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Estimating Diversification Rates on Incompletely Sampled Phylogenies: Theoretical Concerns and Practical Solutions
Jonathan Chang1,2,3, Daniel L Rabosky2, Michael E Alfaro3
1School of Biological Sciences, Monash University, 25 Rainforest Walk, Melbourne, VIC 3800, Australia.
Systematic Biology
|December 6, 2019
Summary
Estimating species diversification rates from incomplete phylogenies can be biased. Stochastic polytomy resolution, like the new TACT method, improves accuracy by better handling unsampled taxa.
Area of Science:
- Evolutionary Biology
- Phylogenetics
- Computational Biology
Background:
- Molecular phylogenies are crucial for understanding species diversification dynamics.
- Empirical phylogenies often lack complete species representation, leading to biased diversification rate estimates.
- Statistical properties of methods correcting for incomplete sampling are not well understood.
Purpose of the Study:
- To identify theoretical concerns with analytical sampling corrections in sparsely sampled phylogenies.
- To introduce and evaluate stochastic polytomy resolution as an alternative to sampling fraction corrections.
- To present a new stochastic polytomy resolution method, Taxonomic Addition for Complete Trees (TACT).
Main Methods:
- Theoretical analysis of sampling fraction corrections and their impact on statistical power.
- Evaluation of stochastic polytomy resolution methods for inferring diversification rate shifts.
- Development of the TACT method using birth-death-sampling estimators and taxonomic data for unsampled taxa.
Main Results:
- Sampling fraction corrections can lead to low power to detect rate variation and spurious diversification patterns.
- Stochastic polytomy resolution significantly enhances the power to estimate diversification rate shifts.
- TACT effectively estimates branching times for unsampled taxa and integrates them into phylogenies.
Conclusions:
- Standard sampling fraction corrections are problematic for sparsely sampled phylogenies.
- Stochastic polytomy resolution offers a more robust approach for diversification inference.
- TACT provides a practical tool for improving diversification analyses with incomplete phylogenetic data.
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