The overarching goal of phylogeography and the Earth-life sciences is to understand how geological and climatic processes contribute to the generation and distribution of the diversity of life on Earth. This question, at its heart, is one of causation. Causal structures are used to explain the cause-effect relations within natural systems and can be quantitatively evaluated through structural equation modeling. Here, I suggest that causality provides an organizing framework for linking extrinsic (geological) processes with genetic diversification and species richness that can be broadly applied. By using causal structures within individualistic taxonomic and geographic studies, we can tackle higher-order questions to reveal how Earth shapes life through time. Causal diagrams and structural equation modeling allow the abstraction of variables to accommodate (1) the heterogeneity of individual study systems, and (2) the need to reduce the complexity in interdisciplinary studies. Using directed acyclic graphs to articulate these relationships yield actionable hypotheses that feed directly back into Earth-life theory. I suggest many classically studied features, such as mountain ranges, are aggregate features whose causal effects can be decomposed into networks of indirect causal paths that are empirically testable. Formalizing causal relationships mitigates against the risk of mis-assigning causality, which can cloud our understanding of how the Earth-life system functions. Finally, this approach formalizes a way to test ideas about the top-down causation of biodiversity. Knowing how much of life is extrinsically forced would in turn reveal the importance of biotic-biotic interactions as well as intrinsic organismal and stochastic effects in shaping the diversity we see today.
Phylogeography needs extrinsic causal theory