The beginning of plant cultivation is one of the most important cultural transitions in human history 1 – 4 . Based on molecular markers showing the genetic similarities between domesticated plants and wild relatives, south-western Amazonia has been proposed as one of the early centres of plant domestication 4 – 6 . However, the nature of the early human occupation and the history of plant cultivation in south-western Amazonia are still little understood. Here, we document the cultivation of Cucurbita at ca. 10,250 cal yr BP, Manihot at ca. 10,350 cal yr BP and Zea mays at ca. 6,850 cal yr BP in the Llanos de Moxos. We show that, starting ca. 10,850 cal yr BP, pre-Columbians created an anthropic landscape made of approximately 4,700 artificial forest islands within a treeless seasonally flooded savannah. Our results confirm the Llanos de Moxos as a hotspot for early plant cultivation and demonstrate that ever since their arrival, humans have caused a profound alteration of Amazonian landscapes, with lasting repercussions for habitat heterogeneity and species conservation.

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Anthropogenic soils known as Amazonian Dark Earths (ADEs) have long been known as a key component of subsistence systems for various pre-Columbian Amazonian populations. Often treated as a single category, ADE systems consist of two broad anthrosols (human-modified soils): the darker ADE (traditionally known as terra preta) and a lighter brown Amazonian Brown Earth (ABE; traditionally known as terra mulata). Data on the characteristics and spatial distribution of these anthrosols are severely lacking. Transects of soil test pits at the Triunfo and Versalles archaeological sites in the Iténez Forest, in the Bolivian Amazon, show variability in the distribution of soil types, revealing aspects of settlement organisation and resource management. Geochemical, isotopic and archaeobotanical data from an ADE, ABE and control soil profile from the Triunfo site, established ca. 500 cal BCE, characterise the two anthrosols as distinct components of a polyculture agroforestry subsistence system that combines anthropogenic soil fertilisation, closed-canopy forest enrichment, limited forest clearance for crop cultivation and low-severity fire management.

Recent advances in the archaeology of lowland South America are furthering our understanding of the Holocene development of plant cultivation and domestication, cultural niche construction, and relationships between environmental changes and cultural strategies of food production. This article offers new data on plant and landscape management and mobility in Southwestern Amazonia during a period of environmental change at the Middle to Late Holocene transition, based on archaeobotanical analysis of the Monte Castelo shellmound, occupied between 6000 and 650 yr BP and located in a modern, seasonally flooded savanna–forest mosaic. Through diachronic comparisons of carbonized plant remains, phytoliths, and starch grains, we construct an ecology of resource use and explore its implications for the long-term history of landscape formation, resource management practices, and mobility. We show how, despite important changes visible in the archaeological record of the shellmound during this period, there persisted an ancient, local, and resilient pattern of plant management which implies a degree of stability in both subsistence and settlement patterns over the last 6000 years. This pattern is characterized by management practices that relied on increasingly diversified, rather than intensive, food production systems. Our findings have important implications in debates regarding the history of settlement permanence, population growth, and carrying capacity in the Amazon basin.

The southwestern Amazon Rainforest Ecotone (ARE) is the transitional landscape between the tropical forest and seasonally flooded savannahs of the Bolivian Llanos de Moxos. These heterogeneous landscapes harbour high levels of biodiversity and some of the earliest records of human occupation and plant domestication in Amazonia. While persistent Indigenous legacies have been demonstrated elsewhere in the Amazon, it is unclear how past human–environment interactions may have shaped vegetation composition and structure in the ARE. Here, we examine 6000 years of archaeological and palaeoecological data from Laguna Versalles (LV), Bolivia. LV was dominated by stable rainforest vegetation throughout the Holocene. Maize cultivation and cultural burning are present after ca 5700 cal yr BP. Polyculture cultivation of maize, manioc and leren after ca 3400 cal yr BP predates the formation of Amazonian Dark/Brown Earth (ADE/ABE) soils (approx. 2400 cal yr BP). ADE/ABE formation is associated with agroforestry indicated by increased edible palms, including Mauritia flexuosa and Attalea sp., and record levels of burning, suggesting that fire played an important role in agroforestry practices. The frequent use of fire altered ADE/ABD forest composition and structure by controlling ignitions, decreasing fuel loads and increasing the abundance of plants preferred by humans. Cultural burning and polyculture agroforestry provided a stable subsistence strategy that persisted despite pronounced climate change and cultural transformations and has an enduring legacy in ADE/ABE forests in the ARE. This article is part of the theme issue ‘Tropical forests in the deep human past’.