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DiagnoDating: diagnostics for dated phylogenies in microbial population genetics.

Xavier Didelot1,2, Jake Carson3, Paolo Ribeca4,5

  • 1School of Life Sciences, University of Warwick, Coventry, United Kingdom.

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Summary
This summary is machine-generated.

This study introduces diagnostic tools for evaluating dated phylogenies in microbial population genetics. The new methods assess inference quality in absolute terms, improving reliability for genomic relationship studies.

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Area of Science:

  • Genomics
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Dated phylogenies are crucial for microbial population genetics, but existing tools rely on assumptions that can compromise reliability.
  • Model comparison is used to assess relative inference accuracy, but evaluating absolute quality remains a challenge.

Purpose of the Study:

  • To develop and evaluate methods for assessing the absolute quality of dated phylogenies, independent of model comparison.
  • To provide robust diagnostic tools for microbial population genetic analyses.

Main Methods:

  • Application of established statistical diagnostic tools: outlier detection, posterior predictive checking, and residual analysis.
  • Testing methods on simulated datasets under correct and incorrect model assumptions to assess specificity and sensitivity.
  • Implementation of these diagnostics in a new R package, DiagnoDating.

Main Results:

  • Demonstrated the utility of outlier detection, posterior predictive checking, and residual analysis for dated phylogenies.
  • Quantified the specificity and sensitivity of these diagnostic methods using simulated data.
  • Showcased the practical application and issue-detection capabilities on three real-world datasets.

Conclusions:

  • The developed diagnostic tools offer a reliable way to evaluate dated phylogenies in absolute terms.
  • The DiagnoDating R package provides accessible implementation for researchers.
  • Adoption of these diagnostics is recommended for all microbial population genetic studies using dated phylogenies.