Uncovering Africa’s complex genetic legacy

Stretching along the southwest coast of Africa, the Namib Desert, with its unique landscapes and harsh environment, has long fascinated scientists and adventurers alike.

But behind the sand dunes and barren terrain, the rich tapestry of human history and migration patterns remained hidden. While previous research has unraveled the genetic structure of Africa before the expansion of agriculturalists, the impact of the extinct hunter-gatherer and herder societies on the genetic makeup of modern Africans remained unclear.

A genomic study published in Science Advances, however, provided insights into the origins of people living in the Angolan Namib Desert before the expansion of agriculturalists, revealing a deeply divergent ancestry that is exclusively shared between groups from the Angolan Namib Desert and adjacent areas of Namibia.

Using ancestry analysis techniques, an international research team from the University of Bern in Switzerland, the University of Porto in Portugal, and the Max Planck Institute for Evolutionary Anthropology (MPI EVA) in Germany was able to reconstruct the history of contact emerging from the migration of a pastoral community .

“The unique genetic heritage of the Namib peoples show how modern DNA research targeting understudied regions of high ethnolinguistic diversity can complement ancient DNA studies in probing the deep genetic structure of the African continent,” explained the study .

The study revealed that the population of the Angolan Namib Desert is genetically distinct from other contemporary populations, and that most of the diversity at the genome level was influenced by socioeconomic status.

The researchers analysed saliva samples to discover whether each individual from the study cohort has roots from each reference population.

The common ancestry of click languages  

The researchers conducted the genetic study on a pastoral group known as the Kwepe, living in the Angolan Namib Desert as well as Bantu-speaking groups, which are part of the dominant pastoral traditions of southwest Africa. They also included marginalized groups whose origins are linked to foraging traditions.

The Kwepe group speaks the Kwadi language, a kind of click language which shares a common ancestral language with the Khoe languages spoken by foragers and herders all over Southern Africa.

“Anthropological surveys conducted during the first half of the 20th century confirm that the group that speaks the Kwadi language has a common origin with groups that had been speaking a similar language and disappeared from the region. Therefore, we assumed the possibility of finding traces of the genetic heritage of extinct human groups in the modern peoples living in the region at the present time,” Sandra Oliveira, a researcher in the Department of Evolutionary Genetics at the MPI EVA and co-author of the study, tells Nature Middle East.

Scientists had believed that the Kwadi language became extinct around 1960. However, the new study found two speakers of the Kwadi language with the help of Antonio Mbebe[NE1] , a leader of the Kwepe group. They coordinated with a local institution called the Center for Desert Studies in Curoca that had established good relations with the Kwepe group, where more than 100 Kwepes still follow a semi-nomadic lifestyle in the Namib Desert.

Understanding the Bantu impact

The study showed that "the population of the Angolan Namib Desert is very different from other contemporary populations, as it retains a unique pre-Bantu lineage found only in the population of the Namib Desert."

The term ‘pre-Bantu lineage’ refers to the genetic and cultural heritage of populations in Africa, existing before the large-scale Bantu migrations that began around 2,000 to 3,000 years ago.

The Bantu migrations were a series of population movements and expansions of Bantu-speaking people across much of sub-Saharan Africa. Understanding pre-Bantu origins is essential to unravel the complexity of human history on the African continent.

Before the Bantu migrations, Africa was home to a wide range of ethnic groups and diverse cultures and languages. Pre-Bantu populations varied in their lifestyles, social structures, and geographic distribution, and included hunter-gatherer and early agricultural communities. Some groups relied on searching for food, while other groups practiced the cultivation of crops such as sorghum and potatoes.

Bantu migration had a profound impact on the demographic and linguistic landscape of Africa. As Bantu-speaking groups expanded, they interacted with, and sometimes absorbed or displaced, pre-Bantu populations, leading to the spread of Bantu languages and the fusion of cultures.

Complexity revealed

The new discovery underscores the complexity of human genetic history in the region. One of the most compelling aspects of this study is to be able to reconstruct precise contact dates, arising from the migration of pastoral Khoe-Kwadi-speaking herders and Bantu-speaking farmers to southern Africa.

These migrations played a crucial role in shaping the region's linguistic and cultural diversity. By tracing the genetic fingerprints of these populations, the study sheds light on the interactions, mixing and adaptations that occurred over the centuries.

The importance of this study extends beyond the genetic discoveries themselves, according to Carina Schlebusch, a researcher in genetic human history at Uppsala University in Sweden, who was not involved in the study.

Schlebusch says the discovery highlights the power of modern DNA research, especially in areas with high ethnolinguistic diversity. While ancient DNA studies have made invaluable contributions to our understanding of human history, they often have limitations due to scarcity of ancient specimens and preservation challenges. Recent DNA research, as demonstrated in this study, can complement these efforts by examining the deep genetic structure of the African continent.

With Africa being the birthplace of modern humans who expanded to other parts of the world, these findings have wider impacts.

“Fossils with modern anatomical features appeared in Africa before they appeared in other parts of the world,” Oliveira says.

The continent can therefore shed light on our common ancestors and the journey that has brought us to where we are today. Genetic studies of the modern human’s African origins and analysis of the DNA of diverse populations around the world point to Africa as the source of our genetic diversity.

That diversity, she explains, is needed to reconstruct human demographic history and understand human origins and the genetic basis of adaptation or susceptibility to disease.

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