Data from: From fossils to phylogenies: Exploring the integration of paleontological data into Bayesian phylogenetic inference

Incorporating paleontological data into phylogenetic inference can greatly
enrich our understanding of evolutionary relationships by providing
insights into the diversity and morphological evolution of a clade over
geological time scales. Phylogenetic analysis of fossil data has been
significantly aided by the introduction of the fossilized birth-death
(FBD) process, a model that accounts for fossil sampling through time. A
decade on from the first implementation of the FBD model, we explore its
use in over 170 empirical studies, summarising insights gained through its
application. We identify a number of challenges in applying the model in
practice: it requires a working knowledge of paleontological data and its
complex properties, Bayesian phylogenetics, and the mechanics of
evolutionary models. To address some of these difficulties, we provide an
introduction to the Bayesian phylogenetic framework, discuss important
aspects of paleontological data, and finally describe the assumptions of
the models used in paleobiology. We also present a number of exemplar
empirical studies that have used the FBD model in different ways. Through
this review, we aim to provide clarity on how paleontological data can
best be used in phylogenetic inference. We hope to encourage communication
between model developers and empirical researchers, with the ultimate goal
of developing models that better reflect the data we have and the
processes that generated them.