Human evolution (© adrenalinapura – stock.adobe.com)
In a nutshell
- All modern humans share DNA from two ancient populations that split 1.5 million years ago and reunited through interbreeding about 300,000 years ago.
- The genetic mixture is approximately 80% from one ancient population and 20% from another, forming a foundation that all humans share regardless of ethnicity or geography.
- This discovery rewrites our understanding of human evolution, revealing a complex history of separation and reunion that predates the emergence of our species.
CAMBRIDGE, England — Before there was modern humanity, there was a genetic divorce and remarriage that shaped us all. Cambridge University researchers have uncovered evidence that two distinct populations of ancient hominins, separated for over a million years, before reuniting around 300,000 years ago. It’s a missing chapter of evolution that left its mark in the DNA of every human alive today.
This discovery by researchers at the University of Cambridge, published in Nature Genetics, rewrites our understanding of where we all come from. Using innovative computational techniques, they detected genetic patterns that reveal this ancient mixing event, which happened around the time the earliest anatomically modern humans were appearing on Earth.
The Mystery of Our Shared Ancestry
The research team—Trevor Cousins, Aylwyn Scally, and Richard Durbin from Cambridge’s Department of Genetics—created a new computational tool called “cobraa” (coalescence-based reconstruction of ancestral admixture) that detects population separation and mixing events from patterns in our DNA.
Modern humans appear to be a genetic mixture with approximately 80% ancestry from one ancient population and 20% from another. This mixing occurred long before today’s distinct human populations emerged, meaning this particular ancestral combination forms part of the genetic foundation for all human diversity we see today.
“Our research shows clear signs that our evolutionary origins are more complex, involving different groups that developed separately for more than a million years, then came back to form the modern human species,” says Durbin, a computational biologist and professor at Cambridge, in a statement.
This differs from other known mixing events in human history. For example, the interbreeding between Neanderthals and non-African humans occurred roughly 50,000 years ago and affected only specific populations. In contrast, this newly discovered ancient admixture event is part of the genetic heritage of every human on Earth.
Previous research established that modern humans originated in Africa and that different human populations began to diverge from one another roughly 100,000 to 200,000 years ago. This new finding reveals a much deeper structural layer in human ancestry that predates these more recent splits.
Genetic Bottlenecks and Uneven Distribution
An unexpected finding emerged from their analysis. Immediately after the two populations split around 1.5 million years ago, the researchers spotted signs of a severe bottleneck—a sharp reduction in population size—in the population that would later contribute the majority (80%) of modern human ancestry. This bottleneck would have drastically cut genetic diversity in this lineage.
The genetic material from the minority population (contributing 20% of our ancestry) isn’t evenly distributed across the genome either. It tends to be located farther from genes, hinting that natural selection favored the majority population’s genetic material in functionally important regions.
“We inferred regions of the present-day genome derived from each ancestral population, finding that material from the minority correlates strongly with distance to coding sequence, suggesting it was deleterious against the majority background,” the authors note.
The team also found a telling connection between regions derived from the majority ancestral population and patterns of genetic divergence between humans and our cousins, the Neanderthals and Denisovans. This connection indicates the majority population was also the main ancestral population to these archaic humans.
Fossil Identification
Who exactly were these two ancient populations? The fossil record shows several human-like species existed around 1.5 million years ago, including different populations of Homo erectus and later Homo heidelbergensis. The researchers propose the bottleneck they detected in the majority lineage might represent a founder event connected to migration and physical separation.
“What’s becoming clear is that the idea of species evolving in clean, distinct lineages is too simplistic,” notes Dr. Cousins. “Interbreeding and genetic exchange have likely played a major role in the emergence of new species repeatedly across the animal kingdom.”
To verify their discoveries weren’t just artifacts of their methodology, the researchers applied their model to data from other species—bats, dolphins, gorillas, and chimpanzees. The results varied considerably, with some species showing little evidence of ancient structure while others showed completely different patterns. This variation across species strengthens the credibility of the specific pattern found in humans.
The researchers also examined which genes had unusually high or low amounts of ancestry from the minority population. Genes rich in minority ancestry often had functions related to neural development, including neuron cell connections, startle response, and neurotransmitter transport.
