Integration of several geologic lines of evidence reveals the prevalence of a lowland trans-Andean portal communicating western Amazonia and the westernmost Andes from at least middle Miocene until Pliocene times. Volcanism and crustal shortening built up relief in the southernmost Central and Eastern Cordilleras of Colombia, closing this lowland gap. Independent lines of evidence consist first, of field mapping in the Tatacoa Desert with a coverage area of ∼381 km2, 1,165 km of geological contact traces, 164 structural data points, and 3D aerial digital mapping models. This map documents the beginning of southward propagation of the southernmost tip of the Eastern Cordillera’s west-verging, fold-and-thrust belt between ∼12.2 and 13.7 Ma. Second, a compilation of new and published detrital zircon geochronology in middle Miocene strata of the Tatacoa Desert shows three distinctive age populations: middle Miocene, middle Eocene, and Jurassic; the first two sourced west of the Central Cordillera, the latter in the Magdalena Valley. Similar populations with the three distinctive peaks have now been recovered in western Amazonian middle Miocene strata. These observations, along with published molecular and fossil fish data, suggest that by Serravallian times (∼13 Ma), the Northern Andes were separated from the Central Andes at ∼3°N by a fluvial system that flowed into the Amazon Basin through the Tatacoa Desert. This paleogeographic configuration would be similar to a Western Andean, or Marañon Portal. Late Miocene flattening of the subducting Nazca slab caused the eastward migration of the Miocene volcanic arc, so that starting at ∼4 Ma, large composite volcanoes were built up along the axis of today's Central Cordillera, closing this lowland Andean portal and altering the drainage patterns to resemble a modern configuration.

Alpine provenance studies based on conventional methods such as sandstone framework grain and heavy mineral analyses are now enhanced by improved techniques in laser ablation inductively coupled plasma mass spectrometry detrital zircon analysis. Although the conventional methods appear to have reached their limits of resolution in palaeogeographic problems, laser ablation inductively coupled plasma mass spectrometry U–Pb dating of detrital zircons adds the time dimension to the provenance analysis. Hafnium‐isotope ratios measured on dated zircons give further information on the origin of the magmas in which the detrital zircons have grown. This study reports detrital zircon U–Pb dating and Hf‐isotope results from sandstone formations related to rifting, drifting and subduction settings at different stages of the Alpine Tethys development. This study is a first evaluation of the correlation between U–Pb age and isotopic features of detrital zircons aimed at describing source terranes in different palaeogeographic domains in the Alpine Tethys area. Pan‐African/Cadomian (Ediacaran–Ordovician), Variscan (Middle Devonian–Carboniferous) and Post‐Variscan (Permian) detrital zircon populations are present in nearly all palaeogeographic settings, but in varying amounts. Single Mesoproterozoic and Palaeoproterozoic detrital zircons are found as minor populations. When comparing the northern and southern margins of the Alpine Tethys, the southern margin detrital sources are characterized mostly by a decreased occurrence or by the absence of Silurian–Devonian zircons. A major distinction between northern (Helvetic, North and Middle Penninic domains) and southern (Austro‐Alpine and South Alpine domains) detrital sources is the occurrence of Triassic zircons at the southern Alpine Tethys margin during rifting and subduction stage sedimentation. Hafnium‐isotope ratios measured on uppermost Permian–Triassic zircons from the South Alpine domain suggest a continental crust derivation of the hosting magmas, as expected in a continental rift environment. In the late stage of Alpine convergence (Late Cretaceous–Palaeogene), the Permian–Triassic zircons are reworked into basins situated on the northern Alpine Tethys margin.

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