ArticleMolecular biology and evolution2021
Robustness of Phylogenetic Inference to Model Misspecification Caused by Pairwise Epistasis.
Article in Molecular biology and evolution, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
6 citing papers in PubMed.
- A General Substitution Matrix for Structural Phylogenetics.Molecular biology and evolution · 2025Article
- Subspecies phylogeny in the human gut revealed by co-evolutionary constraints across the bacterial kingdom.Cell systems · 2025Article
- Insertions and Deletions: Computational Methods, Evolutionary Dynamics, and Biological Applications.Molecular biology and evolution · 2024Review
- CNETML: maximum likelihood inference of phylogeny from copy number profiles of multiple samples.Genome biology · 2023Article
- Epistasis Creates Invariant Sites and Modulates the Rate of Molecular Evolution.Molecular biology and evolution · 2022Article
- Shifts in amino acid preferences as proteins evolve: A synthesis of experimental and theoretical work.Protein science : a publication of the Protein Society · 2021Review
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Authors and funding
3 authors.
Funding
Abstract
Likelihood-based phylogenetic inference posits a probabilistic model of character state change along branches of a phylogenetic tree. These models typically assume statistical independence of sites in the sequence alignment. This is a restrictive assumption that facilitates computational tractability, but ignores how epistasis, the effect of genetic background on mutational effects, influences the evolution of functional sequences. We consider the effect of using a misspecified site-independent model on the accuracy of Bayesian phylogenetic inference in the setting of pairwise-site epistasis. Previous work has shown that as alignment length increases, tree reconstruction accuracy also increases. Here, we present a simulation study demonstrating that accuracy increases with alignment size even if the additional sites are epistatically coupled. We introduce an alignment-based test statistic that is a diagnostic for pairwise epistasis and can be used in posterior predictive checks.
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Registered trials
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