Estimating Diversity Through Time Using Molecular Phylogenies: Old and Species-Poor Frog Families are the Remnants of a Diverse Past

The probability distribution of the ancestral population size conditioned on the reconstructed phylogenetic tree with occurrence data

We consider a homogeneous birth-death process with three different sampling schemes. First, individuals can be sampled through time and included in a reconstructed phylogenetic tree. Second, they can be sampled through time and only recorded as a point 'occurrence' along a timeline. Third, extant individuals can be sampled and included in the reconstructed phylogenetic tree with a fixed probability. We further consider that sampled individuals can be removed or not from the process, upon sampling, with fixed probability. We derive the probability distribution of the population size at any time in the past conditional on the joint observation of a reconstructed phylogenetic tree and a record of occurrences not included in the tree. We also provide an algorithm to simulate ancestral population size trajectories given the observation of a reconstructed phylogenetic tree and occurrences. This distribution can be readily used to draw inferences about the ancestral population size in the field of epidemiology and macroevolution. In epidemiology, these results will allow data from epidemiological case count studies to be used in conjunction with molecular sequencing data (yielding reconstructed phylogenetic trees) to coherently estimate prevalence through time. In macroevolution, it will foster the joint examination of the fossil record and extant taxa to reconstruct past biodiversity.