Practical Guide and Review of Fossil Tip-Dating in Phylogenetics

Phylogenetic tip-dating has been and still is revolutionizing evolutionary biology in several ways. Fossil tip-dating, where fossils are placed into a phylogeny as tips based on morphological and/or molecular character information, provides a more principled approach to infer time-calibrated phylogenies compared with node-dating. Additionally, phylogenetic trees with fossils as tips become more and more important to elucidate evolutionary processes in macroevolutionary studies (e.g., deciphering diversification patterns and directional phenotypic evolution). Fossil tip-dating is slowly gathering popularity in empirical applications and has progressed substantially since its first demonstration in 2011, with respect to improved statistical models, software, and data sets. Nevertheless, executing a phylogenetic fossil tip-dating analysis is complicated and comes with many challenges. Here, we provide an extensive review and overview of methods and models for phylogenetic tip-dating analyses with fossils. We focus both on data collection and preparation and on modeling choices. We start with a survey of all published phylogenetic tip-dating studies to date, showing common data and modeling choices as well as trends toward new approaches. Then, we walk readers through sections of molecular evolution, morphological evolution (both for discrete and continuous data), and lineage evolution (the fossilized birth-death process). In each section, we describe the data and standard models with their underlying assumptions, and provide an outlook and practical recommendations.