Reconstructing Prehistoric African Population Structure

Area of Science:

• Paleogenomics
• Population Genetics
• African Prehistory

Background:

• Understanding the deep history of human populations in Africa is crucial for reconstructing global human migration and adaptation.
• Previous studies have suggested complex admixture events, but ancient genomic data from diverse African regions remains limited.

Purpose of the Study:

• To reconstruct the demographic history of prehistoric Africans using genome-wide data.
• To investigate the ancestral contributions of ancient lineages to past and present African populations.
• To document the spread of agricultural and pastoralist groups and identify instances of natural selection.

Main Methods:

• Assembly and analysis of genome-wide data from 16 individuals from prehistoric Africa.
• Ancient DNA (aDNA) sequencing and bioinformatics analyses.
• Population genetic modeling to infer ancestry and migration patterns.

Main Results:

• The anciently divergent lineage of the San people had a broader past distribution than previously known, contributing significantly to hunter-gatherers in Malawi and Tanzania.
• The expansion of West African farmers led to the replacement of local hunter-gatherer populations in certain areas.
• A Tanzanian pastoralist from ~3,100 years ago contributed ancestry across eastern and southern Africa, including to a ~1,200-year-old southern African pastoralist, indicating widespread herder movements.

Conclusions:

• The deep diversification of African lineages was complex, involving extensive gene flow and potentially more deeply diverged lineages than the San contributing to Western African populations.
• Ancient genomes provide direct evidence for population replacement and long-distance migrations associated with the spread of farming and herding.
• Analysis of ancient genomes from southern Africa revealed specific episodes of natural selection in these populations.