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Aim We advocate an interdisciplinary approach to biogeography, integrating geology and paleobiology to examine how biodiversity dynamics evolved as mountain ranges formed through (geological) time. Location Global; case study: Anatolia (Turkey). Methods We discuss the links between surface uplift and biodiversity dynamics and review recent developments for reconstructing the history of geography and biodiversity. To illustrate an integrative approach to biogeography, we present a case study of Neogene Anatolia. In particular, we reconstruct Anatolian paleogeography based on a synthesis of both quantitative and qualitative evidence, and review the fossil record of the regional flora and fauna, to identify changes in compositions that might be induced by surface uplift and associated environmental changes. Results The Central Anatolian Plateau and its mountainous margins display different histories of surface uplift during the late Miocene to Pliocene, which are detectable in the regional fossil record of large mammals. Overall changes in vegetation and climatic conditions for the whole region also align with the general time frame of surface uplift. Main conclusions Our discussion and case study highlight the value of an integrative biogeographic framework, by combining knowledge and techniques from geology and paleobiology to simultaneously consider the biotic and environmental dynamics in space and time. Neogene surface uplift in Anatolia has affected the regional biota, particularly the diversity of plants and large mammals, along with well-known global and regional changes in climate and other environmental factors. To disentangle the effects of different, but most likely interactive environmental changes at various scales, we call for rigorous examination of the geological record in a biogeographic framework, using innovative methods to uncover how environmental and biotic processes have shaped mountain biodiversity.