THE FOSSILIZED BIRTH-DEATH PROCESS FOR ESTIMATING SPECIATION AND EXTINCTION RATES

Estimating speciation and extinction rates is essential for understanding the past, present and future of biodiversity. Critical interest in this topic has led to a divergent suite of independent methods – paleontological estimates are based on sampled stratigraphic occurrences, while phylogenetic estimates are based on the observed branching times in a given phylogeny, typically derived using the genes of living species. Surprisingly, these competing approaches have never been tested – therefore it is not known how independent data sources could be most effectively combined. The fossilized birth-death (FBD) process is a model that explicitly recognizes that the branching events in a phylogenetic tree and the fossils sampled from the rock record were generated by the same underlying diversification process. Here, we present a flexible extension of the FBD model. First, we incorporate the possibility that a sampled fossil may belong to the stem or crown of a given total group, appropriate when some degree of phylogenetic information is available. Second, we allow for the branching process to be modelled in the absence of any phylogenetic information – this is referred to as the fossil-lineage graph FBD. This eliminates entirely the requirement for anything about the underlying phylogeny to be known, such that the method can be applied when only occurrence data is available, but still allows the inherent phylogenetic structure of the data to be considered. We tested this new method using simulations and here we focus on the impact of non-uniform preservation and taxonomic uncertainty. We compared this method to fossil-based alternatives, including the widely implemented boundary-crosser method. We show that our new method is both accurate and precise, but that the performance of all approaches is sensitive to the model of preservation. Furthermore, we demonstrate that results are extremely sensitive to taxonomy, specifically the way in which species are defined with respect to the true underlying branching process. Finally, we demonstrate that the most precise results are recovered when some knowledge of the underlying phylogeny is incorporated explicitly. The most promising strategy to illuminating the processes that have shaped the Tree of Life will be to take advantage of both fossil and phylogenetic evidence.