DOI:10.1093/sysbio/syu006 Bayesian Estimation of Speciation and Extinction from Incomplete Fossil Occurrence Data

Abstract.—The temporal dynamics of species diversity are shaped by variations in the rates of speciation and extinction, and there is a long history of inferring these rates using first and last appearances of taxa in the fossil record. Understanding diversity dynamics critically depends on unbiased estimates of the unobserved times of speciation and extinction for all lineages, but the inferenceof theseparameters is challengingdue to the complexnature of the availabledata.Here,wepresent a new probabilistic framework to jointly estimate species-specific times of speciation and extinction and the rates of the underlying birth–death process based on the fossil record. The rates are allowed to vary through time independently of each other, and the probability of preservation and sampling is explicitly incorporated in themodel to estimate the true lifespan o