For decades, the predominant view of human evolution held that Homo sapiens emerged in Africa between 200,000 and 300,000 years ago, descending from a single ancestral lineage. However, recent research from the University of Cambridge has challenged this perspective, suggesting a far more intricate evolutionary history than previously thought.
Based on an advanced analysis of complete genome sequences, scientists have identified evidence of a genetic mixing event between two ancient human populations that had separated approximately 1.5 million years ago.
Later, around 300,000 years ago, these groups met again, giving rise to modern Homo sapiens. From this event, one of the populations contributed 80% of the genetic makeup of present-day humans, while the other contributed the remaining 20%.
According to Dr. Trevor Cousins, lead author of the study and a member of Cambridge’s Department of Genetics, the question of our species’ origins has intrigued humanity for centuries. For a long time, it was assumed that we evolved from a single continuous ancestral lineage, but the specific details of our origins remain uncertain, explains Cousins.
The study, published in the journal Nature Genetics, challenges the traditional hypothesis of a unique and continuous human lineage. Our research provides clear evidence that our evolutionary origins are more complex and involve different groups that developed separately for over a million years before reuniting to shape the modern human species, notes Professor Richard Durbin, co-author of the study.
A Genetic Mixing Event Before Neanderthals and Denisovans
While previous research had already demonstrated that Neanderthals and Denisovans interbred with Homo sapiens around 50,000 years ago, this new finding suggests that a far more significant genetic mixing event occurred about 300,000 years ago. Compared to the Neanderthal DNA contribution—about 2% of the genome of modern non-African humans—this ancestral event provided up to ten times more genetic material and is present across all of humanity.
The researchers employed a novel method based on analyzing the DNA of living individuals instead of extracting genetic material from ancient skeletal remains. Using data from the 1000 Genomes Project—a global effort to sequence the DNA of populations from Africa, Asia, Europe, and the Americas—they inferred the existence of these ancestral populations, which may not have left obvious physical traces.
To model these complex patterns of divergence and recombination, the team developed a computational algorithm called “cobraa.” This tool allowed them to reconstruct human evolutionary history from modern genetic data, detecting the timing and magnitude of separations and fusions among prehistoric human populations.
Immediately after these two ancestral populations separated, one of them experienced an extreme genetic “bottleneck”—meaning its population size drastically declined before gradually recovering over a million years. This population, which eventually contributed 80% of modern human DNA, also appears to have been the source from which Neanderthals and Denisovans evolved, explains Professor Aylwyn Scally, co-author of the study.
Additionally, the researchers observed that genes inherited from the second ancestral population tend to be located far from genomic regions associated with essential functions. This phenomenon suggests that some of these genes may have been less compatible with the rest of the human genetic material, possibly indicating a process of purifying selection, in which evolution gradually eliminates harmful mutations over time.
However, certain genes from this minority population appear to have played a crucial role in human evolution. Some of these genes are related to brain functions and neural processes, suggesting they may have influenced the development of advanced cognitive abilities, adds Cousins.
The researchers also applied the cobraa model to genetic data from other species, such as bats, dolphins, chimpanzees, and gorillas. The results indicated that while some species have followed cleaner, more distinct evolutionary lines, in other cases, genetic interactions and mixing events similar to those detected in humans occurred.
It is becoming increasingly evident that the idea of species evolving in pure, well-defined lineages is overly simplistic, says Cousins. Genetic exchange between groups may have played a key role in the emergence of new species throughout natural history.
Who Were Our Mysterious Ancestors?
The exact identity of these ancestral populations remains uncertain. Fossil records suggest that species such as Homo erectus and Homo heidelbergensis inhabited Africa and other regions during the same period, making them possible candidates for these ancient genetic populations. However, further studies will be needed to precisely determine which hominin groups correspond to each identified lineage.
The Cambridge team hopes to improve their model in the future by incorporating data that better represents gradual genetic exchanges between populations instead of abrupt separations and reunions. Additionally, they aim to connect their discoveries with recent paleontological findings indicating that early humans may have been far more diverse than previously thought.
It is astonishing that we can reconstruct events from hundreds of thousands or even millions of years ago just by analyzing today’s DNA, concludes Scally. Our history is far richer and more complex than we ever imagined.
SOURCES
Cousins, T., Scally, A. & Durbin, R. A structured coalescent model reveals deep ancestral structure shared by all modern humans. Nat Genet (2025). doi.org/10.1038/s41588-025-02117-1
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