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Stone Age Moroccan Genomes Reveal Sub-Saharan African, Near Eastern Ancestry

NEW YORK (GenomeWeb) – New genome sequence data from North African individuals living up to 15,000 years ago suggests that Stone Age Moroccans carried ancestry from both sub-Saharan Africa and the Near East.

"Our analysis shows that North Africa and the Near East, even at this early time, were part of one region without much of a genetic barrier," co-senior author Choongwon Jeong, a researcher in the Department of Archaeogenetics at the Max Planck Institute for the Science of Human History, said in a statement.

As they reported online today in Science, Jeong and colleagues from Germany, Morocco, and the UK performed mitochondrial genome sequencing and genome-wide SNP analyses on remains from nine anatomically modern humans, dated at 13,900 to 15,100 years old, that were found in present-day Morocco. Their results suggested that members of the so-called "Iberomaurusian" culture living near Morocco's Taforalt cave genetically resembled individuals from the Levantine Natufian population in the Near East and a sub-Saharan African group with ties to populations that currently reside in West Africa.

The ancient individuals "provide a crucial reference point to understand the deep genetic history of North Africa and the broader Middle East," Jeong and co-authors explained.

The researchers used in-solution capture to take a crack at sequencing double-indexed, single-stranded mitochondrial DNA in petrous bone samples from nine ancient individuals at the Grotte des Pigeons burial site associated with the Taforalt cave. They used a similar strategy to target more than 1.2 million SNPs across the nuclear genome.

"[M]odern humans frequently inhabited this cave intensively during prolonged periods throughout the Middle and Later Stone Age," co-author Louise Humphrey, an earth sciences researcher that London's Natural History Museum, said in a statement, noting that "there is evidence for more intensive use of the site and the Iberomaurusians started to bury their dead at the back of the cave" roughly 15,000 years ago.

The team's approach yielded informative mitochondrial genome sequence data for seven of the individuals, generating between 102-fold and 1,701-fold average coverage. For five of the individuals, the group successfully generated SNP profiles from across the nuclear genome — marking the oldest known ancient DNA analysis done in Africa to date.

"Due to challenging conditions for DNA preservation, relatively few ancient genomes have been recovered from Africa and none of them so far predate the introduction of agriculture in North Africa," first author Marieke van de Loosdrecht, an archaeogenetics researcher at the Max Planck Institute for the Science of Human History, said in a statement.

When they considered the ancient Moroccan SNP patterns alongside available Affymetrix Human Origins array data for present-day individuals or ancient populations in Europe, the Near East, and sub-Saharan Africa, the researchers found that the Grotte des Pigeons samples formed a cluster between existing populations in North Africa and East Africa. Similarly, mitochondrial and Y chromosome haplogroups detected in the ancient Moroccans corresponded to those currently found in the same regions.

Digging down into the data, the team saw ancestry from Natufian populations living in the Levant during the early Holocene epoch, along with ancestry resembling Mende and Yoruba populations in West Africa. On the other hand, additional ancestry from Paleolithic European populations did not appear necessary to explain the genetic features found in ancient Morocco.

"[W]e provide genomic evidence for a Late Pleistocene connection between North Africa and the Near East, predating the Neolithic transition by at least four millennia, while rejecting a potential Epigravettian gene flow from southern Europe into northern Africa within the resolution of our data," the authors wrote. "We speculate that the Natufian-related ancestral population may have been widespread across North Africa and the Near East."