Supergene validation: A model-based protocol for assessing the accuracy of non-model-based supergene methods.

Area of Science:

• Phylogenetics
• Computational Biology
• Genomics

Background:

• Genome-scale species tree inference relies on heuristic methods using estimated gene trees.
• A key assumption is the error-free estimation of gene trees.
• Supergene methods concatenate loci to improve gene tree accuracy but lack validation protocols.

Purpose of the Study:

• To develop and present a generalizable, model-based protocol for validating supergenes and supergene methods.
• To assess the accuracy of supergene concatenation steps in phylogenomic analyses.
• To introduce model-based tests of phylogenetic congruency for supergene validation.

Main Methods:

• Adoption of model-based tests of topological congruence for supergene validation.
• Development of a generalizable supergene validation protocol.
• Comparison of model-based procedures against non-model-based methods for supergene construction.

Main Results:

• Model-based phylogenetic congruency tests effectively validate supergenes.
• The proposed model-based procedures outperform non-model-based methods in supergene construction.
• The protocol provides a means to assess supergene method performance across phylogenomic datasets.

Conclusions:

• Model-based supergene validation is essential for reliable species tree inference.
• The developed protocol enhances the accuracy and reliability of phylogenomic analyses.
• This approach improves the assessment of supergene methods in computational biology.