Assessing the effect of model specification and prior sensitivity on Bayesian tests of temporal signal
Fig 6
Prior predictive simulations and marginal priors of root heights, given the prior on the effective population size, θ.
Each panel corresponds to a different prior on θ, as described on Table 1 (Exponential(μ = 1.0), Log-normal(μ = 1.0, σ = 5.0), and Γ(κ = 0.001, θ = 1000)). We show five simulated trees from our analysis using sampling times (heterochronous analyses) and overlaid them (similar to densitree plots [56]). The violin plots show the prior densities of the root height and the hollow circles denote 100 randomly drawn samples from the prior. The y-axis is the time from the present, but note that the scales are different. Tip nodes are shown with solid grey circles. The densities and trees on the left, in orange, do not include an explicit prior on the root height (Th), while those to the right, in purple, have a hard bound on the root height in the form of a uniform prior between 0.0 and 5.0 units of time.