AI interpretationAI-generated
Ancient southern African genomes reveal lost human variation and early Homo sapiens evolution.
Researchers sequenced 28 ancient southern African genomes, some up to 25x coverage, dating from 10,200 to 150 years ago. Genomes older than 1,400 years fall outside the genetic range of all modern humans, including Khoe-San. They carry many Homo sapiens-specific variants unseen today. These ancient people showed little population structure for 9,000 years, suggesting a large, stable Holocene population. Gene flow out of southern Africa occurred over 8,000 years ago, but inward flow only after 1,400 years ago.
- Ancient southern Africans older than 1,400 years carry genetic variants outside the range of all modern humans, including Khoe-San.
- Homo sapiens-specific variants fixed in all humans are enriched in kidney function genes; those fixed in ancient southern Africans are enriched in ultraviolet protection genes.
- Ancient southern Africans showed little spatiotemporal stratification for 9,000 years, indicating a large, stable Holocene population.
- Outward gene flow from southern Africa occurred over 8,000 years ago, but inward gene flow only after around 1,400 years ago.
Sample interpretation
The study reports whole-genome data for 28 ancient southern African individuals, including six with high coverage (25x to 7.2x). They date from 10,200 to 150 calibrated years before present. No site sample statistics are provided in the given data. These genomes are key to understanding Homo sapiens evolution and human genomic variation.
For genealogy enthusiasts
This study shows that ancient southern Africans preserved genetic diversity lost in modern humans, offering a direct window into early Homo sapiens evolution. For ancestry enthusiasts, it highlights that modern Khoe-San retain up to 80% of this ancient ancestry, and that southern Africa was a long-term refugium with complex gene flow.
Abstract
Homo sapiens evolved hundreds of thousands of years ago in Africa, later spreading across the globe, but the early evolutionary process is debated. Here we present whole-genome sequencing data for 28 ancient southern African individuals, including six individuals with 25× to 7.2× genome coverage, dated to between 10,200 and 150 calibrated years before present (cal. bp). All ancient southern Africans dated to more than 1,400 cal. bp show a genetic make-up that is outside the range of genetic variation in modern-day humans (including southern African Khoe-San people, although some retain up to 80% ancient southern African ancestry), manifesting in a large fraction of Homo sapiens-specific variants that are unique to ancient southern Africans. Homo sapiens-specific variants at amino acid-altering sites fixed for all humans—which are likely to have evolved rapidly on the Homo sapiens branch—were enriched for genes associated with kidney function. Some Homo sapiens-specific variants fixed in ancient southern Africans—which are likely to have adapted rapidly on the southern African branch—were enriched for genes associated with protection against ultraviolet light. The ancient southern Africans show little spatiotemporal stratification for 9,000 years, consistent with a large, stable Holocene population transcending archaeological phases. While southern Africa served as a long-standing geographical refugium, there is outward gene flow over 8,000 years ago; however, inward gene flow manifests only after around 1,400 years ago. The ancient genomes reported here are therefore key to the evolution of Homo sapiens, and are important for advancing our understanding of human genomic variation.