Phylogenetic methods are central to the study of biology and in recent years more formal techniques involving computational methods have been developed and widely applied. While these have focused on building the Tree of Life from molecular data, other approaches have extended to phenotypes, behaviour, cultural evolution, and languages. However, underlying these methods, are some issues that relate to the structure and nature of the trees. This thesis sets out to explore some of these issues, and particularly how trees behave under conditions which may stretch the boundaries of phylogenetic approaches. In the first set of analyses, I tackle the problem of asymmetry in trees. It has been observed in many contexts that phylogenetic trees are asymmetrical – that is, descendants are not shared equally across sister clades. This asymmetry, known as phylogenetic imbalance, has been widely studied but primarily concerning trees that include only living lineages. In this chapter, I look at trees that include both extinct and extant lineages and explore how diversification dynamics and preservation biases influence phylogenetic imbalance. Trees were simulated and sampled under a variety of diversification and preservation models and compared with a range of empirical phylogenies. I find that while multiple model combinations can make combined-evidence phylogenies more imbalanced, only a few make them as imbalanced as empirical trees. The second set of analyses also looks at combined-evidence trees. In this case, I explore the impact of imbalance, and specifically long branches, on the ability of current methods to resolve combined-evidence phylogenies. Including extinct lineages appears to mitigate some of the problems associated with long branches and thus improve reconstructions of highly imbalanced trees. Another aspect of phylogenetic methods relates to how trees can be used to explore ecological and evolutionary patterns. A simple assumption might be that lineages that are more distantly related will also be more different in terms of their phenotypes and their ecological functions, however, empirical support for this is mixed. Using a near-complete morphological database and phylogeny for birds, and over 16000 bird assemblage recordss, I systematically explore the relationship between phylogenetic diversity and functional dispersion. Globally, I find that while phylogenetic diversity and functional dispersion are negatively correlated the relationship varies with latitude and longitude and is largely driven by the morphological constraints placed on birds by migration. Recently uplifted tropical mountains show exceptional levels of functional dispersion and regions with exceptionally high phylogenetic diversity fall along established biogeographical boundaries. These analyses indicate the power of linking phylogenetic approaches with morphological studies on a global scale. Phylogenetic approaches were developed initially for biological systems where gene-based heritability is well-understood. Anthropologists and linguists have also applied these methods to contexts where different systems of heritability are in place – for example, vertical transmission of material culture. The evolution of stars in the galaxy offers an interesting and untested field in which to explore the applicability of phylogenetic methods in an entirely new setting. Using separate chemical surveys of Milky Way stars, I evaluate the phylogenetic signal within each dataset and systematically explore how measurement error influences the resolution of two stellar phylogenies. The broader implications of these analyses are discussed in terms of the power, potential and limits of phylogenetic methods, and, how the structures of trees themselves provide more than simply an opportunity to rebuild the Tree of Life.