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Tree balance in phylogenetic models.

Sophie J Kersting1, Kristina Wicke2, Mareike Fischer1

  • 1Institute of Mathematics and Computer Science, University of Greifswald, Greifswald 17487, Germany.

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|February 20, 2025
PubMed
Summary
This summary is machine-generated.

Choosing the right phylogenetic tree balance index is crucial for accurate evolutionary analysis. This study groups indices by tree model suitability, aiding researchers and introducing the R package poweRbal for easier selection.

Keywords:
Yule modelmacroevolutionphylogenetic modelstree balance

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Area of Science:

  • Phylogenetics and Evolutionary Biology
  • Computational Biology
  • Statistical Modeling

Background:

  • Tree shape statistics, especially measures of phylogenetic tree balance, are vital for analyzing evolutionary processes.
  • Numerous (im)balance indices (over 30) exist, posing challenges for researchers in selecting appropriate measures and avoiding multiple testing issues.
  • Applications span evolutionary models, trait inheritance, tumor development, and language evolution.

Purpose of the Study:

  • To systematically evaluate the power of a comprehensive set of established phylogenetic tree balance indices.
  • To identify which indices are most effective for different types of phylogenetic tree models, including trait-based models.
  • To provide guidance for researchers in selecting appropriate balance indices and to introduce a new software tool.

Main Methods:

  • Expanded previous power analyses of tree balance indices to include almost all known indices.
  • Incorporated a broader range of alternative evolutionary models, including various trait-based models.
  • Developed the R software package `poweRbal` to facilitate the inclusion of new indices and models.

Main Results:

  • Identified distinct groups of balance indices that perform better with specific tree models.
  • Demonstrated that informed selection of balance indices based on prior knowledge of the tree model enhances analytical decisions.
  • The `poweRbal` package offers a flexible platform for future research on tree shape statistics.

Conclusions:

  • The choice of phylogenetic balance index significantly impacts the analysis of evolutionary models.
  • Researchers can improve their analyses by understanding which balance indices are best suited for different phylogenetic tree models.
  • The `poweRbal` package provides a valuable resource for the community to advance research in phylogenetic tree shape analysis.