Robustness of Phylogenetic Inference to Model Misspecification Caused by Pairwise Epistasis.

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 e

SUBMITTER: Magee AF 

PROVIDER: S-EPMC8476159 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature