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Related Experiment Videos

How meaningful are Bayesian support values?

Mark P Simmons1, Kurt M Pickett, Masaki Miya

  • 1Department of Biology, Colorado State University, Fort Collins, USA. p.simmons@lamar.colostate.edu

Molecular Biology and Evolution
|November 5, 2003
PubMed
Summary
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This study compared phylogenetic tree support methods in teleost fishes. Parsimony-based jackknife values underestimate support, while Bayesian methods overestimate it, suggesting caution when interpreting Bayesian results.

Area of Science:

  • Evolutionary biology
  • Bioinformatics
  • Phylogenetics

Background:

  • Accurate phylogenetic tree reconstruction is crucial for understanding evolutionary relationships.
  • Branch support values quantify the reliability of inferred evolutionary relationships.
  • Jackknife and Bayesian methods are commonly used for estimating branch support.

Purpose of the Study:

  • To compare the accuracy of parsimony-based jackknife values with Bayesian support values in phylogenetic analyses.
  • To quantify the accuracy of branch support values from both methods with respect to basal clades in teleost fishes.
  • To evaluate the performance of these methods under different taxon and character sampling scenarios.

Main Methods:

  • Phylogenetic analyses were conducted on 100 mitochondrial genomes from teleost fishes.

Related Experiment Videos

  • 366 partitions were analyzed using differential taxon and character sampling.
  • Tree topology and branch support values were compared between jackknife and Bayesian methods.

    • Main Results:

    • Both jackknife and Bayesian methods deviated from ideal support values.
    • Jackknife values consistently underestimated support.
    • Bayesian methods consistently overestimated support, with a greater magnitude of overestimation than underestimation by jackknife.
    • Both methods performed poorly with increased taxon sampling and unchanged character sampling.

    Conclusions:

    • Bayesian support values are often inappropriately high and should not be interpreted as probabilities of correct clade resolution.
    • Parsimony-based jackknife and bootstrap methods are recommended for estimating branch support due to their conservative nature compared to Bayesian overestimation.