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Palaeoecological records suggest that humans have been in the Andes since at least 14 000 years ago. Early human impacts on Andean ecosystems included an increase in fire activity and the extinction of the Pleistocene megafauna. These changes in Andean ecosystems coincided with rapid climate change as species were migrating upslope in response to deglacial warming. Microrefugia probably played a vital role in the speed and genetic composition of that migration. The period from ca 14 500 to 12 500 years ago was when novel combinations of plant species appeared to form no-analogue assemblages in the Andes. By 12 000 years ago most areas in what are today the Andean grasslands were being burned and modified by human activity. As the vegetation of these highland settings has been modified by human activity for the entirety of the Holocene, they should be regarded as long-term manufactured landscapes. The sharp tree lines separating Andean forests from grasslands that we see today were probably also created by repeated burning and owe their position more to human-induced fire than climatic constraints. In areas that were readly penetrated by humans on the forested slopes of the Andes, substantial modification and settlement had occurred by the mid-Holocene. In hard-to-reach areas, however, the amount of human modification may always have been minimal, and these slopes can be considered as being close to natural in their vegetation. This article is part of the theme issue ‘Tropical forests in the deep human past’.

Palaeoecological records suggest that humans have been in the Andes since at least 14 000 years ago. Early human impacts on Andean ecosystems included an increase in fire activity and the extinction of the Pleistocene megafauna. These changes in Andean ecosystems coincided with rapid climate change as species were migrating upslope in response to deglacial warming. Microrefugia probably played a vital role in the speed and genetic composition of that migration. The period from ca 14 500 to 12 500 years ago was when novel combinations of plant species appeared to form no-analogue assemblages in the Andes. Human populations increased in size and by 12 000 years ago most areas in what are today the Andean grasslands were being burned and modified. As the vegetation of these highland settings has been modified by human activity for the entirety of the Holocene, they should be regarded as long-term manufactutred landscapes. The sharp tree lines separating Andean forests from grasslands that we see today were probably also created by repeated burning and owe their position more to human-induced fire than climatic constraints. In areas that were readly penetrated by humans on the forested slopes of the Andes, substantial modification and settlement had occurred by the mid-Holocene. In hard-to-reach areas, however, the amount of human modification may always have been minimal, and these slopes can be considered as being close to natural in their vegetation.This article is part of the theme issue ���Tropical forests in the deep human past���.

Our understanding of the climatic teleconnections that drove ice-age cycles has been limited by a paucity of well-dated tropical records of glaciation that span several glacial–interglacial intervals. Glacial deposits offer discrete snapshots of glacier extent but cannot provide the continuous records required for detailed interhemispheric comparisons. By contrast, lakes located within glaciated catchments can provide continuous archives of upstream glacial activity, but few such records extend beyond the last glacial cycle. Here a piston core from Lake Junín in the uppermost Amazon basin provides the first, to our knowledge, continuous, independently dated archive of tropical glaciation spanning 700,000 years. We find that tropical glaciers tracked changes in global ice volume and followed a clear approximately 100,000-year periodicity. An enhancement in the extent of tropical Andean glaciers relative to global ice volume occurred between 200,000 and 400,000 years ago, during sustained intervals of regionally elevated hydrologic balance that modified the regular approximately 23,000-year pacing of monsoon-driven precipitation. Millennial-scale variations in the extent of tropical Andean glaciers during the last glacial cycle were driven by variations in regional monsoon strength that were linked to temperature perturbations in Greenland ice cores1; these interhemispheric connections may have existed during previous glacial cycles.

A 42,000-year record of coprophilous fungal (Sporormiella, Podospora, Cercophora), fossil pollen and charcoal data assessed megafaunal use of woodland versus grassland settings in Central American landscapes by Pleistocene megafauna. The sedimentary record from Lake Petén-Itzá showed that vegetation growing around the lake shifted between scrub grasslands, Pinus-dominated woodlands, Quercus-dominated woodlands, and tropical seasonal forest. A series of regression analyses and probabilistic models revealed that vegetation assemblages and temperature influenced the abundance of coprophilous fungus, a proxy for megafaunal abundance. We found that megafaunal populations were almost continuously present around Petén-Itzá during the Pleistocene, and that the peak abundances appear to have been associated with cool, moist Quercus-rich parklands. In contrast, the lowest inputs of coprophilous fungi occurred during cold, dry events when scrub grasslands expanded. The dry grasslands may have been nutrient-limited, offering poor quality grazing for megafauna. The decline of the Pleistocene megafauna at Petén-Itzá was a multi-stage event, with a series of population collapses prior to an inferred local extirpation c. 13,600 years ago.

Controversy exists over the cause and timing of the extinction of the Pleistocene megafauna. In the tropical Andes, deglaciation and associated rapid climate change began ~8,000 years before human arrival, providing an opportunity to separate the effects of climate change from human hunting on megafaunal extinction. We present a paleoecological record spanning the last 25,000 years from Lake Pacucha, Peru (3,100 m elevation). Fossil pollen, charcoal, diatoms, and the dung fungus Sporormiella, chronicle a two-stage megaherbivore population collapse. Sporormiella abundance, the proxy for megafaunal presence, fell sharply at ~21,000 years ago, but rebounded prior to a permanent decline between ~16,800 and 15,800 years ago. This two-stage decline in megaherbivores resulted in a functional extinction by ~15,800 years ago, 3,000 years earlier than known human occupation of the high Andes. Declining megaherbivore populations coincided with warm, wet intervals. Climatic instability and megafaunal population collapse triggered an ecological cascade that resulted in novel floral assemblages, and increases in woody species, fire frequency, and plant species that were sensitive to trampling. Our data revealed that Andean megafaunal populations collapsed due to positive feedbacks between habitat quality and climate change rather than human activity.