Question: Under what circumstances are local communities and metacommunities phylogenetically clustered, overdispersed or random assemblages in terms of phylogenetic relatedness? Methods: An individual-based eco-evolutionary model was used to explain the link between system properties, ecological and evolutionary processes, and phylogenetic patterns in a spatially explicit competitive metacommunity. We simulated adaptive radiation dictated by local ecological dynamics (intra- and inter-specific competition) and dispersal. Phylogenies were constructed from the resulting metacommunities and phylogenetic community structure was analysed. Conclusions: Phylogenetic clustering, dictated by the relative rate between eco-evolutionary processes such as colonization, invasion, and local radiation, are more likely if both intra- and inter-habitat heterogeneity is high. The amount of dispersal between habitats is also an important structuring parameter, but mainly so if intra-habitat heterogeneity is high and inter-habitat heterogeneity is low. Our results are based on a more rigorous and quantitative analysis of the ecological and evolutionary conditions dictating the phylogenetic signal and explain the continuous variability of phylogenetic clustering and overdispersion found in natural systems.