Assessing the effect of model specification and prior sensitivity on Bayesian tests of temporal signal
Fig 3
Phylogenetic tree extension for a simulation replicate with no temporal signal.
Highest clade credibility trees from a data set simulated with no sampling times (isochronous) and under a strict molecular clock model (SC). The prior on effective population size (θ) is a Γ(κ = 0.001, θ = 1000), which resulted in high classification errors using BETS. The y-axis is the time from the present. Tip nodes have solid grey circles. Including sampling times that span 0.5 units of time and about 1/4 of the true root height induces dramatic overestimation of the root height, compared to the true model (SC, isochronous). This effect occurs under both molecular clock models, the SC and the relaxed molecular clock with an underlying log-normal distribution (UCLD), but it is markedly less pronounced in the UCLD. Note that the y-axis is in logarithmic scale (log10).