of which only one has been published to date, would help sharpen the picture further, and protein sequences recently recovered from Homo erectus fossils could potentially help identify who the super-archaic ancestor actually was.
“I think these new computational methods that allow us to reconstruct genealogical relationships are really the next frontier in this field because they are allowing us to uncover hidden episodes from our past without requiring ancient DNA,” Moorjani said. She also noted that the TRACE method isn’t limited to humans, and should work for reconstructing similarly hidden ancestry across other branches of the tree of life as well.
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