Resolving the Tree of Life, in particular understanding the sequence of events taking place in its deepest branches, is currently a major research objective. Herein lie the answers to many fundamental questions about evolution: how do new groups originate, how are complex body-plans assembled and how do novelties such as legs and wings originate? The fossil record plays a pivotal role in this research by yielding transitional forms and providing a timeline for events, but are there particular dangers in the way we evaluate the filtered data they provide? Might fossils even be positively misleading if they are poorly interpreted? Interpretation of fossils can be distorted by biases caused by death, decay and preservation (taphonomy) - inevitable processes in the formation of fossils. Fossilizable and non-fossilizable data can contain very different 'signals' which could distort our ability to reconstruct evolutionary trees and transitions (phylogeny). Furthermore, decay and decomposition can cause fossils to appear more primitive than they were in life. Taphonomic filters therefore have very profound effects upon our ability to reconstruct evolution, but they have not been systematically investigated in this context. The key question I will address is therefore: do palaeontological filters have any effect upon our ability to reconstruct evolutionary trees and the evolutionary events that are inferred from them? If so, which groups of organisms are affected and in what way? Is the supposed importance of particular fossils a result of misinterpretation? When taphonomic filters are taken into account, is our understanding of specific evolutionary hypotheses, such as those relating to the origins of major clades, transformed? In order to address this questions, I will 1) Quantify the effect of taphonomic filters upon our ability to reconstruct the evolutionary relationships of fossil organisms using empirical and theoretical approaches; 2) Identify which types of data and groups of organisms are most disrupted by decay biases, thereby enabling focused study in some areas and encouraging caution in others; 3) Use knowledge of taphonomic filters to re-evaluate the Tree of Life. These combined approaches will allow me to test specific hypotheses relating to the origin and evolution of major groups. More broadly, they will enable a fundamental assessment of the quality of the fossil record. By quantifying the scale and distribution of these problems, we can refine and radically overhaul the way in which we use fossils to inform our understanding of the history of life.