ArticleMolecular biology and evolution2025
A Phylogenetic Method Identifies Candidate Drivers of the Evolution of the SARS-CoV-2 Mutation Spectrum.
Article in Molecular biology and evolution, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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2 citing papers in PubMed.
- Graph transformer for ancient ancestry inference.bioRxiv : the preprint server for biology · 2026Article
- The core-pivotal index: a geometry-first approach to academic impact.Molecular biology and evolution · 2026Article
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Abstract
The molecular processes that generate new mutations evolve, but the causal mechanisms are largely unknown. In particular, the relative rates of mutation types (e.g. C > T), the mutation spectrum, sometimes vary among closely related species and populations. I present an algorithm for subdividing a phylogeny into distinct mutation spectra. By applying this approach to a SARS-CoV-2 phylogeny comprising approximately 8 million genome sequences, I identify ten shifts in the mutation spectrum. I find strong enrichment consistent with candidate causal amino-acid substitutions in the SARS-CoV-2 polymerase, and strikingly three appearances of the same homoplasious substitution are each associated with decreased C > T relative mutation rates. With rapidly growing genomic datasets, this approach and future extensions promise new insights into the mechanisms of the evolution of mutational processes. Keywords: Mutation Spectrum; Phylogenetic Analysis; SARS-CoV-2 Evolution.
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