Chapter 22: Preparing Paleontological Datasets for Phylogenetic Comparative Methods

by David W. Bapst


The fossil record holds considerable promise for furthering our understanding of macroevolutionary patterns, particularly allowing us to analyze hypotheses which cannot be tested with phylogenies of extant taxa alone. However, although there is a growing number of paleontological studies that use phylogenetic comparative methods to address questions of trait evolution, there is little documentation on obtaining the time-scaled phylogenies of fossil taxa required for such analyses. This chapter is an attempt to introduce interested readers to the issues involved with that process, including the uncertainties and biases involved with fossil data, which some might inadvertently overlook. In addition, I illustrate how the fossil records of different groups can be very different in terms of the datasets available, including the issues of that data, and stress that there is no ‘one size fits all’ solution. Instead, for several hypothetical examples, I recommend several approaches that explicitly consider potential uncertainties, unavailable data and biasing factors.