Common ancestry is a central tenet of evolutionary theory; phylogenies allow us to view this history, and more importantly, they provide a framework for generating and testing hypotheses of evolution. Hypotheses of macroevolution are centred on biodiversity: understanding and maintaining biodiversity is a key challenge of biology, whilst palaeobiology is mainly concerned with understanding the processes that generated this diversity. In recent years phylogenies have been employed to provide a timescale for evolution, and understand morphologicaJ evolution using Phylogenetic Comparative Methods (PCMs). However, whilst fossils were instrumental in initially integrating macroevolutionary thought into the modem evolutionary synthesis, the majority of PCMs have been applied to extant species only. Therefore, the main theme of this thesis is to incorporate fossils into analyses of major patterns in macroevolution, and simultaneously test the effectiveness of these method we use to do this. In Chapters One and Five, I study times of large macroevolutionary change - the origin of birds and the Permo- Triassic mass extinction - using phylogenies composed mainly of fossils. In Chapter Three, I investigate macroevolutionary patterns using extant taxa only, but incorporating modem PCMS. In Chapters Two and Four, I investigate the effects fossils and alternative methods can have on our understanding of modem macroevolutionary change. Overall, I show fossils are important in the understanding of past macroevolutionary change. The continued use of fossils in phylogenetics has great promise for our understanding species' diversification and trait evolution, but it is still possible to elucidate patterns from extant taxa. Throughout, I keep a firm focus on the appropriateness of methods, and consider best ways to integrate from the present day into deep time, and to combine modem genomic trees with sparse fossil data.