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Angolan Namib Desert Population Analysis Uncovers New Ancestry Group With Deep Divergence

NEW YORK – With genetic profiles of hundreds of individuals from present-day populations in a desert region of southwestern Africa that spans Angola and Namibia, an international team has retraced interactions between forager, pastoral, and farming populations, uncovering genetic remnants of a previously unidentified ancestral population.

"The unique genetic heritage of the Namib peoples shows 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," senior and corresponding author Jorge Rocha, a researcher at the University of Porto in Portugal, and his colleagues wrote in Science Advances on Friday.

Using array-based genotyping, along with an ancestry decomposition method, the team profiled genetic patterns across the genomes of 208 individuals from nine present-day ethnic groups in the Angolan Namib Desert, analyzing the data in combination with available genotyping data from populations in other parts of Africa.

Building on prior mitochondrial DNA-based research, which pointed to genetic differentiation between a dominant pastoral group and populations with lower socioeconomic status such as the Kwepe stock herders, the researchers saw a combination of genetic drift and previously unidentified ancestry in marginalized groups in the region.

"There is no extant population that could be identified as the original bearer of the Namib-ancestry," Rocha said in an email. "All we have are genome fragments that became part of the gene pool of migrants who arrived to the area and most likely admixed with its original inhabitants."

Together, the team's results supported a model in which an early-branching human lineage spread across southern Africa, diverging before the split between click language-speaking groups in the Kx’a language family, currently found in the northern Kalahari Basin, or the Tuu language family in the southern Kalahari.

"The finding that the Angolan Namib was once inhabited by foragers with a genetic composition distinct from Kx’a- and Tuu-speaking groups shows that the genetic diversity of the oldest population layer of Southern Africa was higher than previously assumed," Rocha said.

"This added diversity is important for reconstructing the genetic history of Africa before the spread of food production," he explained, "including the origins and relationships between coastal peoples that relied on the exploration of maritime resources."

The study also provided clues to the past relationships between pastoral groups, particularly Khoe-Kwadi language family speakers, and a more recently-arriving farming groups with Bantu ancestry, highlighting genetic ties between Kwadi speakers and the ancient ancestry group that were not found in other areas profiled in the past.

"We found that the Kwadi people admixed with peoples bearing the older Namib-related ancestry and became quite distinct from their Khoe-Kwadi-speaking relatives settling in other regions of southern Africa," Rocha explained.

"Based on our genetic and linguistic results," he noted, "we were now able to propose a model for the dispersion of Khoe-Kwadi-speaking peoples in which admixture with local foragers and later Bantu incomers played a key role in their genetic differentiation."

More broadly, the findings are expected to provide genetic insights to complement archeological studies in the Angolan Namib region and beyond, hinting that mysterious rock art and shell midden deposits previously found in the area may have been left by the newly-detected ancestral group.

"Together, our results show that contact areas associated with the confluence of different migratory waves can harbor the ancestry of vanished groups predating the arrival of food production in Africa," the authors wrote. "While the full diversity and geographical extension of these early foragers may ultimately be revealed by ancient DNA, detailed studies of highly admixed small-scale communities can still provide unique opportunities to probe the deep genetic structure of the continent."