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Updated: Aug 30, 2025
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Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
Published on: December 7, 2021
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Robust Phylodynamic Analysis of Genetic Sequencing Data from Structured Populations
Jérémie Scire1,2, Joëlle Barido-Sottani1,2,3, Denise Kühnert4
1Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland.
Viruses
|August 26, 2022
Summary
The phylodynamic model "bdmm" now analyzes larger genetic datasets, improving population dynamic inference. This enhanced tool provides more precise estimates for complex models and migration patterns.
Area of Science:
- Computational phylodynamics
- Evolutionary biology
- Bioinformatics
Background:
- Phylodynamic models quantify population dynamics from phylogenetic trees.
- The BEAST 2 package 'bdmm' computes tree probability densities under these models.
- Previous 'bdmm' versions were limited to ~250 genetic samples.
Purpose of the Study:
- To enhance the computational efficiency and robustness of the 'bdmm' phylodynamic model.
- To enable the analysis of significantly larger genetic datasets.
- To improve the precision of parameter estimates in structured population models.
Main Methods:
- Implemented algorithmic improvements to the 'bdmm' package.
- Focused on enhancing numerical robustness and computational efficiency.
- Extended the model with new features inspired by empirical data.
Main Results:
- Dramatically increased the number of analyzable genetic samples.
- Achieved improved numerical robustness and calculation efficiency.
- Demonstrated higher precision in parameter estimates with larger datasets, especially for complex models.
- Applied the enhanced 'bdmm' to Influenza A virus HA sequence data (175 and 500 samples).
Conclusions:
- The updated 'bdmm' enables robust, faster, and more general phylodynamic inference for larger datasets.
- Analyzing larger datasets provides more precise estimates of population dynamics and migration patterns.
- 'bdmm' facilitates deeper insights into viral evolution and global spread.
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