INCORPORATING FOSSIL RICHNESS INFORMATION INTO DIVERSIFICATION ESTIMATES FROM MOLECULAR PHYLOGENIES

Understanding the disparity in clade sizes across the tree of life is a principle issue in evolutionary biology. Traditionally, such understanding of relative speciation and extinction rates came from studying fossil richness data. However, this approach is insufficient for lineages with poor or absent fossil records. Alternatively, the past decade has seen a flurry of activity fitting birth-death models to molecular phylogenies, using information from extant species richnesses and inferred branching times. However, molecular phylogenies, being composed of non-extinct taxa, impose a necessary monotonic increase in taxon richness over time. As we know from the fossil record that some lineages previously enjoyed higher diversity than today, the strict increase in diversity implied from molecular data may obfuscate genuine past diversification patterns, and for some clades may mislead inference altogether. An ideal approach would utilize a marriage of fossil and molecular data. fossilMEDUSA, building upon the original MEDUSA method of Alfaro et al. (2007; PNAS), supplements molecular phylogenies with past richness information from the fossil record, fitting piecewise birth-death models to better extract information on past diversification dynamics. The new method, part of the GEIGER 2.0 R package, is described and demonstrated using a large Carnivore data set.