New research from the University of Cambridge suggests that modern humans evolved from not just one, but two ancient populations that split more than a million years ago before reuniting in a complex genetic exchange. The findings challenge the long-standing idea that Homo sapiens emerged from a single continuous lineage and instead point to a more intricate ancestry shared by all modern humans.
According to the study, published in Nature Genetics, the modern humans evolved from two ancestral populations that diverged around 1.5 million years ago and came back together roughly 300,000 years ago. One of these ancestral groups contributed about 80% of our genetic makeup, while the other contributed around 20%. Unlike Neanderthal DNA, which makes up just 2% of non-African genomes, this earlier genetic mixture is present in all modern humans across the globe.
Dr Trevor Cousins from Cambridge’s Department of Genetics explained:
“For a long time, it’s been assumed that Homo sapiens evolved from a single African lineage. What we found shows the story is far more layered, involving ancient populations that developed independently before eventually merging.”
The team used a method that doesn’t rely on ancient bones or fossils but instead analyses modern DNA using a new computational tool called cobraa. This allowed them to detect deep ancestral structure by modelling how populations split and reconnected. The data came from the 1000 Genomes Project, which includes diverse genetic samples from around the world.
Their results showed signs of a population bottleneck, one group shrank to a very small size shortly after the initial split, only to grow again over a million years. This same group would later give rise to Neanderthals and Denisovans. The second group, which contributed a minority of the DNA, appears to have played a key role in traits related to brain function, suggesting its legacy might be more significant than the numbers alone imply.
The full study, A structured coalescent model reveals deep ancestral structure shared by all modern humans was co-authored by Professors Aylwyn Scally and Richard Durbin, also of Cambridge. Both are Fellows at Darwin College, where Cousins is a current member.
Speaking about the significance of the findings, Scally said: “The fact that we can use modern DNA to reconstruct genetic events that took place hundreds of thousands of years ago is extraordinary. Our origins are not a straight line. They’re a network, shaped by interbreeding and adaptation.”
The research also has implications beyond human evolution. The team applied the same model to other species, including bats, chimpanzees, and dolphins and found that deep population structure is more common than previously thought, challenging the idea that species evolve in tidy, linear paths.
So who were these ancestral groups that shaped our species? Fossil candidates include Homo erectus and Homo heidelbergensis, both of which lived in and outside of Africa during the relevant period. But with few direct links between fossil finds and genetic evidence, identifying the exact populations may take further breakthroughs.
While studies on Neanderthal and Denisovan DNA have already changed our understanding of recent human history, this new work stretches that story even further back, reinforcing how dynamic and diverse our ancestry truly is. According to Cousins, “some of the genes inherited from the minority group are located in regions of the genome associated with neural activity, hinting at their significance in human evolution.”
For more insights into the ancient structure of our species and updates from the world of genetics and anthropology, visit EyeOnLondon.
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