Assessing the effect of model specification and prior sensitivity on Bayesian tests of temporal signal
Fig 2
Relative log marginal likelihoods of simulations.
The polygons represent the relative log marginal likelihood under three possible priors on the effective population size (θ) parameter of the constant-size coalescent tree prior. The top row is for heterochronous simulations, where temporal signal is present. The bottom row is for isochronous simulations that do not have temporal signal. Within each panel the corners correspond to a combination of model and sampling times, either a strict (SC) or relaxed molecular clock with an underlying log-normal distribution (UCLD), and with (heterochronous) or without (isochronous) sampling times. The correct model used to generate the data is the SC heterochronous (SC/het) for the top row and the SC isochronous (Iso/SC) for the bottom row. Each polygon is for one simulation replicate (a total of ten) and the colours denote whether we employed a hard bound on the root height of the form Uniform(0.0, 5.0), as shown in the legend.