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Discoveries in the Sahara Desert continue to unveil the region’s rich past. Recent scientific advancements in genetic analysis have allowed researchers to recover the first whole genomes from ancient human remains found at the Takarkori rock shelter in Libya. Sign up for science newsletters to explore fascinating findings and stay updated on scientific progress.
Unearthing the Secrets of the Green Sahara Through Ancient Genomes
The present-day landscape surrounding the Takarkori rock shelter in southwestern Libya is characterized by expansive sand dunes and arid terrain. However, approximately 7,000 years ago, this area, now part of the Sahara Desert, presented a vastly different environment – a more verdant and hospitable region known as the “Green Sahara.”
Scientists endeavoring to decipher the origins of the inhabitants of this “Green Sahara” have achieved a significant breakthrough. They successfully extracted and analyzed the first complete genomes – comprehensive genetic blueprints – from the remains of two women interred at Takarkori.
During that era, the region flourished as a lush savanna, abundant with trees, perennial lakes, and rivers. This fertile ecosystem sustained diverse wildlife, including large creatures like hippopotamuses and elephants.
This area also provided a home for early human communities. Archaeologists have discovered the remains of 15 women and children within the Takarkori rock shelter, revealing a society that subsisted on fishing and animal husbandry, tending to sheep and goats.
Savino di Lernia, a coauthor of the study published in “Nature,” explained the selection of these two skeletons: “We initiated our research with these individuals because of their exceptional preservation – their skin, ligaments, and tissues were remarkably intact.”
According to di Lernia, a professor at Sapienza University of Rome specializing in African archaeology and ethnoarchaeology, these findings represent a landmark achievement. It is the first instance where archaeologists have successfully sequenced whole genomes from human remains discovered in such a hot and dry climate.
The detailed genomic analysis yielded unexpected insights for the research team. It indicated that the Green Sahara’s inhabitants were a previously unidentified and geographically isolated population. This group likely resided in the region for tens of millennia.
Mummified Remains Offer Glimpses into Sahara’s Past
Excavations at the Takarkori rock shelter, an area accessible only by four-wheel drive vehicles, commenced in 2003. The two female mummies were among the initial discoveries. “On the second day of excavation, we unearthed the first mummy,” di Lernia recounted. “We brushed away the sand and exposed the mandible.”
Scientists extracted samples from the mummified remains of two 7,000-year-old women, including the skeleton pictured, discovered at the Takarkori rock shelter. – Archaeological Mission in the Sahara/Sapienza University of Rome
The small community inhabiting the rock shelter possibly migrated to the region during humanity’s initial major dispersal from Africa over 50,000 years ago. Study coauthor Harald Ringbauer noted the rarity of encountering such genetically isolated ancestry, especially in contrast to regions like Europe, which experienced extensive population mixing. Ringbauer is a researcher and group leader specializing in archaeogenetics at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, a pioneering institution in developing techniques for retrieving genetic material from ancient bones and fossils.
This genetic isolation, the study authors posit, suggests that the region was likely not a significant migration route connecting sub-Saharan Africa to North Africa, despite the Sahara’s favorable conditions at the time.
Previous examinations of cave paintings and animal remains at Saharan archaeological sites indicated that its inhabitants were pastoralists, herding sheep, goats, or cattle. This led some researchers to propose that herders migrated from the Near East, the birthplace of farming.
However, the researchers suggest that such a migration is improbable given the genetic distinctiveness of the Takarkori group. They propose instead that pastoralism was adopted through cultural diffusion, possibly through interactions with other groups already practicing animal domestication.
“We now understand their genetic isolation, but not cultural isolation. We recognize extensive networks across different parts of the continent, evidenced by pottery originating from sub-Saharan Africa, the Nile Valley, and surrounding areas,” di Lernia stated.
He further explained, “They possessed a lineage that is quite ancestral, indicating a Pleistocene legacy that warrants further investigation,” referencing the epoch concluding approximately 11,000 years ago, preceding the current Holocene Epoch.
Louise Humphrey, a research leader at the Natural History Museum’s Centre for Human Evolution Research in London, corroborated the study’s conclusions. She affirmed that the Takarkori population remained largely genetically isolated for millennia, and that pastoralism in this area arose through cultural exchange rather than population replacement.
Humphrey, who was not involved in this research but has worked at Taforalt cave in eastern Morocco – a site where 15,000-year-old hunter-forager remains were found – stated that “DNA extracted from two pastoralist women buried at the rock shelter around 7,000 years ago reveals that the majority of their ancestry traces back to a previously unknown ancient North African genetic lineage.”
“Future investigations integrating archaeological and genomic data will likely provide deeper insights into human migration patterns and cultural shifts within this region,” Humphrey concluded.
Christopher Stojanowski, a bioarchaeologist and professor at Arizona State University, highlighted another significant aspect of the study: “the inference of a moderately substantial population size and the absence of inbreeding evidence.”
Stojanowski, who was not part of the study, added that “The limited evidence of inbreeding suggests a degree of mobility and interconnectedness, somewhat conflicting with the notion of a long-term, isolated Green Sahara population.”
The Takarkori rock shelter is among numerous archaeological sites dispersed across the Sahara. – Archaeological Mission in the Sahara/Sapienza University of Rome
Challenges in Ancient DNA Recovery
Experts have extensively examined skeletons and artifacts unearthed at the Takarkori site for years. However, previous attempts to retrieve DNA from these remains proved unsuccessful.
In 2019, scientists managed to extract mitochondrial DNA, which provides information about the maternal lineage. Yet, according to Ringbauer, this genetic material offered only a partial understanding.
“Several years ago, the samples were sent to Leipzig because we continually refine our methodologies to maximize the information extracted from minimal DNA quantities. These samples contained very limited DNA,” Ringbauer, an expert in computational genetic data analysis, explained.
Ancient DNA is often degraded and contaminated. It typically preserves best in cool environments, unlike the severe temperature variations found in the world’s largest hot desert. Nonetheless, Ringbauer and his colleagues at the Max Planck Institute for Evolutionary Anthropology successfully extracted sufficient DNA from the two mummies to sequence their entire genomes. This more comprehensive genetic dataset allowed geneticists to reconstruct details about a population’s ancestry, extending beyond individual lineage.
“The complete genome encapsulates the DNA of numerous ancestors,” Ringbauer clarified. “Examining the genome reveals the diverse ancestral lineages. Each genome carries within it a multitude of ancestral narratives.”