Green Sahara Ancient DNA Reveals Isolated North African Lineage
Ancient genomes from Libya’s Takarkori shelter uncover a unique North African lineage, challenging migration theories.
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In the middle of the 19th century, the German explorer Heinrich Barth discovered prehistoric Saharan rock sculptures and engravings while traveling through the Sahara Desert in North Africa.
Barth, who is considered one of the great explorers of Africa, reported how one sculpture included depictions of “oxen”, or ox, moving towards a pond or well from which they were to be watered. “Some of these bulls are admirably executed, and with a fidelity which can scarcely be accounted for, unless we suppose that the artist had before his eyes the animals which he chiseled,” he wrote.
Barth was curious; the landscapes depicted in the sculptures and engravings appeared very different to the dry, almost lifeless desert he had encountered.
Hundreds of years later, scientists would learn that these images portray life in the Sahara during the African Humid Period (AHP).
What was the African Humid Period?
The AHP began ~14,500 years ago. It was primarily caused by orbital changes in the Earth’s axial tilt, which strengthened the African monsoon system. Moist air was drawn further north into the Sahara, which turned the desert into a green savannah, filled with trees and dotted with large lakes. Aridification slowly turned the Sahara into a desert, ending the AHP ~5,000 years ago. Researchers now know that the Sahara and North Africa more generally swing between wet and dry climates every 20,000 years.
The AHP ultimately promoted human settlement across the Sahara, leading to the spread of pastoralism – a shift from a hunter-gatherer lifestyle to one primarily based on food production through the domestication of animals and plants.
Ancient DNA analysis from archaeological sites around the world is helping scientists build a more accurate picture of the genetic history and demographic past of different regions and populations. The process of extracting and analyzing DNA from Saharan sites, however, has historically proven difficult – the harsh conditions mean that DNA rarely preserves well.
In 2019, mitochondrial DNA (mtDNA) was analyzed from the remains of two female individuals extracted from the Takarkori rock shelter in the Tadrart Acacus Mountains of southwestern Libya. The remains were estimated to be ~7,000 years old, making this study the first successful ancient DNA analysis from pastoralists of the Green Sahara.
mtDNA is only passed down by the mother and doesn’t change much from generation to generation. Therefore, using it to infer population dynamics can provide a limited view of the past.
Now, a collaborative team of researchers has successfully obtained the first genome-wide data from the same two female individuals.
“Two factors allowed us to generate DNA data even from one of the harshest climates on earth: First, the human remains in this site were exceptionally well preserved, being one of the oldest natural mummies in the world. Second, the ancient DNA field has made truly remarkable progress in the last years. Using cutting-edge DNA extraction and processing protocols we were now able to extract and amplify even the very small amounts of preserved DNA,” Dr. Harald Ringbauer, a population geneticist at the Max Planck Institute for Evolutionary Anthropology (MPI-EVA) and a co-author of the study, told Technology Networks.
“This revealed completely new insights into who the Pastoralists of the Green Sahara were and where they came from,” Ringbauer added.
Ancient North African genomes rewrite Sahara’s genetic history
According to Ringbauer, a long-standing hypothesis has suggested that the Pastoralists of the Green Sahara originated from sub-Saharan Africa or from people of the eastern Mediterranean and the Nile Valley.
The ancestry of the Takarkori rock shelter individuals paints a different picture, however.
“The ancient genomes revealed that they were part of a distinct, isolated and previously unknown North African lineage. While this lineage became extinct, present-day North Africans still carry substantial parts of this ancestry, highlighting their unique heritage,” Ringbauer said.
The females are also related to foragers from the Taforalt Cave in eastern Morocco, whose 15,000-year-old remains had been sequenced in a previous study. These individuals lived during the Ice Age, before the AHP.
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Interestingly, the Takarkori rock females and the Taforalt Cave individuals are equally distant regarding their relation to sub-Saharan African lineages. It appears that gene flow between North African and sub-Saharan individuals was limited, despite the Sahara’s greening, which contradicts previous hypotheses.
The Takarkori women also demonstrated a 10-fold reduction in Neanderthal DNA compared to populations living outside of Africa. They have more Neanderthal DNA than contemporary sub-Saharan Africans.
“Our findings suggest that while early North African populations were largely isolated, they received traces of Neandertal DNA due to gene flow from outside Africa,” said senior author Professor Johannes Krause, director at MPI-EVA.
"Our research challenges previous assumptions about North African population history and highlights the existence of a deeply rooted and long-isolated genetic lineage," added first author Nada Salem, a PhD student at MPI-EVA. "This discovery reveals how pastoralism spread across the Green Sahara, likely through cultural exchange rather than large-scale migration."
The research not only reshapes our understanding of North African ancestry and the movement of early pastoralist communities but also marks a significant achievement in ancient DNA research.
Successfully extracting and analyzing genome-wide data from remains preserved in one of the world’s harshest environments demonstrates how far the field has come. “The extreme Sahara climate is a unique challenge for ancient DNA. But using cutting edge ancient DNA technologies allowed us to squeeze out enough genetic data for our analysis,” concluded Ringbauer.
About the interviewee
Dr. Harald Ringbauer is a population geneticist who develops and applies computational tools to analyze genetic data. A key research interest of his is human ancient DNA. This field is rapidly growing – by now thousands of genomes of past humans are being published every single year. Ringbauer develops new ways to study these ancient genomes to study the human past, e.g., to learn about past population and social structure. Currently, he works at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, where he leads a research group in the department of Archaeogenetics.
