Abstract
Rapidly evolving pathogens, such as viruses and bacteria, accumulate genetic change at a similar timescale over which their epidemiological processes occur, such that, it is possible to make inferences about their infectious spread using phylogenetic time-trees. For this purpose it is necessary to choose a phylodynamic model. However, the resulting inferences are contingent on whether the model adequately describes key features of the data. Model adequacy methods allow formal rejection of a model if it cannot generate the main features of the data. We present TreeModelAdequacy, a package for the popular BEAST2 software that allows assessing the adequacy of phylodynamic models. We illustrate its utility by analyzing phylogenetic trees from two viral outbreaks of Ebola and H1N1 influenza. The main features of the Ebola data were adequately described by the coalescent exponential-growth model, whereas the H1N1 influenza data were best described by the birth–death susceptible-infected-recovered model.
Highlights
Model selection methods only allow a relative comparison of a set of models, but they cannot determine whether any of the models in question could have generated key features of the data at hand
Absolute model fit can be assessed via model adequacy methods, where a model is considered “adequate” if it is capable of generating the main features of the empirical data
Phylodynamic and diversification models are fitted to phylogenetic trees and their parameters depend on the distribution of nodes, such that some useful test statistics include the ratio of external to internal branch lengths, the tree height, and measures of phylogenetic tree imbalance (Revell et al 2005, 2008; Drummond and Suchard 2008; Höhna 2015)
Summary
Model selection methods only allow a relative comparison of a set of models, but they cannot determine whether any of the models in question could have generated key features of the data at hand (i.e., absolute model fit). In full Bayesian phylogenetic analyses, the tree, parameters for the molecular clock, the substitution model, and the phylodynamic model can be estimated simultaneously using molecular data. Phylodynamic and diversification models are fitted to phylogenetic trees and their parameters depend on the distribution of nodes, such that some useful test statistics include the ratio of external to internal branch lengths, the tree height, and measures of phylogenetic tree imbalance (Revell et al 2005, 2008; Drummond and Suchard 2008; Höhna 2015).
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