The study, published in Nature in 2023, compared genetic material from present day African populations with fossil evidence from early Homo sapiens populations. The result was a model of human evolution that replaces a clean family tree with something more like a network of deeply connected branches.

A More Complex Beginning in Africa

Scientists broadly agree that Homo sapiens originated in Africa. The harder question is how early human groups separated, moved, reconnected, and shaped one another across the continent.

Brenna Henn, professor of anthropology and the Genome Center at UC Davis and corresponding author of the study, said the uncertainty comes from gaps in both fossils and ancient DNA.

"This uncertainty is due to limited fossil and ancient genomic data, and to the fact that the fossil record does not always align with expectations from models built using modern DNA," she said. "This new research changes the origin of species."

The work was co led by Henn and Simon Gravel of McGill University. Their team tested several competing ideas about human evolution and migration in Africa, drawing from models proposed in paleoanthropology and genetics. The analysis included genome data from southern, eastern and western Africa.

The Nama Genomes Added a Key Clue

A major part of the study came from 44 newly sequenced genomes from modern Nama individuals in southern Africa. The Nama are an Indigenous population known for carrying unusually high levels of genetic diversity compared with many other living groups.

Researchers collected saliva samples from people in their villages between 2012 and 2015, while participants were going about daily life. Those samples helped the team examine whether human origins fit a single source model or something broader and more interconnected.

The best fitting model suggested that the earliest population split among early humans still detectable in living people happened roughly 120,000 to 135,000 years ago. Before that split, two or more weakly differentiated Homo populations had been exchanging genes for hundreds of thousands of years.

Even after the split, movement and mating continued between these early groups. The researchers describe this as a weakly structured stem, meaning the roots of modern humans were not one isolated population, but a loose set of connected populations with ongoing gene flow.

Not One Branch, But a Network

That network like model may explain human genetic diversity better than older models, according to the authors. Instead of needing to assume major contributions from an unknown archaic hominin population in Africa, the model shows how patterns in modern DNA could have emerged from structure within ancestral human populations themselves.

"We are presenting something that people had never even tested before," Henn said of the research. "This moves anthropological science significantly forward."

Co-author Tim Weaver, a UC Davis professor of anthropology who studies early human fossils, said the results shift how scientists should think about older explanations.

"Previous more complicated models proposed contributions from archaic hominins, but this model indicates otherwise," he said.

Weaver contributed comparative fossil expertise to the study, helping connect genetic models with what early human remains looked like.

What This Means for Ancient Fossils

The model also has consequences for how scientists interpret the fossil record. According to the authors, only 1 to 4% of genetic differentiation among living human populations can be traced to variation between these ancestral stem populations.

Because the early branches continued mixing, they were probably similar in appearance. That means fossils with very different physical traits (such as Homo naledi) are unlikely to represent lineages that directly contributed to the evolution of Homo sapiens, the authors said.

In other words, the roots of humanity may have been geographically and genetically widespread, but not necessarily divided into sharply different human forms. The deeper picture is one of movement, contact, and repeated mixing across Africa.

Later Research Adds More Depth

Work published after the 2023 study has continued to show how important African genomic diversity is for understanding human origins. A 2024 Nature Ecology & Evolution study reported 9,000 years of genetic continuity in southernmost Africa, highlighting the region's long and unusually deep human population history.

A later Nature study analyzed genomes from 28 ancient southern African individuals dated between 10,200 and 150 years before present. That work found that ancient southern Africans carried genetic variation outside the range seen in living people and identified Homo sapiens specific variants that may shed light on adaptation and evolution within Africa.

Together, these findings strengthen a bigger message: human origins were not a single spark in one place. They were shaped by many populations, deep African diversity, and long periods of connection across the continent.

Additional co-authors of the 2023 study include Aaron Ragsdale, University of Wisconsin, Madison; Elizabeth Atkinson, Baylor College of Medicine; and Eileen Hoal and Marlo Möller, Stellenbosch University, South Africa.