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Study of Medieval Swahili Peoples Finds African, Asian Genetic Ancestry

NEW YORK – An international team has detected both African and Southwest Asian genetic ancestry in medieval individuals from the Swahili culture of eastern Africa, combining sex-biased ancestry and other genetic patterns with archaeological data to better understand interactions between cultures at the time.

"[T]he results presented here provide unambiguous evidence of ongoing cultural mixing on the East African coast for more than a millennium, in which African people interacted and had families with immigrants from other parts of Africa and the Indian Ocean world," co-senior and co-corresponding author Chapurukha Kusimba, an anthropology researcher affiliated with the National Museums of Kenya, the University of South Florida, and the University of Nairobi, and his colleagues wrote in Nature on Wednesday.

"Narratives of ancestry on the eastern African coast have a complex history," the authors explained, "and the genetic findings of long-standing, sex-biased mixtures adds to this complexity."

Using targeted sequencing, the researchers profiled some 1.2 million SNPs across the genome in 80 ancient individuals from half a dozen medieval and early modern sites along East Africa's Swahili coast or nearby islands that span present-day locations such as southern Somalia, northern Mozambique, Madagascar, and several archipelagos. They analyzed the sequence data in combination with array-based genotypes for 93 individuals from present-day Swahili-speaking populations.

"Our results do not provide simple validation for the narratives previously advanced in archaeological, historical, or political circles. Instead, they contradict and complicate all of them," Kusimba and co-senior author David Reich, a human evolutionary biology and genetics researcher affiliated with Harvard University and the Broad Institute, wrote in a related op-ed published in The Conversation on Wednesday.

The duo noted that the Swahili language and culture have persisted in Kenya, Tanzania, and other East African countries, though much of the Swahili civilization's history has been interpreted and told by individuals from outside the group, who often classified the culture as mainly African or primarily non-African.

Analyzing a combination of genetic and non-genetic data, the researchers found signs of admixed African and Asian ancestry stretching back thousands of years in the ancient Swahili representatives they studied, including Asian ancestry from India and Persia in elite members of the medieval Swahili population.

"Contradicting what we had expected, the ancestry of the people we analyzed was not largely African or Asian," Kusimba and Reich wrote. Instead, they suggested, the groups were "intertwined, each contributing about half of the DNA of the people we analyzed."

The team's analysis also highlighted incoming Arabian ancestry within the last 300 years, during a period of Omani control, followed by increased interactions with populations from other parts of Africa.

Even so, the ancestry patterns they identified pointed to an overrepresentation of Asian ancestry originating from males, combined with African female ancestry. Coupled with the matriarchal features found in the culture, the authors speculated that Persian men may have married women from elite families, who shared the Swahili language and matrilineal traditions with their offspring.

"We find evidence of predominantly male Southwest Asian ancestors mixing with predominantly female African and, to a much lesser extent, female Indian ancestors in the lineages of medieval people on the Swahili coast," the authors reported. "This provides evidence for asymmetric social interactions between groups as cultural contact occurred, although such genetic data cannot reveal the processes contributing to these patterns."