ArticleJournal of molecular evolution2025
Stochastic Character Mapping: An Under-Exploited Approach to the Study of Molecular Evolution.
Article in Journal of molecular evolution, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
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1 citing paper in PubMed.
- Summarizing Evolutionary Trajectories from Phylogenetic Character Maps of Discrete Traits.bioRxiv : the preprint server for biology · 2026Article
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2 authors.
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Abstract
Methods for the probabilistic mapping of the history of state changes over a phylogeny have been available for the study of molecular evolution for over two decades. In spite of this, such methods have yet to be adopted at large by most molecular evolutionary biologists. Here, we re-emphasize the potential of these stochastic mappings with examples pertaining to the study of the amino acid replacement process. We show how the features targeted by today's top-performing models could have been highlighted in a full phylogenetic context with an amino acid-level Jukes-Cantor model. We also demonstrate how stochastic mappings could be used for detecting CpG hypermutability, a site-dependent feature. We hope for a larger project utilizing mapping-based methods to provide of more fulsome characterization of molecular evolution, and to prioritize and assess modeling efforts. Finally, we draw attention to the options available within the PhyloBayes(-MPI) software for producing mappings under a large set of evolutionary models.
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