Assessing the effect of model specification and prior sensitivity on Bayesian tests of temporal signal
Table 3
Correctly classified simulation replicates under heterochronous and isochronous trees.
A total of twenty simulations were generated in each configuration. Ten under heterochronous trees that are expected to display temporal signal, and ten under isochronous trees that they are not expected to support temporal signal. A number of ten represents perfect classification according to the Bayesian evaluation of temporal signal, BETS, and a log Bayes factor of at least 3 (strong evidence for temporal signal) for heterochronous trees. For isochronous trees, the threshold is a log Bayes factor of at most -3 (strong evidence against temporal signal). The rows correspond to three possible priors on the effective population size of the constant-size coalescent, θ. The ‘Best clock model’ is a situation where we consider the best heterochronous and isochronous model, take their log Bayes factor, and determine temporal signal if the absolute value in favour of the correct model is at least 3. The value to the left of / is the number of correctly classified heterochronous simulations, and the value right of / is the number of correctly classified isochronous simulations.