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 interactions among inhabitant groups. Its subsequent desertification created the largest geographic barrier in Africa, driving the evolutionary divergence of North Africa and Sahel. To explore the genetic impact of these transformations, we sequenced 118 high-coverage (30x) human modern genomes from five North African and seven Sahelian countries, integrating them with 43 previously analyzed samples (D’Atanasio et al. 2023) and >2,400 modern and ancient genomes from literature.This dataset reveals strong genetic heterogeneity, with notable stratification in Sudan—where genetic signals link it to both North Africa and Sahel—and the presence of a sub-Saharan ancestry in culturally Berber populations like nomadic Tuareg and Egyptian Siwa, suggesting possible early movements. The inclusion of >150 African ancient genomes, from the Neolithic to the Early Christian period, provides a crucial temporal framework for reconstructing past population dynamics. However, Africa remains underrepresented in genomic research, and many analytical methods, often developed for non-African populations, can be challenging to apply in this context. Addressing these challenges will be crucial for optimizing the best strategies to analyze the diversity of this dataset, leading to a more precise reconstruction of trans-Saharan genetic trajectories.