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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
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Gene Tree Discord, Simplex Plots, and Statistical Tests under the Coalescent.

Elizabeth S Allman1, Jonathan D Mitchell1,2, John A Rhodes1

  • 1Department of Mathematics and Statistics, University of Alaska Fairbanks, Fairbanks, AK 99709, USA.

Systematic Biology
|February 9, 2021
PubMed
Summary

A new simplex plot visualizes gene tree discordance, aiding comparisons to the multispecies coalescent model. This method helps identify significant gene tree inference errors or incomplete lineage sorting in evolutionary studies.

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Area of Science:

  • Phylogenetics
  • Evolutionary Biology
  • Computational Biology

Background:

  • Gene tree discordance complicates evolutionary history reconstruction.
  • The multispecies coalescent model (MSC) explains discordance via incomplete lineage sorting.
  • Visualizing and statistically testing gene tree discordance against MSC expectations is challenging.

Purpose of the Study:

  • Introduce a simplex plot for visualizing gene tree discordance.
  • Provide a statistical method to test gene tree data against the MSC.
  • Aid in identifying gene tree inference errors or complex evolutionary histories.

Main Methods:

  • Developed a simplex plot using quartet concordance factors.
  • Implemented a statistical procedure to quantify deviations from MSC predictions.
  • Applied the method to simulated and empirical multilocus datasets.

Main Results:

  • The simplex plot effectively summarizes gene tree discordance.
  • The statistical test identifies datasets incongruent with the MSC.
  • The approach distinguishes between gene tree error and significant incomplete lineage sorting.

Conclusions:

  • The simplex plot is a valuable tool for exploring gene tree collections.
  • The statistical test aids in model selection for evolutionary inference.
  • This method enhances the analysis of species tree reconstruction.