A Mysterious 'Population B' Split From Humans 1.5 Million Years Ago—and Its DNA Is Still Inside You

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20-03-2025

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Using a new method of modeling genetic data, researchers identified a split in human ancestry dating back 1.5 million years. The two populations later reconnected.
The mystery population (Population B) could make up as much as 20% of the modern human genome.
Genes from Population B may have improved human brain function, researchers suggest.
Research on evolution is... well... ever-evolving, to say the least. According to a study published in the journal Nature Genetics, a new method of modeling genomic data recently identified a split in modern human (Homo sapien) ancestry. The split occurred over 1.5 million years ago, when the ancestor of modern humans split off from an unknown population. The two groups eventually re-converged, and the mystery population may have increased our brain function, the study suggests.
'The question of where we come from is one that has fascinated humans for centuries,' Trevor Cousins, first author of the study, said in a statement. '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.'
The study used new modeling techniques to analyze vast amounts of data from both the 1000 Genome Project and the Human Genome Diversity Project. In the end, two ancestral populations emerged, which researchers inventively called Population A and Population B. Once the groups split (remember, just a short 1.5 million years ago), the study found that Population A experienced a 'bottleneck,' or a drastic drop in population size and genetic diversity. Population A eventually recovered, however, and groups like the Neanderthal and Denisovans branched off from it.
Researchers estimate the two populations re-converged around 300,000 years ago. Genetic analysis suggests that Population A contributed roughly 80% of modern humans' genome, and Population B makes up around 20%. This genetic mixing is especially significant in comparison to other instances of interbreeding. For instance, prior research has shown that Neanderthals mixed with Homo sapiens around 50,000 years ago. But Neanderthal DNA makes up less than 2% of the modern human genome.
Interestingly, the genes that Population B contributed—especially 'those related to brain function and neural processing'—could have played a crucial role in human evolution, according to Cousins. Notably, Population B's genetic material decreased individuals' ability to have children, but 'the genome is a complicated place, and regions outside of genes can still do important things,' Cousins told Live Science.
Unfortunately, researchers were unable to run their models on available Neanderthal and Denisovans data sets, which continues to be an ongoing research challenge.
'The fact that we can reconstruct events from hundreds of thousands or millions of years ago just by looking at DNA today is astonishing,' Aylwyn Scally, co-author on the study, said in the statement. 'And it tells us that our history is far richer and more complex than we imagined.'
Outside of just human history, the team suggests that their findings could help contribute to our understanding of evolution more broadly.
'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.'
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