Chapter 8 illustrates the importance of considering the phylogeny of species when investigating different ecological questions related to species traits. First, the concept of phylogenetic trees is provided with the notion that, in some cases, species that share a common ancestor share some common traits, while in others distantly related species have evolved similar adaptations independently. Models of evolution, in particular the Brownian motion model, are introduced to set a reference for comparing the extent of trait conservatism. The importance of phylogeny is first discussed with respect to ‘species level’ analyses (Chapter 4) relating traits, species environmental preferences and species fitness. Tests such as Phylogenetic Independent Contrasts (PICs) are discussed in terms of whether they provide, or not, a way to ‘correct’ for the phylogenetic non-independence between species. Then the concept of phylogenetic relatedness between species is discussed in the context of Phylogenetic Diversity (PD) indices and combined with functional diversity measurements. Different R tools are described to support these types of analyses in the material accompanying this book.