New technique pinpoints human DNA inherited from 'ghost' ancestors

A team of researchers from UC Berkeley has identified regions of human DNA that originated from two previously unknown ancestral populations, revealing evidence of interbreeding between early modern humans and archaic hominins that left no sequenced genomes behind. The discovery, made using a novel method called TRACE, highlights how modern humans inherited genetic material from these so-called “ghost” ancestors, whose identities remain uncertain. The findings suggest that interbreeding occurred far earlier than previously thought and involved multiple hominin groups across Africa and Eurasia. The study, published in Science on July 30, used genealogical relationships within modern human genomes to detect traces of DNA from these unknown ancestors. One of the ghost lineages interbred with modern humans in Africa more than 50,000 years ago, before the major migration out of the continent. This genetic contribution accounts for approximately 1% of the modern human genome, similar to the proportion of Neanderthal DNA found in contemporary humans. The lineage diverged from the modern human line roughly 800,000 years ago, around the same time Neanderthals and Denisovans split off from the human family tree. Another discovery involves a super-archaic ancestor, a hominin group that existed nearly 1.8 million years ago. This lineage interbred with Denisovans in Eurasia, and its genetic legacy eventually reached modern humans through subsequent interbreeding with Homo sapiens. Researchers noted that this finding is especially significant because it demonstrates that genetic contributions can persist even when no direct fossil or sequenced DNA from the original population exists. Yulin Zhang, a graduate student at UC Berkeley and one of the lead authors of the study, emphasized that while earlier studies hinted at the presence of such ghost ancestry, this research definitively mapped specific genomic regions inherited from these unknown lineages. Importantly, the study showed that this genetic influence is not limited to African populations but is present in all modern humans worldwide. Arjun Biddanda, a postdoctoral researcher at Johns Hopkins University and co-author of the paper, described the super-archaic finding as particularly exciting. He explained that the genetic contributions come from a lineage that predates the emergence of known hominin species, yet its impact can still be detected in today’s human genome. The researchers speculate that this lineage could be linked to Middle Pleistocene Homo groups in Africa or early Homo erectus in Eurasia, based on estimated divergence times. Priya Moorjani, an associate professor of molecular and cell biology at UC Berkeley, pointed out that the results challenge traditional views of human evolution as a simple branching tree. Instead, she argued that the data support a more complex picture involving frequent migrations and interbreeding among different hominin populations over millions of years. The study suggests that modern humans did not evolve in isolation but interacted extensively with other hominin groups, leading to a deeply interconnected evolutionary history. The TRACE method used in the study relies on analyzing patterns of genetic variation across hundreds of modern human genomes. By identifying unique genealogical relationships, the researchers were able to trace back the origins of certain genetic segments to these unknown ancestors. This approach allows scientists to infer historical interbreeding events even in the absence of direct genetic samples from the extinct populations. The implications of the study extend beyond understanding human ancestry. It provides a framework for uncovering additional genetic contributions from uncharacterized hominin lineages, potentially reshaping our knowledge of human prehistory. As more genomes are analyzed using similar techniques, further insights into the complexity of human evolution are expected to emerge. Researchers plan to refine the TRACE method to explore other potential genetic legacies from unknown hominin groups. They hope to identify additional instances of interbreeding and better understand the genetic diversity shaped by these ancient interactions. Future work will focus on expanding the dataset and applying the method to non-African populations to see if similar patterns exist elsewhere.