Conversely, genes with little minority ancestry were often involved in RNA processing, cell structure organization, and immune functions. These patterns hint that the two ancestral populations may have adapted to different environments before reuniting, with certain genetic variants from each population offering advantages for specific biological functions.
A New Chapter in Human Evolution
This discovery joins other recent findings showing human evolution is more complex than we once thought. Rather than populations simply splitting from one another in a tree-like pattern, human evolution increasingly appears to involve repeated separation and remixing of populations.
The admixture event identified in this study is much older than previously detected interbreeding events, such as those between modern humans and Neanderthals or between modern humans and a proposed “ghost population” in West Africa. Unlike these more recent events that affected only certain human populations, the ancient admixture event described here is shared by all humans.
“The fact that we can reconstruct events from hundreds of thousands or millions of years ago just by looking at DNA today is astonishing,” says Scally. “And it tells us that our history is far richer and more complex than we imagined.”
Paper Summary
Methodology
The Cambridge team developed “cobraa” to analyze DNA patterns. This tool examines how genetic similarities and differences are distributed across an individual’s genome. When comparing two copies of a chromosome, the time since their common ancestor varies along the chromosome due to past recombination events (when chromosomes exchange genetic material during reproduction). By studying these patterns, researchers can reconstruct population history. The breakthrough came when the team showed that even when structured models (separate populations) and unstructured models (continuous population) produce the same average rates of genetic similarity, they differ in how similarity patterns transition from one location to another along the genome. The team built a mathematical model to detect these differences and applied it to high-quality genome sequences from 26 individuals representing diverse populations from the 1000 Genomes Project and Human Genome Diversity Project.
Results
The analysis showed clear evidence of an ancient split about 1.5 million years ago followed by mixing around 300,000 years ago. This structured model fit the data better than models assuming a continuously mixed population. About 80% of modern human ancestry comes from one ancient population (population A) and 20% from the other (population B). The team also found a dramatic bottleneck in population A right after the split. To figure out which parts of our genome came from each ancestral population, the researchers extended their model to track ancestry at each position. Regions from the minority population (B) tended to be farther from genes, suggesting selection against this genetic material over time. Regions from the majority population (A) showed less difference when compared to Neanderthal and Denisovan DNA, indicating population A was also ancestral to these archaic humans.
Limitations
The researchers acknowledge their model simplifies what was likely a more complex evolutionary history. Even focusing just on older events shared by all humans, our actual past was probably more complicated than the clean split-and-mix model they used. Their analysis also assumes no selection and consistent mutation and recombination rates across the genome, which we know isn’t true. However, previous studies show that realistic variation in mutation and recombination rates doesn’t significantly affect this type of analysis. Technical issues prevented them from applying their method to available Neanderthal and Denisovan data, limiting their ability to directly test hypotheses about relationships between these ancient populations and the two ancestral groups they identified.
Discussion and Takeaways
This discovery adds a deeper layer to our understanding of human origins. While we knew modern humans originated in Africa and spread worldwide, this finding reveals complexity in our evolutionary history that predates the emergence of distinct human populations. The admixture event identified is shared by all modern humans, meaning it happened before today’s population diversity emerged. The uneven distribution of DNA from the two ancestral populations suggests natural selection has shaped our genome since the mixing event, with certain functional regions favoring genetic material from one population over the other. The researchers wonder which fossil species might match the two ancestral populations, noting various Homo erectus and Homo heidelbergensis groups existed during this period. The bottleneck in the majority population after splitting might represent a founder event linked to migration. Their model fits genetic patterns across all human populations, including the San people of southern Africa, who have the most divergent ancestry among living humans.
Funding and Disclosures
The research received funding through a Wellcome Postgraduate Studentship (108864/B/15/Z) for Trevor Cousins and a Wellcome Investigator Award (207492/Z/17/Z) for Richard Durbin. The funders weren’t involved in study design, data collection and analysis, publication decisions, or manuscript preparation. The authors reported no competing interests.
Publication Information
The study, “A structured coalescent model reveals deep ancestral structure shared by all modern humans,” was published in Nature Genetics on March 18, 2025. The research team included Trevor Cousins, Aylwyn Scally, and Richard Durbin from the Department of Genetics at the University of Cambridge, UK. The paper is available online at https://doi.org/10.1038/s41588-025-02117-1.
