Substitution model adequacy and assessing the reliability of estimates of virus evolutionary rates and time scales

Abstract

Determining the time scale of virus evolution is central to understanding their origins and emergence. The phylogenetic methods commonly used for this purpose can be misleading if the substitutionmodel makes incorrect assumptions about the data. Empirical studies consider a pool ofmodels and select that with the highest statistical fit. However, this does not allow the rejection of all models, even if they poorly describe the data. An alternative is to use model adequacy methods that evaluate the ability of a model to predict hypothetical future observations. This can be done by comparing the empirical data with data generated under the model in question. We conducted simulations to evaluate..