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.

Aim Lakes in the Ecuadorean Andes span different altitudinal and climatic regions, from inter Andean plateau to the high‐elevation páramo, which differ in their historical evolution in the several centuries since the pioneering Humboldt expeditions. Here, we evaluate temporal and spatial patterns of change in diatom assemblages between historical (palaeolimnological) and modern times. Location Ecuadorean Andes Methods We compared historical (pre‐1850) and modern (2017) diatom assemblages from 21 lakes and determined the relative role of environmental (water chemistry and climate) and spatial factors (distance‐based Moran's eigenvectors maps) on both assemblages using non‐metric multidimensional scaling (NMDS) with environmental fitting. In addition, we used redundancy analysis (RDA) with variance partitioning to estimate the historical (measured using downcore assemblage composition) effects on modern diatom assemblages and identified diatom species that contributed most to dissimilarity between the two times. Results Diatom changes between the two time points were limited across the group of lakes, as indicated by the NMDS ordination. Variance partitioning indicated that modern diatom assemblages were affected by environmental and spatial effects, but with non‐significant effects of past diatom species composition. Ordination results showed that variables related to elevation and water chemistry affected both modern and historical diatom assemblages. Diatom species with the best fit on NMDS axes (i.e. >70%) were influenced by elevation and climatic variables. The most distinctive change between the two time periods was the higher relative abundance of planktic diatom species in top‐core assemblages of some lakes, but in a highly variable fashion across gradients of increased elevation and water depth. Main conclusions Landscape palaeolimnological analyses of varied Ecuadorean Andean lakes demonstrate both environmental and spatial controls on diatom metacommunities. The multi‐faceted ecological control of the altitudinal gradient on both historic and contemporary diatom assemblages suggests species sorting and dispersal constraints operating at centennial time‐scale. Although a few individual lakes show substantive change between the 1850s and today, the majority of lakes do not, and the analysis suggests the resilience of lakes at a regional scale. We emphasize the potential of diatom palaeolimnological approaches in biogeography to test ecologically relevant hypotheses of the mechanisms driving recent limnological change in high‐elevation tropical lakes.

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