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Bayesian support is larger than bootstrap support in phylogenetic inference: a mathematical argument.
Tom Britton1, Bodil Svennblad, Per Erixon
1Department of Mathematics, Stockholm University, SE-106 91 Stockholm, Sweden. tomb@math.su.se
Mathematical Medicine and Biology : a Journal of the IMA
|November 6, 2007
Summary
Bayesian posterior probabilities (BPPs) often appear higher than bootstrap support (BS) values in phylogenetic inference. This study provides a mathematical explanation for this common observation using likelihood properties and simulations.
Area of Science:
- Phylogenetic inference and computational evolutionary biology.
- Statistical modeling in bioinformatics.
Background:
- Phylogenetic tree support is crucial for understanding evolutionary relationships.
- Non-parametric bootstrap support (BS) and Bayesian posterior probabilities (BPPs) are common measures.
- Empirical studies consistently show BPPs are higher than BS values for the same data.
Purpose of the Study:
- To provide a theoretical, mathematical explanation for the observed difference between BS and BPP values.
- To support empirical findings with a heuristic argument based on likelihood theory.
Main Methods:
- Developed a heuristic mathematical argument.
- Utilized properties of marginal and profile likelihoods for the normal distribution.
- Conducted a simulation study to validate the theoretical argument.
Main Results:
- Presented a mathematical argument explaining why BPPs tend to be higher than BS values.
- The argument leverages the behavior of likelihood functions under different estimation frameworks.
- Simulation results supported the key steps and conclusions of the heuristic argument.
Conclusions:
- The study offers a theoretical basis for the systematic inflation of BPPs compared to BS.
- Understanding this difference is vital for accurate phylogenetic tree interpretation.
- The findings contribute to the methodological rigor of phylogenetic inference.
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