Ancient Genomes from Southern Africa Reveal Unique Human Lineage

Research has unveiled a unique lineage of ancient humans in southern Africa, shedding light on the continent’s complex evolutionary history. A collaborative study between South African and Swedish scientists successfully extracted genetic material from ancient skeletons, providing crucial insights into a distinct population that thrived in the region until about 1,000 years ago.

The findings challenge previous understandings of human genetic diversity, particularly in light of the Bantu expansion, which significantly altered the genetic landscape of populations south of the Sahara. The team analyzed skeletons dating from approximately 10,000 years ago to more recent periods, revealing a population that was not only sizable but also genetically distinct from known lineages.

Insights into Human Evolution

Understanding how modern human features developed has long been a challenge for researchers. Fossil evidence from various sites across Africa demonstrates a mix of archaic and modern traits, complicating the timeline of human evolution. Adding to the complexity, DNA preservation issues in the continent’s warmer climates have limited the ability to study ancient lineages.

The Khoe-San, one of the earliest branches of modern humans, are known for their high genetic diversity. This study, however, offers a glimpse into a previously unrecognized population that existed independently until recent times. Using principal coordinate analysis, the researchers found that genetic variations from these ancient skeletons formed a cluster distinct from those of East and West African populations, indicating significant isolation.

Of particular interest is the finding that the genomes from these ancient skeletons showed no evidence of genetic input from outside populations until approximately 1,200 years ago. This suggests that for millennia, this southern African group remained largely insulated from the genetic mixing that characterized other regions of the continent.

Climate as a Factor in Isolation

The research indicates that climate and geographical factors may have contributed to this population’s isolation. Southern Africa might have served as a climate refuge during periods of environmental change, allowing modern humans to expand from this area when conditions improved. This hypothesis is supported by evidence of southern African genetic variants appearing in eastern and western African populations around 5,000 years ago.

Genetically, the ancient population resembled many of their contemporaries, exhibiting traits common among early humans, such as brown eyes and high skin pigmentation. Notably, none displayed genetic resistance to malaria or sleeping sickness, traits found in some modern groups. While the study identified variations in genes related to immune function, it did not reveal any particularly unique characteristics that set this population apart from others of the time.

The significance of this research lies in its potential to reshape our understanding of human evolution. As additional evidence emerges, it will likely help piece together the complex narrative of how diverse human populations interacted and evolved over hundreds of thousands of years. The presence of this large, stable group in southern Africa adds a new layer to the already intricate story of human ancestry.

The study was published in the journal Nature on March 15, 2025, contributing vital information to the ongoing exploration of our species’ origins and migrations across the globe.