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Approximate Bayesian computation with deep learning supports a third archaic introgression in Asia and Oceania
Mayukh Mondal1, Jaume Bertranpetit2, Oscar Lao3,4
1Institute of Genomics, University of Tartu, Riia 23b Tartu, Tartu, 51010, Estonia.
Nature Communications
|January 18, 2019
Summary
Genetic studies reveal a third archaic human introgression event in Asian and Oceanian populations beyond Neanderthals and Denisovans. Deep learning models uncover complex human evolutionary history and archaic admixture.
Area of Science:
- Human evolutionary genomics
- Population genetics
- Paleoanthropology
Background:
- Anatomically modern humans experienced archaic hominin introgressions during Out of Africa dispersal.
- Neanderthal and Denisovan introgressions are known, but evidence suggests others from unidentified archaic groups.
- Understanding these admixture events is crucial for reconstructing human evolutionary history.
Purpose of the Study:
- To infer the evolutionary history of Eurasian populations, including past introgression events.
- To identify potential novel archaic hominin admixture in human populations.
- To apply deep learning methods to complex evolutionary genomics problems.
Main Methods:
- Developed a demographic model using deep learning within an Approximate Bayesian Computation (ABC) framework.
- Analyzed genetic diversity in current human populations to infer demographic history.
- Integrated ancient genome data with population genetic analyses.
Main Results:
- Confirmed previously identified Neanderthal and Denisovan introgressions.
- Provided strong evidence for a third introgression event affecting all Asian and Oceanian populations.
- The source of this third introgression is an archaic population related to, or an early offshoot of, the Denisova lineage.
Conclusions:
- Deep learning-based demographic modeling is effective for uncovering complex introgression events in human evolution.
- A previously unrecognized archaic introgression significantly shaped the genetic makeup of Asian and Oceanian populations.
- Further research is needed to fully characterize the archaic population responsible for this third admixture event.
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