Working with the tree of life in comparative studies: How to build and tailor phylogenies to interspecific datasets

Abstract

All comparative analyses rely on at least one phylogenetic hypothesis. However, the reconstruction of the evolutionary history of species is not the primary aim of these studies. In fact, it is rarely the case that a well-resolved, fully matching phylogeny is available for the interspecific trait data at hand. Therefore, phylogenetic information usually needs to be combined across various sources that often rely on different approaches and different markers for the phylogenetic reconstruction. Building hypotheses about the evolutionary history of species is a challenging task, as it requires knowledge about the underlying methodology and an ability to flexibly manipulate data in diverse formats. Although most practitioners are not experts in phylogenetics, the appropriate handling of phylogenetic information is crucial for making evolutionary inferences in a comparative study, because the results will be proportional to the underlying phylogeny. In this chapter, we provide an overview on how to interpret and combine phylogenetic information from different sources, and review the various tree-tailoring techniques by touching upon issues that are crucial for the understanding of other chapters in this book. We conclude that whichever method is used to generate trees, the phylogenetic hypotheses will always include some uncertainty that should be taken into account in a comparative study.