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Macroecology, as a relatively new field in Ecology, holds distinct methodological characteristics that lead to profound philosophical changes in the nature of evidence to support and build theories and models. One reason for this is the impracticability of controlled or manipulative experimental studies at broad spatial and temporal scales, as well as historical contingencies and the complexity of ecological dynamics at these scales. We follow here a model-based reasoning for building scientific theories and show in particular how computer simulation models, applied to different case studies in diversity gradients, can be successfully used in macroecology as mediating theory and data.