The North African maternal genetic diversity enriched by historical migrations: insights from a comprehensive analysis of complete mitogenomes.

North Africa has experienced significant gene flow throughout history, with Morocco occupying a strategic location at the crossroads of Africa and Europe. In this study, we compiled 869 complete mitogenome sequences from six North African populations to explore genetic diversity, haplogroup distributions, and phylogenetic relationships, with a specific emphasis on the Moroccan population. We obtained a high haplotype diversity across all populations, and neutrality tests yielded significant negative values, consistent with demographic expansion. We identified 56 haplogroups, dominated by U6, H, and L. Genetic differentiation between populations was low (FST = 0.001-0.014), and analysis of molecular variance indicated that most genetic variation occurs within populations, and reinforces the presence of a genetically cohesive Maghreb core. Phylogenetic and NeighborNet analyses showed that Moroccan sequences are widely distributed across haplogroups, with deep branching of macro-haplogroup L subclades, indicating early human migration patterns, including out-of-Africa dispersal and subsequent back-migrations. Bayesian demographic analysis of the prevalent haplogroups in Morocco revealed distinct evolutionary trajectories: an expansion of haplogroup L, a decline of U6, and an expansion of H. To complement the maternal perspective, we analyzed published Y-chromosome STR data from 2114 North African males. Haplotypic diversity remains high (> 0.97), and the haplogroup E-M81 predominates in Moroccan, Algerian, and Tunisian populations. Low pairwise Rst values further confirm the genetic homogeneity of North Africa and reinforce the strong cohesion of the Maghreb core. This study highlights a rich genetic heritage shaped by ancient and ongoing gene flow in North Africa.