Robustness of Phylogenetic Inference to Model Misspecification Caused by Pairwise Epistasis |
| |
Authors: | Andrew F Magee Sarah K Hilton William S DeWitt |
| |
Institution: | 1.Department of Biology, University of Washington, Seattle, WA, USA;2.Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA;3.Department of Genome Sciences, University of Washington, Seattle, WA, USA |
| |
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. |
| |
Keywords: | phylogenetics epistasis model adequacy posterior predictive simulation |
|
|