New research has uncovered genetic traces of two previously unidentified human ancestor lineages, offering a breakthrough in understanding our evolutionary history. While scientists have long known that Homo sapiens interbred with extinct relatives like Neanderthals and Denisovans, other ancestral groups have remained elusive. These so-called “ghost” lineages have left no fossilized DNA for direct comparison, making them difficult to identify until now.
A study By analyzing more than 500 modern human genomes from Africa, Europe, and Asia, the team identified evidence of two distinct, unknown ancestral groups. One lineage appears to have interbred directly with Homo sapiens in Africa more than 50,000 years ago, while the other is a much older group that contributed DNA to humans indirectly through Denisovans.
Priya Moorjani, a study coauthor and associate professor of molecular and cell biology at the University of California, Berkeley, noted that these genealogies provide an unprecedented window into the past. “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,” she said. Understanding these genetic contributions helps explain how early humans adapted to their environments and why certain health conditions persist today.
The more recent ghost lineage, which interbred with humans in Africa before the major migration out of the continent 50,000 years ago, accounts for approximately 0.5% to 1% of the genomes of people living today. This percentage is comparable to the amount of Neanderthal DNA found in many modern populations. Researchers suggest this lineage may be linked to Middle Pleistocene Homo populations in Africa, potentially Homo heidelbergensis, which existed between 700,000 and 200,000 years ago.
The second, “super-archaic” lineage is significantly older, tracing back to a branch of the human family tree that diverged roughly 1.8 million years ago. This group likely interbred with Denisovans in Eurasia more than 200,000 years ago, with their genetic material eventually reaching modern humans through subsequent interbreeding. Arjun Biddanda, a postdoctoral researcher at Johns Hopkins University and co-first author of the study, highlighted the significance of this finding: “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.”
The TRACE method functions by mapping how different segments of DNA were inherited, effectively identifying “mosaics” of ancestral history within our own genetic code. As study co-first author Yulin Zhang, a doctoral student at UC Berkeley, explained, the method reveals shared ancestry that was previously invisible. “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. From this mysterious ancestor, we have something in common from another angle,” Zhang said.
Paleoanthropologist John Hawks of the University of Wisconsin–Madison, who was not involved in the research, emphasized that while modern humans may appear different on the surface, these deep ancestral lineages underscore our shared genetic heritage. He noted that the discovery of the younger ghost lineage confirms that interbreeding occurred well before the well-documented mixing with Neanderthals and impacts all current human populations. The research team intends to apply the TRACE method to further investigate hidden lineages across both human and other animal species, potentially uncovering more secrets hidden within the genome. The report also notes that clues emerging from DNA could unlock the mystery of human ancestors that are missing from the fossil record yet present in the genes of people living today. The report also notes that because — unlike Neanderthals and Denisovans, whose DNA has been recovered from prehistoric remains — they are essentially genetic “ghosts,” with no DNA proof of their existence to compare with the hints spotted in our genomes, but some lineages have been difficult to identify. The report also notes that the researchers reported their findings July 30 in the journal Science. The report also notes that however, the newly detected lineages add more to the story. The report also notes that for example, sits on these deeper branches, dNA inherited from ancient relatives such as Neanderthals. The report also notes that “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.