Does time matter in phylogeny? A perspective from the fossil record
The role of time (i.e. taxa ages) in phylogeny has been a source of intense debate within palaeontology for decades and has not yet been resolved fully. The fossilised birth-death range process is a model that explicitly accounts for information about species through time. It presents a fresh opportunity to examine the role of stratigraphic data in phylogenetic inference of fossil taxa. Here, we apply this model in a Bayesian framework to an exemplar dataset of well-dated conodonts from the Late Devonian. We compare the results to those obtained using traditional unconstrained tree inference. We show that the combined analysis of morphology and stratigraphic data under the FBD range process reduces overall phylogenetic uncertainty, compared to unconstrained tree inference. We find that previous phylogenetic hypotheses based on parsimony and stratophenetics are closer to trees generated under the FBD range process. However, the results also highlight that irrespective of the inclusion of age data, a large amount of topological uncertainty will remain. Bayesian inference provides the most intuitive way to represent the uncertainty inherent in fossil datasets and new flexible models increase opportunities to refine hypotheses in palaeobiology.