Bony labyrinth morphology reveals deep population history and isolation among Homo sapiens in prehistoric northeastern Africa (44-3 ka).

Understanding the population history of Homo sapiens in northeastern Africa has been hindered by the scarcity of human remains and ancient DNA data. Here, we analyse bony labyrinth morphology, a reliable proxy for population affinities, in 148 individuals dating from the Late Pleistocene to the Late Holocene from the Nile Valley region, the Horn of Africa, Central Africa, comparative Pleistocene fossils from Africa and Eurasia, and recent South Africans. Shape analyses reveal morphological continuity among Middle Nile Valley foragers and close affinities with earlier African H. sapiens fossils, suggesting deep regional ancestry. In contrast, local Neolithic food producers exhibit distinct morphologies, supporting a major demographic shift beginning 8000 years ago. A subgroup of Early Holocene Nile Valley foragers displays unusual bony labyrinth morphology and congenital inner ear-specific pathological changes consistent with possible syndromic conditions. This may result from several demographic scenarios, including prolonged endogamy and geographic isolation under environmental constraints. Comparative data from the Horn of Africa and Central Africa reveal high morphological diversity, suggesting strong population substructure and dynamic demographic trajectories during the Holocene. These findings provide rare insights into prehistoric population structure in the region, and demonstrate the usefulness of bony labyrinth morphology where ancient DNA is unavailable.