Lauren Fuge
Modern humans may have descended from at least two ancestral populations, which diverged 1.5 million years ago and then reconnected 300,000 years ago.
Up until now, evidence has suggested that Homo sapiens descended from a single lineage, with some genetic mixing with two extinct human relatives (Neanderthals and Denisovans) around 50,000 years ago. But the story may have a hidden chapter – one that contains more substantial genetic mixing earlier on.
“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 Richard Durbin from Cambridge’s Department of Genetics, co-author of the new study in Nature Genetics.
The paper finds evidence for a genetic mixing event between two separate populations, which split about 1.5 million years ago and then mixed again about 300,000 years ago.
This result is based on an analysis of the full genome sequence of modern human DNA – not from ancient DNA (the extraction of genetic material from ancient specimens). The team developed an algorithm that modelled how human populations diverged and came back together, and first tested it with simulated data.
When they applied it to real data drawn from the 1000 Genomes Project, which has sequenced DNA from humans across multiple continents, they found evidence for two ancestral populations.
“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 co-author Aylwyn Scally, also from Cambridge. “And it tells us that our history is far richer and more complex than we imagined.”
Their findings also showed an unexpected bottleneck.
“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,” says Scally. “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.”
The other population contributed about 20% of the genetic material of modern humans.
Yassine Souilmi, researcher at the Australian Centre for Ancient DNA at the University of Adelaide, says these findings are “consistent with existing fossil evidence and timelines inferred using other genetic methods”.
“The manuscript represents a major methodological advancement in DNA-based demographic history reconstruction,” says Souilmi, who was not involved in the research.
However, he adds, while the method seems to match the available fossil evidence, “it likely under-estimates the real complexity of the events that occurred that far back in time”.
Palaeontologist Giorgio Manzi of Sapienza University of Rome, who was also not involved in this study, draws attention to the complexity of our origins too.
He points back to the 1987 Nature paper that pioneered using a coalescence approach to the origins of our species – that is, a method that traces populations back through time using DNA to find their most recent common ancestor.
“Much has been done since then and the new interesting work … is an important step along this path, showing that the phenomenon was much more complex than a simple bottleneck event,” Manzi says.
“The molecular data must, however, be combined with the prehistoric and paleoanthropological ones, involving the emergence of a new biological model. I believe this is represented by the first appearance in the fossil record of the globular form of the cranium (with all its cascading effects), which current data indicate occurred in East Africa about 250 thousand years ago.”
Another outstanding question is who these two ancestral populations were. Potential candidates include Homo erectus and Homo heidelbergensis, though more evidence is needed in order to make a link.
The Cambridge team also applied the algorithm to genetic data from gorillas, chimps, dolphins and bats, to try and understand their deep histories.
“What’s becoming clear is that the idea of species evolving in clean, distinct lineages is too simplistic,” says Cambridge’s Trevor Cousins. “Interbreeding and genetic exchange have likely played a major role in the emergence of new species repeatedly across the animal kingdom.”