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Updated: Jul 23, 2025
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A Practical Guide to Phylogenetics for Nonexperts
Published on: February 5, 2014
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Computational Reproducibility of Molecular Phylogenies
Sudhir Kumar1,2, Qiqing Tao1,2, Alessandra P Lamarca1,2,3
1Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA.
Molecular Biology and Evolution
|July 19, 2023
Summary
Molecular phylogenetics can produce different evolutionary trees from the same data. However, these varied phylogenies show similar accuracy and do not hinder downstream research, suggesting irreproducibility is not a major issue.
Area of Science:
- Molecular Biology
- Computational Biology
- Evolutionary Biology
Background:
- Inferred molecular phylogenies can vary between analytical runs even with identical data and conditions.
- This lack of reproducibility impacts downstream research in comparative genomics, systematics, and functional biology.
Purpose of the Study:
- To assess the relative accuracies and log-likelihoods of alternative phylogenies generated from simulated and empirical data.
- To determine the relationship between computational irreproducibility and phylogenetic inaccuracy.
Main Methods:
- Generated alternative phylogenies using identical data sets and analytical conditions.
- Compared accuracies and log-likelihoods of inferred phylogenies against the true tree.
- Analyzed the influence of phylogenetic information content on reproducibility and accuracy.
Main Results:
- Alternative phylogenies reconstructed evolutionary relationships with comparable accuracy.
- Inferred phylogenies exhibited similar log-likelihoods, not inferior to the true tree's log-likelihood.
- Both irreproducibility and inaccuracy depend on the amount of phylogenetic information in the data.
Conclusions:
- Computational irreproducibility plays a minor role in the accuracy of molecular phylogenetics.
- Enhancing computational reproducibility through extended searches does not improve phylogenetic accuracy.
- The accuracy of inferred phylogenies is primarily influenced by the data's inherent phylogenetic information.
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