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Split-specific bootstrap measures for quantifying phylogenetic stability and the influence of taxon selection
Huai-Chun Wang1, Edward Susko2, Andrew J Roger3
1Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada; Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada; Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Canada.
Molecular Phylogenetics and Evolution
|August 29, 2016
Summary
New phylogenetic stability measures evaluate taxon sampling effects on evolutionary trees. These tools help identify influential taxa and improve phylogenetic accuracy by guiding sampling strategies.
Area of Science:
- Phylogenetics
- Computational Biology
- Evolutionary Biology
Background:
- Assessing phylogenetic tree robustness is crucial for understanding evolutionary relationships.
- Current methods like bootstrap support and posterior probabilities measure branch uncertainty but don't fully account for taxon sampling impacts.
- Taxon sampling significantly influences phylogenetic stability and the accuracy of inferred evolutionary histories.
Purpose of the Study:
- To develop novel, split-specific measures for evaluating phylogenetic stability.
- To assess how taxon sampling affects the robustness of internal branches in phylogenetic trees.
- To provide diagnostic tools for optimizing taxon sampling in phylogenetic studies.
Main Methods:
- Development of split-specific stability measures, including BPtaxon_split, BPsplit, BPtaxon, and RBIC-taxon, based on bootstrap support for quartets.
- Introduction of a pruned-tree distance metric.
- Application and validation of these measures using empirical and simulated phylogenetic datasets.
Main Results:
- Existing overall stability measures can mask taxon-specific instabilities.
- The new split-specific measures effectively identify taxa that destabilize phylogenetic inference.
- Analyzing reduced sets of quartets is vital for detecting the influence of combined taxa, not just individual ones.
Conclusions:
- The developed split-specific measures offer valuable diagnostic insights into phylogenetic robustness.
- These tools guide experimental design for optimal taxon sampling in phylogenetics.
- Improved taxon sampling strategies enhance the reliability of inferred evolutionary relationships.
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