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MSMS: a coalescent simulation program including recombination, demographic structure and selection at a single locus.

Gregory Ewing1, Joachim Hermisson

  • 1Department of Mathematics, University of Vienna, Vienna, Austria. gregory.ewing@univie.ac.at

Bioinformatics (Oxford, England)
|July 2, 2010
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Summary

A new simulation program models population structure and selection, enabling studies of adaptation and selective sweeps. This tool enhances population genetics research with its flexible and compatible design.

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Area of Science:

  • Population Genetics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Coalescent simulations are crucial for understanding population genetics.
  • Existing tools like ms excel at modeling population structure and demography.
  • However, incorporating selection, especially deme- and time-dependent selection, requires advanced simulation capabilities.

Purpose of the Study:

  • To introduce a novel coalescent simulation program.
  • To extend existing simulation functionalities by incorporating deme- and time-dependent selection.
  • To provide a versatile tool for studying evolutionary processes in structured populations.

Main Methods:

  • Implementation of a coalescent simulation program.
  • Integration of forward simulations for modeling selection.
  • Compatibility with the established ms simulator's interface and output format.

Main Results:

  • The program successfully simulates structured populations with selection.
  • It enables the study of phenomena like hard and soft selective sweeps.
  • Performance remains comparable to existing simulators, even with the addition of selection.

Conclusions:

  • The new simulation program offers enhanced capabilities for population genetics research.
  • It is designed for extensibility and wide deployment.
  • The tool facilitates the investigation of local adaptation and selective sweeps in complex population structures.