Homo sapiens-specific evolution unveiled by ancient southern African genomes

The study sequenced whole genomes from 28 ancient individuals from southern Africa (10,200–150 calibrated years BP), including six with 7.2×–25× coverage. Individuals older than ~1,400 years BP possess genetic profiles outside the range of present-day human variation, reflecting many Homo sapiens–specific variants unique to ancient southern Africans. Variants fixed across humans, likely emerging rapidly on the Homo sapiens branch, are enriched in genes related to kidney function; variants fixed within ancient southern Africans, likely adapted on the southern African branch, are enriched for ultraviolet protection. Genomes show little spatial or temporal structure over ~9,000 years, consistent with a large, stable Holocene population acting as a long-term refugium, with outward gene flow >8,000 years ago and inward gene flow appearing only after ~1,400 years ago. These ancient genomes are key to understanding Homo sapiens evolution and human genomic variation.