The Green Sahara genomic landscape: insights from whole genome analysis of modern northern African and Sahelian populations

Africa, the cradle of Homo sapiens and the continent with the greatest genetic diversity, has long been underrepresented in large-scale genomic research, limiting our understanding of its demographic and migratory history. Recent advances in sequencing, bioinformatics, and interdisciplinary integration have enabled a more detailed reconstruction of African population dynamics. A key episode was the Last Green Sahara (12,000–5,000 years ago), when humid conditions transformed the desert into a fertile region that fostered mobility and interaction among distant groups. The subsequent aridification reshaped these connections, concentrating exchanges along different geographic axes, particularly the Nile Valley and the Sahelian belt. In this study, 118 new high-coverage whole-genome sequences from Sahelian and North African populations were analysed alongside modern and ancient comparative data. Results show marked genetic continuity along the Nile Valley, confirming its role as a stable demographic corridor. At the same time ancestral components display a clear north–south gradient along the axis, reflecting a stratification shaped by both ancient and later historical events. The central Sahel displays strong genetic cohesion despite cultural and linguistic diversity, indicating long-term interaction and gene flow. An eastern ancestral component, introduced in the region at the end of the Last Green Sahara (around 4,000 years ago), is best represented today by the Nuba people of Sudan and serves as a genetic link between the Sahel and Nile systems. Finally, isolated populations such as the Copts of Sudan and the Berbers of the Siwa Oasis (Egypt) display strong local genetic identities, suggesting evolutionary trajectories divergent from the patterns observed at the regional scale.