stdpopsim

stdpopsim extends population genetics models to incorporate realistic selection and demographic histories for simulating genetic variation across species.

Key Features:

• Selection Mode Simulation: Simulates background selection, selective sweeps, and arbitrary distributions of fitness effects (DFE).
• Species-Specific Models: Provides an extensive catalog of species-specific population genetic models with genomic annotations and published DFE estimates.
• Annotated Genome Subsets: Enables DFEs to act on annotated subsets of the genome, such as exons.
• Reproducibility: Maintains core principles of reproducibility and accessibility in simulation framework design.

Scientific Applications:

• Benchmarking Statistical Methods: Enables benchmarking of methods for demographic inference, DFE estimation, and selective sweep detection.
• Evolutionary Prediction Exploration: Supports exploration of theoretical predictions about the interplay between selection and other evolutionary forces.
• Method Robustness Assessment: Allows assessment of demographic inference method robustness to selection on linked sites.
• DFE-Inference Sensitivity Analysis: Reveals sensitivity of DFE-inference methods to model assumptions.
• Sweep Detection Power Analysis: Evaluates how genomic features like recombination rate and functional sequence density influence power to detect selective sweeps.

Methodology:

The framework extends a community-maintained simulation library to incorporate selection into existing species-specific population genetic models; specific computational algorithms or simulation engines are not detailed in the sources.