Ancient DNA and deep population structure in sub-Saharan African foragers

Area of Science:

• Paleogenomics
• Population Genetics
• African Prehistory

Background:

• Genetic and archaeological evidence indicates significant demographic shifts in sub-Saharan Africa during the Late Pleistocene and early Holocene epochs.
• Understanding ancient population structures is difficult due to later demographic changes over the past 5,000 years.

Observation:

• Genome-wide ancient DNA data from six individuals in eastern and south-central Africa, spanning 18,000 years, were analyzed.
• Data quality was improved for 15 previously published ancient individuals, and analyzed with 13 other published ancient individuals.

Findings:

• Sub-Saharan African ancestry is modeled as a mixture of three divergent source populations from the Pleistocene (80-20 kya).
• These include deeply diverged eastern and southern African lineages, and a widespread ancestry component prominent in modern Central African rainforest hunter-gatherers.
• This genetic structure remained stable with limited gene flow, supporting regionalization hypotheses.

Implications:

• Provides new genetic evidence supporting archaeological hypotheses about increasing regionalization at the end of the Pleistocene.
• Enhances the understanding of deep human population history and genetic diversity in sub-Saharan Africa.
• Doubles the time depth of ancient DNA data available for sub-Saharan Africa.