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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.
Molecular Biology and Evolution
|April 14, 2026
Summary
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.
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.
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