Assessing Phylogenetic Confidence at Pandemic Scales
A new method called subtree pruning and regrafting-based tree assessment (SPRTA) improves the interpretability of phylogenetic analyses by considering evolutionary relationships between lineages, such as those found in SARS-CoV-2 variants.
The Role of Phylogenetics in Science
Phylogenetics plays a central role in evolutionary biology and genomic epidemiology. Reliable assessment of phylogenetic confidence is vital, and traditional methods like Felsenstein’s bootstrap are widely used.
Limitations of Existing Methods
- Require enormous computational power, making them impractical for very large datasets.
- Focus mainly on clade membership, complicating interpretation in genomic epidemiology contexts.
SPRTA: A New Paradigm
SPRTA offers an efficient and more interpretable way to assess confidence in phylogenetic trees. Unlike traditional approaches, it evaluates evolutionary histories and phylogenetic placement rather than just clade support.
"SPRTA shifts the paradigm of phylogenetic support measurement from evaluating the confidence in clades to evolution histories and phylogenetic placement—for example, assessing whether a lineage evolved from another considered lineage, which is particularly valuable in genomic epidemiology."
Significance for Genomic Epidemiology
This method enables clearer insights into the evolutionary paths of pathogens, which is critical for understanding variants and tracking pandemics.
Author's summary: SPRTA enhances phylogenetic analysis by focusing on evolutionary relationships and lineage placement, making large-scale genomic epidemiology more interpretable and computationally feasible.