For decades, the story of modern human origins seemed relatively straightforward: Homo sapiens emerged in Africa roughly 300,000 years ago, evolving as a single, continuous lineage before expanding across the globe. But new research suggests that this narrative is missing an entire chapter.
A study published in Nature Genetics1 by Trevor Cousins, Aylwyn Scally, and Richard Durbin of the University of Cambridge proposes that modern humans did not descend from a single population, but rather from two deeply divergent ancestral groups. These two populations split approximately 1.5 million years ago and remained separate for over a million years before mixing again around 300,000 years ago. One of these groups contributed about 80% of modern human DNA, while the other—now vanished—left a genetic imprint making up the remaining 20%.
"Rather than a single lineage evolving smoothly over time, the evidence suggests a history of separation and recombination," says Cousins. "These groups were apart for a million years—longer than modern humans have been on the planet."
This discovery complicates the long-held assumption that our species emerged from a single, unbroken line of ancestors. It also raises new questions about which fossil hominins—such as Homo erectus and Homo heidelbergensis—might represent these lost populations.
A Hidden Population, a Vanished Legacy
What makes this finding particularly striking is that this ancient genetic mixing event is not just a curiosity of the distant past. It is present in every modern human population, across Africa, Europe, Asia, and the Americas.
Unlike the more familiar interbreeding episodes with Neanderthals and Denisovans—events that contributed only about 2% of the DNA in non-African populations—this deeper ancestral mixture accounts for ten times that amount. And yet, until now, it had remained invisible in our understanding of human evolution.
The researchers made this discovery not by analyzing ancient bones but by studying the DNA of living people. Using data from the 1000 Genomes Project, they applied a computational model called cobraa (Coalescence-Based Reconstruction of Ancestral Admixture), which allowed them to detect subtle genetic signals left by ancient populations. This approach circumvents the need for physical fossils, offering a way to reconstruct population history even when no bones or artifacts remain.
A Genetic Bottleneck and the Fate of Our Ancestors
One of the study’s most intriguing findings is that, immediately after the initial split 1.5 million years ago, one of the two populations went through a severe genetic bottleneck. This group shrank to a tiny size before slowly recovering. Over time, this population eventually gave rise to the majority of Homo sapiens ancestry, as well as to Neanderthals and Denisovans.
"This population bottleneck could be the result of an ecological crisis, a migration event, or simply chance," says Scally. "What’s remarkable is that despite its small size, this group ultimately shaped most of our genetic heritage."
The other group—whose genes now make up the remaining 20% of modern human DNA—appears to have remained larger but was eventually absorbed into the expanding Homo sapiens population.
Interestingly, the researchers found that genetic material from this secondary group tended to be located away from functionally important regions of the genome, suggesting that some of its DNA may not have been fully compatible with the majority genetic background. This pattern hints at a process called purifying selection, in which harmful mutations are gradually removed from a population over time.
Who Were These Lost Ancestors?
This discovery invites a crucial question: If these two populations remained separate for over a million years, what did they look like? Were they physically distinct, akin to separate species? And do they correspond to any known hominin fossils?
Fossil evidence suggests that Homo erectus was widespread across Africa and Eurasia throughout this period. Other species, such as Homo heidelbergensis, also inhabited Africa and Europe. Either of these groups—or even an as-yet-undiscovered lineage—could be the long-lost ancestors detected in this study.
"These populations were likely distinct in ways we don’t yet understand," says Durbin. "We may find fossils that match their genetic legacy, or we may already have them but lack the tools to identify their role in our ancestry."
If this ancient mixing event is confirmed through further research, it could reshape how we classify and think about human evolutionary history. Rather than a single lineage, our origins may have been more like a braided stream—separate currents that merged over time.
Rethinking Species Boundaries in Human Evolution
The idea that modern humans emerged from multiple ancestral populations aligns with a broader shift in how biologists think about evolution. Increasingly, researchers are finding that species do not always evolve in neat, separate branches but often exchange genes across long periods.
"What’s becoming clear is that species don’t evolve in isolation," Cousins explains. "Interbreeding and genetic exchange have likely played a role in the emergence of new species across the animal kingdom, not just in humans."
This study also suggests that similar events may have occurred in other species. The researchers applied their method to genetic data from bats, dolphins, chimpanzees, and gorillas, and found evidence of deep ancestral structure in some of these species as well.
What Comes Next?
With this new model of human origins, researchers now have a fresh set of questions to explore. What conditions allowed these populations to remain separate for so long? What finally brought them back together? Did their reunion contribute to the development of cognitive traits that define modern humans?
To refine these findings, scientists may turn to ancient DNA—if they can find it. Fossils from the crucial period around 300,000 years ago could hold traces of these lost ancestors, offering a direct genetic link to the populations detected in modern DNA.
"The fact that we can reconstruct events from hundreds of thousands or even millions of years ago, just by looking at DNA today, is astonishing," says Scally. "It tells us that our history is far richer and more complex than we ever imagined."
Conclusion
The story of human origins is still being written. As researchers develop new genetic tools and unearth new fossils, the narrative continues to shift. What this study makes clear is that Homo sapiens did not emerge from a single lineage but from the reunion of two deeply ancient populations—distant relatives who came together to form the species that would eventually inhabit every corner of the planet.
If this discovery holds, it could reshape how we define what it means to be human—not as the product of a linear march of progress, but as the outcome of ancient migrations, genetic exchanges, and lost populations that shaped our species in ways we are only beginning to understand.
Additional Related Research
Skoglund, P., & Reich, D. (2020). Ancient DNA and the new science of the human past. Nature, 577, 645–656. https://doi.org/10.1038/s41586-019-1863-2
Hublin, J. J., et al. (2017). "New fossils from Jebel Irhoud, Morocco and the pan-African origin of Homo sapiens." Nature, 546(7657), 289–292.
DOI: 10.1038/nature22336
This study presents evidence from Moroccan fossils suggesting that H. sapiens had a more widespread African origin than previously believed.
Ragsdale, A. P., et al. (2023). "A weakly structured stem for human origins in Africa." Nature, 617(7962), 755–763.
DOI: 10.1038/s41586-023-06184-w
Supports deep population structure within Africa, indicating H. sapiens arose from multiple interconnected groups rather than a single lineage.
Reich, D., et al. (2010). "Genetic history of an archaic hominin group from Denisova Cave in Siberia." Nature, 468(7327), 1053–1060.
DOI: 10.1038/nature09710
First genomic analysis of Denisovans, showing they contributed DNA to modern human populations.
Terhorst, J., et al. (2017). "Robust and scalable inference of population history from hundreds of unphased whole genomes." Nature Genetics, 49(2), 303–309.
DOI: 10.1038/ng.3748
Develops computational tools to analyze population splits and admixture in human evolution.
Cousins, T., Scally, A. & Durbin, R. A structured coalescent model reveals deep ancestral structure shared by all modern humans. Nat Genet (2025). https://doi.org/10.1038/s41588-025-02117-1
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