Assessing the performance of qpAdm: a statistical tool for studying population admixture
Éadaoin Harney1,2,3,4, Nick Patterson4, David Reich3,4,5,6
1Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
Genetics
|March 27, 2021
Summary
qpAdm is a robust statistical tool for analyzing population admixture history. Simulations show it provides accurate ancestry proportions, even with imperfect data, but caution is advised for complex scenarios.
Area of Science:
- Population Genetics
- Computational Biology
- Human Ancestry
Background:
- Admixture is a key process shaping population genetics.
- qpAdm is a widely used statistical tool for modeling admixture.
- Limited performance assessments exist for qpAdm.
Purpose of the Study:
- To rigorously assess the performance of qpAdm across various scenarios.
- To identify potential limitations and weaknesses of the qpAdm tool.
- To establish best practices for utilizing qpAdm in population history studies.
Main Methods:
- A comprehensive simulation study was conducted.
- Various scenarios were simulated to test qpAdm behavior.
- Performance was evaluated under conditions of low data coverage, missing data, and ancient DNA damage.
Main Results:
- qpAdm demonstrates robustness and accuracy in many common scenarios.
- The tool performs well even with low data coverage, high missingness, and ancient DNA damage.
- Accuracy is maintained when diploid calls cannot be made.
Conclusions:
- qpAdm is a reliable tool for population admixture analysis.
- Users should avoid co-analyzing ancient and present-day data.
- Caution is recommended for models with numerous reference populations or prolonged gene flow.
- A user guide with best practices is provided.
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