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Homo sapiens-specific evolution unveiled by ancient southern African genomes
Mattias Jakobsson1,2,3, Carolina Bernhardsson4, James McKenna4,5
1Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden. mattias.jakobsson@ebc.uu.se.
Nature
|December 3, 2025
Summary
Ancient southern African genomes reveal unique Homo sapiens genetic variations predating modern human diversity. These findings are crucial for understanding early human evolution and genomic diversity across Africa.
Area of Science:
- Paleogenomics
- Human Evolution
- Population Genetics
Background:
- The early evolution and global spread of Homo sapiens remain subjects of scientific debate.
- Understanding ancient human genetic variation is key to reconstructing evolutionary history.
Purpose of the Study:
- To analyze whole-genome sequencing data from 28 ancient southern African individuals.
- To investigate the genetic makeup of early Homo sapiens in southern Africa and its relation to modern populations.
Main Methods:
- Whole-genome sequencing of 28 ancient southern African individuals (10,200–150 calibrated years before present).
- Analysis of Homo sapiens-specific variants, including those at amino acid-altering sites.
- Assessment of population structure and gene flow over time.
Main Results:
- Ancient southern Africans (>1,400 cal. BP) exhibit genetic profiles distinct from modern humans, with unique Homo sapiens-specific variants.
- Enrichment of Homo sapiens-specific variants in genes related to kidney function and ultraviolet light protection.
- Evidence of a large, stable Holocene population in southern Africa with limited spatiotemporal stratification over 9,000 years.
Conclusions:
- Southern Africa acted as a long-standing refugium with significant outward gene flow over 8,000 years ago.
- Inward gene flow into southern Africa occurred primarily after 1,400 years ago.
- These ancient genomes are pivotal for understanding Homo sapiens evolution and human genomic diversity.
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