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A Practical Guide to Phylogenetics for Nonexperts
Published on: February 5, 2014
Spurious 99% bootstrap and jackknife support for unsupported clades
Mark P Simmons1, John V Freudenstein
1Department of Biology, Colorado State University, Fort Collins, CO 80523-1878, USA. psimmons@lamar.colostate.edu
Molecular Phylogenetics and Evolution
|June 28, 2011
Summary
Bootstrap and jackknife resampling in phylogenetic analyses can create misleading branch support due to artifacts. Using strict consensus and jackknife resampling, along with multiple tree searches, can improve phylogenetic accuracy.
Area of Science:
- Phylogenetic analysis
- Computational biology
- Evolutionary biology
Background:
- Branch support quantification via bootstrap and jackknife resampling is crucial for phylogenetic analyses.
- Previous research identified the frequency-within-replicates approach as a source of apparent support for unsupported clades.
- The current study addresses potential artifacts in phylogenetic tree support estimation.
Purpose of the Study:
- To demonstrate the 'undersampling-within-replicates' artifact in phylogenetic analyses.
- To illustrate how both frequency-within-replicates and undersampling-within-replicates artifacts can inflate branch support.
- To provide recommendations for more robust phylogenetic inference.
Main Methods:
- Analysis of contrived and empirical datasets to illustrate bootstrap and jackknife artifacts.
- Evaluation of artifacts in both parsimony and maximum likelihood phylogenetic inference methods.
- Testing of outputs from multiple phylogenetic inference software.
Main Results:
- The frequency-within-replicates artifact can lead to overestimation of clade support.
- The undersampling-within-replicates artifact, where non-representative subsets of optimal trees are used, also inflates support.
- These artifacts are present in both parsimony and likelihood analyses and across different phylogenetic programs.
Conclusions:
- Summarize pseudoreplicate trees using strict consensus, not frequency-within-replicates.
- Employ jackknife resampling over bootstrap resampling for more reliable support values.
- Conduct multiple tree searches per pseudoreplicate and map support values onto the strict consensus tree.
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