Bayesian Estimation of Speciation and Extinction Probabilities From (In)complete Phylogenies

Speciation and extinction probabilities can be estimated from molecular phylogenies of extant species that are complete at the species level. Because only a fraction of published phylogenies is complete at the species level, methods have been developed to estimate speciation and extinction probabilities also from incomplete phylogenies. However, due to different estimation techniques, estimates from complete and incomplete phylogenies are difficult to compare statistically. Here I show with some examples how existing likelihood functions can be used to obtain Bayesian estimates of speciation and extinction probabilities, and how this approach is applied to both complete and incomplete phylogenies.