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PickMe: Sample Selection for Species Tree Reconstruction using Coalescent Weighted Quartets.

Joseph Rusinko1, Yu Cai1, Allison Crysler1

  • 1Department of Mathematics and Computer Science, Hobart and William Smith Colleges, Geneva, NY 14456, USA.

Systematic Biology
|May 5, 2025
PubMed
Summary
This summary is machine-generated.

Researchers developed PickMe, a Bayesian framework for selecting samples in phylogenomics. This algorithm improves species tree accuracy by formally assessing sample reliability, outperforming existing methods on simulated and real data.

Keywords:
AsclepiasApocynaceaeBayes factorgene treemilkweedphylogenomicssample selection

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Area of Science:

  • Phylogenomics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Reconstructing species trees requires careful selection of genes and samples from large datasets.
  • Incomplete or unreliable data complicates sample selection, often relying on ad hoc strategies.
  • Accurate species tree inference depends on maximizing sampling while ensuring data sufficiency.

Purpose of the Study:

  • To introduce PickMe, a Bayesian framework for formalizing sample selection in phylogenomics.
  • To develop a method for assigning reliability scores to individual samples for species tree analysis.
  • To improve the accuracy of species tree reconstruction by optimizing sample inclusion.

Main Methods:

  • Developed a Bayesian framework to compute posterior probabilities for quartets in a species tree.
  • Assigned sample reliability scores based on scaled posterior probabilities.
  • Implemented PickMe algorithm to recommend samples for species tree analysis under the Multispecies Coalescent model.

Main Results:

  • PickMe-selected samples produced more accurate species trees compared to unfiltered data or ad hoc cut-offs on simulated data.
  • Analysis of milkweed target capture data suggested PickMe could have included more samples than previously analyzed.
  • PickMe demonstrated superior performance against existing sample selection methods using both simulated and empirical data.

Conclusions:

  • PickMe provides a formal, data-driven methodology for sample selection in phylogenomics.
  • The PickMe algorithm enhances the reliability and accuracy of species tree reconstruction.
  • PickMe is a valuable addition to phylogenomic data analysis pipelines, improving sample selection strategies.