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Ancient Genomes Support Genetic Continuity, European Migrations in North Africa

NEW YORK (GenomeWeb) – Modern North Africans have a complex population history that includes prehistoric admixture with Neolithic Europeans, according to a new genomic analysis.

Archaeological findings have suggested that features linked to the Neolithic period, like farming and pottery, may have been introduced to North Africa from Iberia or the Mediterranean. But it's been unclear whether these innovations were due to the arrival of new people or the adoption of new ideas.

A Stanford University-led team of researchers sequenced and analyzed the genomes of individuals whose remains were excavated from Early and Late Neolithic sites in Morocco and southern Iberia. As they reported yesterday in the Proceedings of the National Academy of Sciences, the researchers found that the genomes of Early Neolithic Moroccans were similar to late Stone Age individuals from the area, suggesting genetic continuity in the region, while Late Neolithic Moroccans harbored an Iberian component, suggesting an influx of new people.

"Our results support the idea that the Neolithization of North Africa involved both the development of Epipaleolithic communities and the migration of people from Europe," Stanford's Carlos Bustamante and his colleagues wrote.

His team sequenced 27 individuals, seven of them from the Early Neolithic site Ifri n'Amr or Moussa that dates to 5,000 BC and eight from the Late Neolithic site Kelif el Boroud that dates to 3,000 BC, both in Morocco. The remaining 12 individuals were from the southern Iberian Early Neolithic site El Toro.

The researchers boosted their coverage of these ancient genomes by relying on baits that targeted sites included in the Multiethnic Genotyping Array (MEGA). After enrichment, they generated 13 low-coverage genomes from the three archaeological sites, with genome-wide coverage ranging from 0.01X to 0.74X and MEGA coverage ranging from 0.04X to 1.72X.

From their initial mitochondrial DNA and Y chromosome haplogroup analysis, the researchers found there was likely either a population replacement or genetic influx into Morocco between 5,000 BC and 3,000 BC, as they noted differences in haplogroups between their Early Neolithic Moroccan and Late Neolithic Moroccan samples.

This finding was further borne out through a principal components analysis using sub-Saharan African, North African, European, and Middle Eastern populations from the Human Genome Diversity Project. The researchers found that the Early Neolithic Moroccan samples clustered near the Mozabites, a Berber group living in southern Algeria, and the Early Neolithic Iberian samples clustered near southern Europeans. The Late Neolithic Moroccan samples, meanwhile, fell between the two Early Neolithic samples from Iberia and Morocco.

Using the Admixture algorithm and further statistical testing, Bustamante and his colleagues teased out additional genetic structures within these populations. For instance, they noted that the Early Neolithic Moroccan samples include a North African component seen in Mozabites and that they clustered between samples from the Taforalt, a 15,000-year-old Stone Age site in Morocco, and modern North Africans. This, the researchers said, indicates long-running genetic continuity in the region.

They also found the Taforalt and Early Neolithic Moroccan samples to share a degree of genetic drift with each other as well as with ancient Levantine samples, suggesting Paleolithic mixture between the groups.

Again, the Late Neolithic Moroccan samples were intermediate between European Early Neolithic and North African ancestries and, more specifically, clustered between the Early Neolithic Moroccan samples and Anatolian/European farmer samples.

Based on this, Bustamante and his colleagues concluded that the first stage of Neolithic expansion in Morocco was likely due to the local population adopting technological advances, such as pottery making or farming, from nearby regions. But then, by 3,000 BC, Mediterranean-like groups arrived in Morocco, via Iberia.

"Future paleogenomic efforts in North Africa will further disentangle the complex history of migrations that forged the ancestry of the admixed populations we observe today," they added.