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Related Concept Videos

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Bootstrap support is not first-order correct.

Edward Susko1

  • 1Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia, Canada. susko@mathstat.dal.ca

Systematic Biology
|June 8, 2010
PubMed
Summary
This summary is machine-generated.

Bootstrap support interpretation is re-evaluated. It is not a first-order correct P value for phylogenetic trees, often being conservative due to tree space properties.

Related Experiment Videos

Area of Science:

  • Phylogenetics
  • Computational Biology
  • Statistical Inference

Background:

  • Bootstrap support is widely used to assess the reliability of splits in phylogenetic trees.
  • A desirable interpretation is that 1-minus bootstrap support represents a P value for the null hypothesis that a split is not well resolved.
  • Previous arguments suggested bootstrap support is first-order correct as a P value.

Purpose of the Study:

  • To investigate the statistical accuracy of bootstrap support as a P value.
  • To determine if bootstrap support is first-order correct under maximum likelihood estimation and neighbor-joining algorithms.
  • To provide insight into the reasons for any observed inaccuracies.

Main Methods:

  • Derivation of the limiting distribution of bootstrap support for splits under maximum likelihood (ML) estimation.
  • Analysis of bootstrap support using the neighbor-joining (NJ) algorithm.
  • Examination of example phylogenetic trees to illustrate findings.

Main Results:

  • Bootstrap support is not first-order correct as a P value for the hypothesis that a split is not well resolved.
  • This inaccuracy holds for both ML and NJ tree reconstruction methods.
  • Bootstrap support is generally conservative as a P value, particularly due to the nature of tree space.

Conclusions:

  • The interpretation of bootstrap support as a first-order correct P value is flawed.
  • The conservative nature of bootstrap support is linked to the properties of phylogenetic tree space.
  • Further understanding of bootstrap support's statistical behavior is needed for accurate phylogenetic inference.