Identifying and addressing methodological incongruence in phylogenomics: A review

Area of Science:

• Evolutionary Biology
• Bioinformatics
• Computational Biology

Background:

• Phylogenetic data availability has surged, shifting research bottlenecks from data acquisition to analytical methods.
• Evaluating new phylogenetic analysis techniques and artefact identification is paramount for robust evolutionary hypotheses.
• Incongruence in phylogenetic reconstructions stems from biological (e.g., horizontal gene transfer) and methodological (e.g., data misassignment) sources.

Purpose of the Study:

• To provide a practical review of recent advancements in detecting phylogenetic artefacts.
• To discuss methods for identifying model violations and data misassignments in phylogenetic analyses.
• To guide researchers in selecting appropriate artefact detection tools based on dataset characteristics and computational resources.

Main Methods:

• Review of recent techniques for detecting artefacts in phylogenetic reconstructions.
• Discussion of methods to identify model violations and poorly assigned data.
• Comparative analysis of the advantages and disadvantages of various detection techniques.

Main Results:

• Identified and reviewed various tools for detecting phylogenetic artefacts.
• Highlighted the importance of distinguishing between biological and methodological sources of incongruence.
• Emphasized that methodological artefacts must be excluded before attributing incongruence to biological processes.

Conclusions:

• Selecting appropriate artefact detection methods is critical for accurate phylogenetic inference.
• No single method is universally applicable; choices depend on the specific dataset and available computational power.
• Informed selection of detection methods enhances the reliability of evolutionary history reconstructions.