For years, scientists have known that modern humans carry genetic traces from Neanderthals and Denisovans—two now-extinct relatives with whom our ancestors interbred tens of thousands of years ago. But a groundbreaking series of studies published July 30 and 31, 2026, in Science has revealed a startling new twist: our DNA also harbors hidden fragments from two other, entirely unknown ancient human lineages. These mysterious ancestors, dubbed the “ghost” and “super-archaic” lineages, have left their mark on the genetic tapestry of people alive today, deepening our understanding of human evolution as a story of tangled roots, not simple branches.
According to the University of California, Berkeley, the story began with a puzzle. While Neanderthal and Denisovan DNA could be identified in modern genomes by comparing them to sequenced remains, there were hints of even older, unaccounted-for DNA segments. The challenge was clear: how could researchers detect ancient genetic contributions from extinct populations for which we have no fossils or sequenced genomes? The answer came in the form of a new computational method called TRACE (TRacking Archaic Contributions via ARG Estimation), developed by a team led by Berkeley’s Priya Moorjani.
TRACE works by analyzing hundreds of modern human genomes from around the world, reconstructing the ancestral recombination graph (ARG) that maps how DNA segments are related over time. By identifying stretches of DNA whose ancestry extends much further back than the rest, the method can spotlight genetic contributions from archaic hominins—even in the absence of ancient DNA. As Moorjani explained in a press release, “Genealogies preserve a record of our evolutionary past. 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 team first validated TRACE by showing it could reliably detect known Neanderthal and Denisovan segments. But when they turned to regions that didn’t match either group, the true surprise emerged. They discovered two distinct patterns of ancient DNA, each pointing to a separate, previously unidentified lineage.
The first, known as the “ghost” ancestor, interbred with the ancestors of all modern humans in Africa more than 50,000 years ago—before Homo sapiens began their final migration out of Africa. This ghost lineage split from the modern human line about 800,000 to 830,000 years ago, roughly the same time Neanderthals and Denisovans diverged from each other. Its genetic legacy persists in every human population examined, accounting for about 0.5 to 1.1 percent of the modern human genome, remarkably similar to the amount of Neanderthal DNA most people carry today. As Yulin Zhang, a Berkeley graduate student and co-first author, put it, “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.”
What’s more, ghost DNA was found in regions of the genome previously thought to be exclusively modern human, such as a segment containing the FOXP2 gene, which is involved in speech and language. According to Discover Magazine, this finding challenges assumptions about what made Homo sapiens unique and suggests that even genes tied to our defining traits have a more complicated history than once believed.
The second mysterious ancestor, called the “super-archaic” lineage, is even older. It separated from our lineage around 1.8 million years ago and interbred with Denisovans in Eurasia more than 200,000 years ago. Some of this super-archaic DNA then entered modern human genomes via Denisovan interbreeding. The researchers found that Denisovans carry between 3 and 5 percent super-archaic ancestry, though only a small fraction—about 0.3 percent—made its way into Homo sapiens, especially in populations from Oceania, who have the highest levels of Denisovan DNA. Arjun Biddanda, a postdoctoral researcher at Johns Hopkins University and co-first author, described the significance: “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.”
Neither the ghost nor the super-archaic ancestors have been identified in the fossil record. The ghost lineage’s divergence overlaps with Middle Pleistocene Homo groups in Africa, such as Homo heidelbergensis, while the super-archaic ancestor may be related to Homo erectus in Eurasia, but the connection remains unconfirmed. As UC Berkeley News reported, “Though it’s unclear who these ghost and super-archaic ancestors were, the inferred divergence time overlaps with the existence of Middle Pleistocene Homo groups in Africa 800,000 years ago and Homo erectus in Eurasia 1.8 million years ago, respectively.”
The impact of these ancient encounters is more than academic. Many of the archaic DNA segments are enriched in regions linked to immunity and metabolism, suggesting that interbreeding may have provided adaptive advantages as early humans encountered new diseases and food sources. As Moorjani noted, “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.”
Interestingly, some ghost segments appear in parts of the genome previously labeled as “Neanderthal and Denisovan deserts”—regions thought to be uniquely modern human. This raises the possibility that selection acted against Neanderthal and Denisovan DNA in these regions, but not against other archaic contributions. The FOXP2 region is a striking example, where ghost ancestry was found in about 13 out of every 100 copies analyzed, according to Discover Magazine.
The findings upend the traditional view of human evolution as a tidy, branching tree. Instead, the evidence points to a “complex web of populations connected by repeated episodes of migration and mixing,” as Moorjani put it. Early modern humans, Neanderthals, Denisovans, and other hominins lived side by side for millennia, close enough—genetically and geographically—to have children together. Their legacies are still written in our DNA.
The research was a collaborative effort involving UC Berkeley, Johns Hopkins University, and other institutions, and was funded by the National Science Foundation. The study’s authors hope that as more diverse genomes are sequenced from around the world, additional hidden lineages may be identified. Protein sequences recently recovered from Homo erectus fossils could also shed light on the identity of the super-archaic ancestor.
“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. TRACE may even help reveal similar patterns in other species, opening new windows onto the tangled branches of the tree of life.
As the mysteries of our ancient ancestry continue to unravel, one thing is clear: the story of Homo sapiens is richer and more interconnected than ever imagined, shaped by encounters with relatives we are only just beginning to meet.