The Green Sahara genomic landscape: tracing ancestries across North Africa and Sahel through joint analysis of modern and ancient genomes

During its last humid phase (12,000–5,000 ya), the Sahara was fertile and widely populated, allowing coexistence and interactions among various inhabitant groups. The subsequent desertification created the largest geographic barrier in Africa, driving the evolutionary divergence of North Africa and the Sahelian belt. In order to characterize at a higher resolution possible genetic signals related to the last Green Sahara and the trajectories of subsequent migrations, we sequenced 118 high-coverage (30x) human modern genomes from five North African and seven Sahelian countries, integrating them with 43 previously analysed samples (D’Atanasio et al. 2023) and >2,400 modern and ancient genomes from literature. The analysis of this comprehensive dataset highlights significant genetic heterogeneity, with notable cases of stratification, such as in Sudan - where genetic signals link this region to both North Africa and Sahel - and the presence of a relevant sub-Saharan ancestry in some culturally Berber populations, like nomadic Tuareg and Egyptian Siwa, that could point to possible early events. Crucially, the inclusion of ancient genomes has revealed that early ancestries are differentially distributed not only between northern and southern regions of the Sahara but also longitudinally following distinct patterns along the Sahel. Further analyses aim to distinguish between older and more recent admixture events and to date them. In particular, >150 ancient African samples, spanning from the Neolithic to the Early Christian period, are essential for uncovering genetic signals across an extensive temporal range and shedding light into the historical trajectories and evolutionary dynamics around the present-day Sahara.