Ancient Genetic Discovery Challenges Single-Lineage Theory of Human Origins

[Micael]

Another piece to the puzzle, but accompanied by more questions. One day we’ll figure out enough details to paint a clear picture of our origins. I hope.

Ancient Genetic Discovery Challenges Single-Lineage Theory of Human Origins

The evolutionary path of modern humans is more complex than previously thought, as new evidence suggests an ancient human ancestral population split into two separate groups that eventually reunited.

According to a new genome sequence analysis conducted by the University of Cambridge, these ancient populations split around 1.5 million years ago before diverging genetically and then reconnecting roughly 300,000 years ago. The modern humans that first arose in Africa between 200,000 and 300,000 years ago were not an even mix, though, as one of these ancestral populations donated 80% of the current genome.

The Origin of Modern Humans

“The question of where we come from is one that has fascinated humans for centuries,” said lead author Dr Trevor Cousins of Cambridge’s Department of Genetics. “For a long time, it’s been assumed that we evolved from a single continuous ancestral lineage, but the exact details of our origins are uncertain.”

Previous genetic studies identified early modern humans intermixing with Neanderthals and Denisovans 50,000 years ago, with modern descendants receiving about 2% of their genetic material from those now-extinct cousins. Despite that limited intermixing, it had long been assumed that modern humans had primarily descended from a single lineage out of Africa.

The new research shows “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,” said co-author Professor Richard Durbin, also of Cambridge’s Department of Genetics.

Global Genetic Sequencing

Instead of sequencing ancient remains, the Cambridge team worked with modern human DNA from the 1000 Genomes Project. That project collected DNA sequences from around the world between 2008 and 2015, creating the most detailed catalog of human genetics. The benefit of such an approach is that it provides the most precise picture of what populations contributed to human genetics, as both preservation and discovery of ancient human remains hold a significant element of chance, with many groups leaving no remaining traces.

Researchers on the project created an algorithm called Cobraa to model how ancient humans diverged into separate populations, which later mingled. The team also discovered notable differences in the two populations shortly after the split.

Geneticists Explain Modern Humans

“Immediately after the two ancestral populations split, we see a severe bottleneck in one of them—suggesting it shrank to a very small size before slowly growing over a period of one million years,” said co-author Professor Aylwyn Scally, of Cambridge’s Department of Genetics.

“This population would later contribute about 80% of the genetic material of modern humans, and also seems to have been the ancestral population from which Neanderthals and Denisovans diverged,” Scally added.

“However, some of the genes from the population which contributed a minority of our genetic material, particularly those related to brain function and neural processing, may have played a crucial role in human evolution,” said Cousins.

The study intriguingly found that the first population locked the incoming genes from the second population away from part of the genome linked to gene function, treating the new genes like harmful mutations and suggesting problematic genetic compatibility.

Identifying the two groups of ancestral humans remains to be done, although the team has some clues. Fossil evidence shows that Homo Erectus and Homo heidelbergensis both occupied Africa and other areas during the correct timeframe. However, further research into the fossil record will be required before an identification can be made.

Continuing Evolutionary Studies

The unusual discoveries illustrate how the Cobraa algorithm could be applied to study evolution in other species, like human primates, but even species as far removed from humans as bats or dolphins.

“What’s becoming clear is that the idea of species evolving in clean, distinct lineages is too simplistic,” said Cousins. “Interbreeding and genetic exchange have likely played a major role in the emergence of new species repeatedly across the animal kingdom.”

While Cobraa has proven adept at identifying sharp splits, the Cambridge team is refining its model to detect more gradual genetic changes. Additionally, they plan to correlate their work to fossil evidence and other anthropological discoveries to investigate ancient human diversity more closely.

“The fact that we can reconstruct events from hundreds of thousands or millions of years ago just by looking at DNA today is astonishing,” said Scally. “And it tells us that our history is far richer and more complex than we imagined.”

The paper “A structured Coalescent Model Reveals Deep Ancestral Structure Shared by All Modern Humans” appeared on March 18, 2025, in Nature Genetics.

Ryan Whalen covers science and technology for The Debrief. He holds an MA in History and a Master of Library and Information Science with a certificate in Data Science. He can be contacted at ryan@thedebrief.org, and follow him on Twitter @mdntwvlf.

[jemhouston]

Fascinating doesn't do it justice.

[kdahm]

This is more or less expected, given the fuzziness on deciding when a species has diverged far enough to be called a species and the hominid propensity to screw anything that doesn't move fast enough. If offspring are possible among a braid of similar populations, they will occur. If it happens often enough, there will be merging. The timing is interesting, though.