AdmixSim 2: a forward-time simulator for modeling complex population admixture

Area of Science:

• Population genetics
• Evolutionary biology
• Genomics

Background:

• Computer simulations are vital in population genetics and evolutionary studies.
• Existing simulation tools are limited for studying population admixture.
• Developing advanced simulation tools is crucial for population admixture research.

Purpose of the Study:

• To develop a flexible and efficient forward-time simulator for population genomics data under complex evolutionary scenarios.
• To provide a tool capable of simulating complex population admixture scenarios with various evolutionary parameters.
• To facilitate downstream analyses such as local ancestry inference and association studies.

Main Methods:

• Developed AdmixSim 2, an individual-based, forward-time simulator.
• Implemented the extended Wright-Fisher model.
• Incorporated gene flow, natural selection, recombination, mutation, and sex-specific chromosome simulation.
• Utilized empirical or simulated genomic data as input for phased haplotype output.

Main Results:

• AdmixSim 2 simulates population genomics data under complex evolutionary scenarios, including admixture.
• The tool supports dioecious or monoecious populations, autosomes, and sex chromosomes.
• Phased haplotype data output facilitates local ancestry inference and association studies.
• Performance was evaluated using simulated and empirical data from diverse populations.

Conclusions:

• AdmixSim 2 is a versatile simulation tool for population admixture studies.
• The simulator is expected to advance research in complex population genetics.
• AdmixSim 2 provides a valuable resource for simulating admixture scenarios.