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A multi-proxy study on a sediment core from Pedro Palo Lake, a mid-altitude endorheic Andean Lake in northern South America, was carried out to understand the effects of human activities and climate variability on tropical mountain freshwater ecosystems. Results indicate that between ~ 7980 and 4110 cal year BP the lake maintained well-mixed, mesotrophic conditions, within which a diverse planktonic and benthic diatom community flourished. From 4110 to about 2050 cal year BP, benthic diatoms almost disappeared, and the planktonic community changed to include small Discostella spp. and large Fragilaria species, suggesting higher nutrient concentrations and possibly, more turbid waters. At this time, peaks in charcoal concentration and in the sedimentary C/N ratio imply that forest fires in the watershed intensified and that more organic matter, derived from terrestrial vegetation, accumulated in the lake. This period coincides with an increase in population, and in the social, technological and agricultural complexity of indigenous peoples. We propose that anthropogenic activities, burning and deforestation, increased the nutrient load to the lake causing the observed changes in the diatom communities. After 2050 cal year BP, periphytic diatoms returned, the intensity and frequency of fires diminished, and a secondary forest grew. We infer an associated decrease in nutrients, resulting from reforestation and/or lower water levels caused by drier climates. Estimations based on the age model of the core suggest that it took approximately 30 years for the lake to change from its most degraded state in the middle Holocene to its state in the late Holocene. However, the much-reduced diversity of the diatom community after ~ 2050 cal year BP indicates that the lake did not rebound to its previous middle Holocene conditions. The record from Pedro Palo is therefore a good example of the detrimental and long-lasting effects of anthropic deforestation. [ABSTRACT FROM AUTHOR]