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Oldest African human genomes sequenced

Published online 28 March 2018

Humans in the Near East, North Africa, and Sub-Saharan Africa were interacting in the Stone Age, DNA from 15,000-year-old skeletons shows.

Meredith Brand

The excavated cemetery is probably the largest and oldest cemetery in Africa. 
The excavated cemetery is probably the largest and oldest cemetery in Africa. 
© Shawn Hempel - Concepts / Alamy Stock Photo
Modern humans from Africa and the Near East appear to have interacted much earlier and in more complex ways than previously thought, a study of the oldest human nuclear DNA yet sequenced in Africa has revealed.1

The new findings emerged from a study on 15,000-year-old skeletons excavated from Grotte des Pigeons, a cave near the town of Taforalt in north eastern Morocco. 

“What makes these results unique is that we’ve managed to get this first glimpse into the prehistoric population genetics in North Africa before the introduction of agriculture,” says Marieke van de Loosdrecht, the study’s first author and a PhD candidate at the Max Planck Institute for the Science of Human History in Jenna, Germany.

Africa’s first cemetery

Grotte des Pigeons was occupied from around 23,000 to 12,000 years ago by the Iberomaurusian culture, which made fine stone tools known as microlithic backed bladelets. 

The Iberomaurusian people lived in the cave’s wide amphitheater-like entrance and buried their dead in a cemetery at the back of the cave, says co-author Nick Barton, archaeology professor at the Institute of Archaeology at the University of Oxford. The cemetery potentially has over 100 burials from the Later Stone Age, making it the largest and oldest cemetery in Africa, he says.

The appearance of the stone tools roughly 25,000 to 20,000 years ago may represent the arrival of a new population in the region. 

“The main aim of this research,” says Abdeljalil Bouzouggar, study co-senior author at the Max Plank Institute for Evolutionary Anthropology in Leipzig, “was to look at the origin of the Iberomaurusian whether it is a local or an exogenous culture.”  

The analysis of mitochondrial and nuclear DNA extracted from seven skeletons revealed a mixture from two ancestral groups: a Near Eastern population, most similar to ancient hunter-gatherers known as Natufians, and a poorly understood ancestry similar to Sub-Saharan African populations. 

“We were expecting some links with Europe from across the Gibraltar or Sicily Straits but our results don't support this theory. In my view, the most important result is that around 15,000 years ago North and West Africa and the Near East were an open space for human migrations and various interactions,” says Bouzouggar.

The Near-Eastern genetic connection is relatively clear, according to Iosif Lazaridis, of the Department of Genetics at Harvard Medical School who was not involved with the study. 

“There are now enough ancient samples from the Middle East and Europe to be fairly sure that the Taforalt samples were indeed more closely related to Natufians than to other non-Africans.”

However, the Taforalt affinity to Sub-Saharan Africans is less clear, since no modern Sub-Saharan Africans appear to be a good source for the ancestry found in the cave samples, says Lazaridis.

To probe this Sub-Saharan connection, the researchers examined genetic similarities between the samples and a variety of modern and ancient populations that represent the human genetic diversity within Sub-Saharan Africa, says Choongwon Jeong, the study’s co-senior author.

Modern West Africans are on average most closely related to the ‘Sub-Saharan African-related’ ancestry in Taforalt, but the match was not perfect, he says.  

More sampling from ancient North and Sub-Saharan African skeletal remains should hopefully clarify the remaining questions surrounding the Sub-Sharan genetic component of the Taforalt individuals, the researchers say. 


  1. van de Loosdrecht, M et al. Pliestocene North African genomes link Near Eastern and sub-Saharan African human populations. Science. (2018)