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Testing Multispecies Coalescent Simulators Using Summary Statistics.

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    New methods validate gene tree simulations for species tree inference. Several popular simulators produced flawed samples, highlighting the need for rigorous testing of the multispecies coalescent (MSC) model. An R package is available for testing.

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    Area of Science:

    • Computational Biology
    • Phylogenetics
    • Bioinformatics

    Background:

    • Genomic-scale data fuels species tree inference research.
    • Multispecies coalescent (MSC) simulators are crucial for evaluating new inference methods.
    • Ensuring the validity of simulator outputs is paramount.

    Purpose of the Study:

    • To develop methods for verifying gene tree collections against the MSC model for a given species tree.
    • To assess the accuracy of existing MSC simulators.
    • To provide tools for validating phylogenetic simulation software.

    Main Methods:

    • Development of statistical tests to compare gene tree distributions to MSC predictions.
    • Evaluation of topological and metric properties of gene trees.
    • Application of tests to established gene tree simulators.

    Main Results:

    • Several widely-used MSC simulators were found to produce invalid samples.
    • The developed tests effectively identify discrepancies between simulated and expected gene tree properties.
    • The study pinpoints specific issues in simulator outputs.

    Conclusions:

    • Rigorous validation of MSC simulators is essential for reliable species tree inference.
    • The new testing methods ensure the accuracy of gene tree samples.
    • The freely available R package MSCsimtester facilitates simulator validation for researchers.