A structured coalescent model reveals deep ancestral structure shared by all modern humans

Area of Science:

• Human evolutionary genetics
• Population genetics
• Ancient DNA analysis

Background:

• Understanding human origins requires analyzing admixture events and population size changes.
• Coalescence-based models are crucial for inferring demographic histories.
• Previous models have limitations in representing complex ancestral population dynamics.

Purpose of the Study:

• To introduce a novel coalescence-based hidden Markov model, cobraa.
• To explicitly model ancestral population split and rejoin events.
• To apply the model to simulated and real genomic data across species.

Main Methods:

• Development of cobraa, a coalescence-based hidden Markov model.
• Application of cobraa to simulated datasets for validation.
• Analysis of real genomic data from multiple species, including modern humans.

Main Results:

• Evidence for an extended period of structure in modern human history.
• An admixture event between two ancestral populations around 300,000 years ago in an ~80:20 ratio.
• A strong bottleneck detected in the major ancestral population shortly after divergence.
• Genomic regions from the minority ancestral population correlate with distance to coding sequences, suggesting negative selection.
• Majority ancestry regions show strong correlation with human-archaic hominin divergence, indicating its ancestral link to Neanderthals and Denisovans.

Conclusions:

• The study provides a new computational tool (cobraa) for detailed demographic inference.
• Modern humans evolved from a structured ancestral population with a significant admixture event.
• The findings shed light on the evolutionary pressures and ancestral components shaping the human genome, including links to archaic hominins.