OSF-Builder: A New Tool for Constructing and Representing Evolutionary Histories Involving Introgression

Area of Science:

• Evolutionary Biology
• Phylogenetics
• Computational Biology

Background:

• Introgression is a key evolutionary process driving innovation.
• Existing methods for detecting introgression are abundant, but few exist for reconstructing evolutionary histories involving it.

Purpose of the Study:

• To develop a novel method for constructing evolutionary histories that explicitly incorporate introgression.
• To create an efficient algorithm that minimizes the number of introgression events in reconstructed histories.

Main Methods:

• The study proposes a new method based on representing introgression as an "overlaid species forest" (OSF).
• An efficient algorithm, OSF-Builder, was developed to construct optimal OSFs by minimizing introgression events.
• The method utilizes a species forest and an allele tree as input.

Main Results:

• OSF-Builder is guaranteed to find an optimal overlaid species forest, minimizing introgression events.
• Simulations were used to assess the performance of the OSF-Builder algorithm.
• The method was successfully applied to a butterfly dataset with known introgression.

Conclusions:

• The developed method and OSF-Builder algorithm provide an efficient way to reconstruct evolutionary histories with introgression.
• This approach enhances our understanding of evolutionary processes and innovation.
• The OSF-Builder software is publicly available for use in phylogenetic research.