A new genetic model suggests that the ancestors of all modern humans split from a mysterious population 1.5 million years ago, only to reunite with them about 300,000 years ago. This unknown group contributed 20% of our genome and may have played a crucial role in enhancing brain function.
Unlocking Evolution Through the Genome
"The fact that we can reconstruct events from hundreds of thousands or even millions of years ago just by examining DNA today is astonishing," said Aylwyn Scally, a geneticist at the University of Cambridge and co-author of the study. "It tells us that our history is far richer and more complex than we ever imagined."
The study, published in Nature Genetics on March 18, introduced a new genetic modeling method called "cobraa," which allowed researchers to trace the evolutionary history of modern humans (Homo sapiens).
By applying this method to DNA data from the 1000 Genomes Project and the Human Genome Diversity Project, the team identified two major ancestral groups that split about 1.5 million years ago. They labeled these groups Population A and Population B.
Shortly after this split, Population A underwent a drastic decline, likely losing significant genetic diversity. Over time, however, it rebounded, eventually giving rise to Neanderthals and Denisovans. Then, around 300,000 years ago, Population A reconnected with Population B, contributing to the genetic makeup of modern humans.
Their findings indicate that approximately 80% of the modern human genome comes from Population A, while 20% can be traced back to Population B.
The Influence of Population B on Human Brain Development
Some of the genes inherited from Population B—particularly those linked to brain function and neural processing—may have played a vital role in human evolution, according to study co-author Trevor Cousins, a genetics researcher at the University of Cambridge.
Interestingly, while genetic material from Population B may have slightly reduced reproductive success, Cousins pointed out that "the genome is a complex space, and even non-coding regions can have significant effects."
The study also noted that early human species such as Homo erectus and Homo heidelbergensis, which lived in Africa and beyond during this critical period, are potential candidates for Populations A and B. However, the genetic model alone cannot determine which fossils belong to which group.
"Phantom Populations" in Human Evolution
Some researchers refer to such groups as "phantom populations"—ancestral groups that diverged and later reconnected, leading to gene flow between them.
"What’s fascinating about this study is that the pattern in the model suggests a deep African structure that is common to all modern humans," said John Hawks, a biological anthropologist at the University of Wisconsin-Madison, who was not involved in the study.
"These aren’t just isolated phantom populations contributing to specific groups; rather, they represent a significant portion of genetic material that merged into the African population from which all modern humans emerged."
However, Hawks pointed out a limitation of the model: it relies on the 1000 Genomes Project, which underrepresents African populations. "I see this more as proof of concept rather than a definitive guide to ancient human history," he explained.
Rethinking Human Origins
The origins of modern humans remain one of the most debated topics in paleoanthropology. Advances in DNA and genome analysis over the past two decades have provided new insights—while also raising new questions.
"What’s becoming increasingly clear is that the idea of species evolving in clean, distinct lineages is far too simplistic," said Cousins. "Interbreeding and genetic exchange likely played a major role in the emergence of new species across the animal kingdom, including in our own evolutionary past."
