Exact calculation of the expected SFS in structured populations.
Armando Arredondo1, Josué Corujo2, Camille Noûs3
1Institut National des Sciences Appliquées, Institut de Mathématiques de Toulouse, Université de Toulouse, Toulouse, France.
Theoretical Population Biology
|March 23, 2025
Summary
We present a novel method to calculate the expected Site Frequency Spectrum (SFS) for structured populations using coalescent theory. This approach overcomes computational challenges, enabling new population genetic inferences.
Area of Science:
- Population Genetics
- Evolutionary Biology
- Computational Biology
Background:
- The Site Frequency Spectrum (SFS) is crucial for understanding genetic variation and making population inferences.
- Calculating the expected SFS in structured populations is computationally challenging due to the large state space in coalescent theory.
Purpose of the Study:
- To develop an efficient method for calculating the expected SFS in structured populations.
- To overcome the limitations of existing methods in handling complex population structures.
Main Methods:
- Formulating the expected SFS calculation as a linear system solution.
- Developing an algorithmic procedure to construct and sort the state space.
- Utilizing the sparsity of the rate matrix and iterative methods for numerical solutions.
- Specializing the method for the symmetrical n-island model.
Main Results:
- The proposed method successfully obtains the expected SFS by solving a linear system.
- An efficient algorithmic procedure is detailed, including state space management and numerical solvers.
- A specialized software, SISiFS, is developed for the n-island model.
Conclusions:
- The developed method provides a computationally feasible approach to calculate the expected SFS in structured populations.
- SISiFS software facilitates demographic parameter inference, advancing population genetic studies.
- This work bridges theoretical coalescent models with practical computational tools for evolutionary inference.
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