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Multiple climate proxies indicate episodic changes in moisture levels within an ~1 Ma duration (early-mid Pliocene) interval. Limestones within the Opache Formation, Calama Basin, Atacama Desert region, Chile, contain evidence for wetter and drier periods on short time scales. Proxies include carbonate lithological changes, paleontology (stromatolites, oncolites, gastropods, ostracods and diatoms), O and C stable isotopes, geochemistry, and mineralogical changes (aragonite, calcite, Mg-calcite, dolomite and gypsum) throughout a 30 m stratigraphic section. Stromatolite fossil cyanobacteria dark and light laminations and mesohaline to hypersaline diatom species suggest Pliocene annual seasonality. Short-term changes between wetter and drier conditions indicate that at least this part of the Atacama region was experiencing relatively rapid early-mid Pliocene climate instability. The predominance of limestone in the Opache Formation, in contrast to the 1500 m of Oligocene-Miocene siliciclastic conglomerates and sandstones, interpreted as arid climate alluvium, that underlie it, indicates a shift from arid or hyperarid climate to a semi-arid climate. Semi-arid conditions promoted limestone deposition in a shallow lacustrine-palustrine environment. In this setting, events such as storms with associated surface water flow, erosion, siliciclastic sand, gravel, and intraclast deposition, coupled with significant biological activity, represent sedimentation during more humid periods in a shallow lacustrine depositional environment. In contrast, limestone characterized by mudcracks, Navicula diatoms, and vadose syndepositional cementation, reflect periods of enhanced evaporation, water shallowing, and episodic desiccation, characteristic of a palustrine depositional system. These facies shifts, in conjunction with geochemical and isotopic proxy evidence, yield a sedimentary record of wetter and drier climate shifts. [ABSTRACT FROM AUTHOR]