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Ancient DNA Gives Insight Into Spread of Pastoralism in Sub-Saharan Africa

NEW YORK (GenomeWeb) – A new genetic analysis of ancient individuals who lived in sub-Saharan Africa has helped shed light on how pastoralism spread through the region.

Archaeological studies have suggested that domesticated animals like sheep, goats, and cattle were first introduced in northeastern Africa about 8,000 years ago, spread into eastern Africa about 5,000 years ago, and to southern Africa by about 2,000 years ago. However, domesticated animals did not appear in what is now northern Ethiopia and Djibouti until about 4,500 years ago and in the Rift Valley of Kenya until about 4,200 years ago.

By analyzing DNA isolated from more than three dozen individuals who lived in what's now Kenya and Tanzania during the Later Stone Age, Pastoral Neolithic, and Iron Age, an international team of researchers modeled how different populations may have spread pastoralism into different regions of Africa. As they reported today in Science, their findings indicate numerous admixture events.

"The origins of food producers in East Africa have remained elusive because of gaps in the archaeological record," co-first author Mary Prendergast from Saint Louis University's Madrid campus said in a statement. "This study uses DNA to answer previously unresolvable questions about how people were moving and interacting."

Prendergast and her colleagues extracted DNA from bone and tooth samples from 41 individuals who had been buried at sites linked to Later Stone Age, early pastoral and Pastoral Neolithic, and Pastoral Iron Age populations in what's now Kenya and Tanzania. They performed targeted sequencing on these samples, focusing on a set of 1.2 million SNPs to a median 0.51X coverage.

Through a principal components analysis of this data alongside data from modern-day Africans and non-Africans, the researchers uncovered different clines of ancestry. Modern-day Sudanese populations, for instance, fall along a cline from Copts to Nilotic speakers — such as Dinka and Nuer populations — while Afro-Asiatic speakers, often from Ethiopia, form a second cline.

Ancient individuals in this analysis cluster with their archaeological associations, the researchers noted. For instance, the three Later Stone Age individuals grouped with other ancient foragers and between individuals from Ethiopia and Tanzania, which the researchers noted was consistent with their geographic location. At the same time, pastoralists clustered separately from foragers, and Iron Age individuals were shifted closer to western Africans and Bantu speakers.

After formal modeling using the qpAdm framework and three proxy groups — present-day Dinka, ancient Chalcolithic-period individuals from Israel, and a 4,500-year-old forager from Mota in southern Ethiopia — to represent potential ancestral populations and admixture dating, the researchers began to piece together how various populations moved in Africa over time, spreading pastoralism.

The researchers proposed that admixture in northeastern Africa of groups associated with pastoralism gave rise to groups with about equal amounts of ancestry linked to present-day Nilotic speakers like the Dinka and Nuer and ancestry linked to ancient and present-day groups from northern Africa and the Levant.

Descendants of these groups, they suggested, then mixed with local foragers in eastern Africa — represented by the Mota-related ancestry in their model — during the Pastoral Neolithic. Then gene flow from Sudan-linked groups occurred before the Iron Age to contribute to the ancestry of the Pastoral Iron Age group. Around the same time, they noted, western African-related ancestry linked to modern-day Bantu speakers then appeared among Rift Valley populations.

"Ancient DNA offers a new source of information about eastern African Holocene prehistory, and an important next direction is to integrate this information rigorously with insights provided by the longer-established disciplines of archaeology and linguistics," the researchers added in their paper.