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Tests for two trees using likelihood methods.

Edward Susko1

  • 1Department of Mathematics and Statistics & Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada.

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Summary
This summary is machine-generated.

This study evaluates tree comparison tests, finding the Kishino-Hasegawa (KH) test often yields incorrect error rates. A new bootstrap method improves KH test accuracy, offering better alternatives for phylogenetic analysis.

Keywords:
KH testSOWH testmaximum likelihoodtopology test

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Area of Science:

  • Phylogenetics
  • Statistical Inference
  • Computational Biology

Background:

  • Comparing phylogenetic trees is crucial for evolutionary studies.
  • Likelihood-based methods, such as the Kishino-Hasegawa (KH) and likelihood ratio (LR) statistics, are commonly used.
  • Determining appropriate thresholds for statistical significance is a key challenge.

Purpose of the Study:

  • To evaluate the accuracy of the KH test and LR statistic for comparing phylogenetic trees.
  • To develop and assess improved methods for setting significance thresholds.
  • To provide more reliable statistical tools for phylogenetic tree comparison.

Main Methods:

  • Analysis of two likelihood-based test statistics: KH and LR.
  • Investigation of various threshold determination methods, including normal theory, parametric bootstrap, and mixture of chi-squares.
  • Simulation studies to assess type I error probabilities and performance.
  • Development of a computationally efficient normal-theory parametric bootstrap method for KH test thresholds.
  • Extension of mixture of chi-squares results for LR statistic thresholds.

Main Results:

  • The standard KH test with normal theory thresholds often produces lower type I error rates than expected.
  • A normal-theory parametric bootstrap method offers improved threshold determination for the KH test.
  • The chi-bar test and KH test with normal bootstrap show good performance but are complex to implement.
  • Two conservative approaches provide a balance between performance and implementation simplicity.
  • An adjustment to the Swofford-Olsen-Waddell-Hillis (SOWH) test is proposed.

Conclusions:

  • Standard KH test thresholds can be unreliable; improved methods are necessary.
  • Parametric bootstrap and chi-bar tests offer more accurate phylogenetic tree comparisons.
  • Simpler conservative methods provide a viable alternative when complex methods are not feasible.
  • The study contributes to more robust statistical practices in phylogenetics.