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Identifying the causes of species diversification and extinction remains a major challenge. Such biodiversity dynamics can be influenced by two major classes of factors:(i) biotic (intrinsic to the species, such as biological traits or species interactions), as in the Red Queen scenario; and (ii) abiotic (extrinsic to the species, such as climatic and geological events), as in the Court Jester scenario. Both classes are likely at play in most montane systems, where the interaction between mountain building and climate change may generate species diversity in a variety of ways; for example, via increased environmental heterogeneity, the generation of local habitats, the immigration of species or the formation of island‐like ecological opportunities. Teasing apart the relative contributions of abiotic and biotic processes is challenging, because both may occur simultaneously and interact with each other, and a statistical framework that enables the separation of their relative contributions is still lacking. Here, we review the origin and evolution of biodiversity within a unified phylogenetic framework that explicitly disentangles the influences of mountain orogeny, climate change and ecological interactions. Relying on recently developed birth–death models, we build a model‐testing approach that compares various diversification scenarios. Our approach includes a series of biologically realistic models to estimate speciation and extinction rates using a phylogeny, while assessing the relationship between diversification in the focal clade with an environmental variable, with growing species diversity within the focal clade or with the diversity of interacting clades. We …