The legacy of pre-Columbian land use in the Amazonian rainforest is one of the most controversial topics in the social and natural sciences. Until now, the debate has been limited to discipline-specific studies, based purely on archaeological data, modern vegetation, modern ethnographic data or a limited integration of archaeological and palaeoecological data. The lack of integrated studies to connect past land use with modern vegetation has left questions about the legacy of pre-Columbian land use on the modern vegetation composition in the Amazon, unanswered. Here, we show that persistent anthropogenic landscapes for the past 4,500 years have had an enduring legacy on the hyperdominance of edible plants in modern forests in the eastern Amazon. We found an abrupt enrichment of edible plant species in fossil lake and terrestrial records associated with pre-Columbian occupation. Our results demonstrate that, through closed-canopy forest enrichment, limited clearing for crop cultivation and low-severity fire management, long-term food security was attained despite climate and social changes. Our results suggest that, in the eastern Amazon, the subsistence basis for the development of complex societies began ~4,500 years ago with the adoption of polyculture agroforestry, combining the cultivation of multiple annual crops with the progressive enrichment of edible forest species and the exploitation of aquatic resources. This subsistence strategy intensified with the later development of Amazonian dark earths, enabling the expansion of maize cultivation to the Belterra Plateau, providing a food production system that sustained growing human populations in the eastern Amazon. Furthermore, these millennial-scale polyculture agroforestry systems have an enduring legacy on the hyperdominance of edible plants in modern forests in the eastern Amazon. Together, our data provide a long-term example of past anthropogenic land use that can inform management and conservation efforts in modern Amazonian ecosystems.

Domesticated maize evolved from wild teosinte under human influences in Mexico beginning around 9000 years before the present (yr B.P.), traversed Central America by ~7500 yr B.P., and spread into South America by ~6500 yr B.P. Landrace and archaeological maize genomes from South America suggest that the ancestral population to South American maize was brought out of the domestication center in Mexico and became isolated from the wild teosinte gene pool before traits of domesticated maize were fixed. Deeply structured lineages then evolved within South America out of this partially domesticated progenitor population. Genomic, linguistic, archaeological, and paleoecological data suggest that the southwestern Amazon was a secondary improvement center for partially domesticated maize. Multiple waves of human-mediated dispersal are responsible for the diversity and biogeography of modern South American maize.

During the last two decades, new archaeological projects which systematically integrate a variety of plant recovery techniques, along with palaeoecology, palaeoclimate, soil science and floristic inventories, have started to transform our understanding of plant exploitation, cultivation and domestication in tropical South America. Archaeobotanical studies are providing a far greater appreciation of the role of plants in the diets of early colonists. Since~13ka, these diets relied mainly on palm, tree fruits, and underground tubers, along with terrestrial and riverine faunal resources. Recent evidence indicates two areas of precocious plant cultivation and domestication: the sub-Andean montane forest of NW South America and the shrub savannahs and seasonal forests of SW Amazonia. In the latter area, thousands of anthropic keystone structures represented by forest islands show a significant human footprint in Amazonia from the start of the Holocene. While radiocarbon date databases show a decline in population during the middle Holocene, important developments happened during this epoch, including the domestication of cacao, the adoption of maize and the spread of manioc across the basin. The late Holocene witnessed the domestication of rice and the development of agricultural landscapes characterised by raised fields and Amazonian Dark Earths (ADEs). Our multi-proxy analysis of 23 late Holocene ADEs and two lakes from southern Amazonia provides the first direct evidence of field polyculture agriculture including the cultivation of maize, manioc, sweet potato, squash, arrowroot and leren within closed-canopy forest, as well as enrichment with palms, limited clearing for crop cultivation, and low-severity fire management. Collectively, the evidence shows that during the late Holocene Amazonian farmers engaged in intensive agriculture marked by the cultivation of both annual and perennial crops relying on organic amendments requiring soil preparation and maintenance. Our study has broader implications for sustainable Amazonian futures.

The discovery of large geometrical earthworks in interfluvial settings of southern Amazonia has challenged the idea that Pre-Columbian populations were concentrated along the major floodplains. However, a spatial gap in the archaeological record of the Amazon has limited the assessment of the territorial extent of earth-builders. Here, we report the discovery of Pre-Columbian ditched enclosures in the Tapajós headwaters. The results show that an 1800 km stretch of southern Amazonia was occupied by earth-building cultures living in fortified villages ~Cal AD 1250–1500. We model earthwork distribution in this broad region using recorded sites, with environmental and terrain variables as predictors, estimating that earthworks will be found over ~400,000 km2 of southern Amazonia. We conclude that the interfluves and minor tributaries of southern Amazonia sustained high population densities, calling for a re-evaluation of the role of this region for Pre-Columbian cultural developments and environmental impact.

The long term response of ancient societies to climate change has been a matter of global debate. Until recently, the lack of integrative studies between archaeological, palaeoecological, and palaeoclimatological data had prevented an evaluation of the relationship between climate change, distinct subsistence strategies, and cultural transformations across the largest rainforest of the world, Amazonia. Here, we review the most relevant cultural changes seen in the archaeological record of six different regions within Greater Amazonia during late pre-Columbian times. We compare the chronology of those cultural transitions with high-resolution regional palaeoclimate proxies, showing that, while some societies faced major reorganisation during periods of climate change, others were unaffected and even flourished. We propose that societies with intensive, specialised land-use systems were vulnerable to transient climate change. In contrast, land-use systems that relied primarily on polyculture agroforestry, resulting in the formation of enriched forests and fertile Amazonian Dark Earths in the long term, were more resilient to climate change.

The late-Holocene expansion of the Tupi-Guarani languages from southern Amazonia to SE South America constitutes one of the largest expansions of any linguistic family in the world, spanning ~4000 km between latitudes 0°S and 35°S at about 2.5k cal. yr BP. However, the underlying reasons for this expansion are a matter of debate. Here, we compare continental-scale palaeoecological, palaeoclimate and archaeological datasets, to examine the role of climate change in facilitating the expansion of this forest-farming culture. Because this expansion lies within the path of the South American Low-Level Jet, the key mechanism for moisture transport across lowland South America, we were able to explore the relationship between climate change, forest expansion and the Tupi-Guarani. Our data synthesis shows broad synchrony between late-Holocene increasing precipitation and southerly expansion of both tropical forest and Guarani archaeological sites -the southernmost branch of the Tupi-Guarani. We conclude that climate change likely facilitated the agricultural expansion of the Guarani forest-farming culture by increasing the area of forested landscape that they could exploit, showing a prime example of ecological opportunism.

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A 50,000-year-old sediment core record from Laguna Chaplin is reanalyzed to explore potential paleoecological methods to detect the extent of pre-Columbian disturbance in the Bolivian Amazon. High-resolution (sub-centennial) macrocharcoal data are analyzed using statistical algorithm software including Regime Shift Detection and CHAR Analysis to detect changes in past fire regimes. These data are compared with existing charcoal records from throughout the Bolivian lowlands to provide a regional scale context of past biomass burning. During the mid-Holocene, changes in precipitation are the dominant driver of fire activity and biomass burning at Laguna Chaplin and across the Bolivian lowlands. During the late Holocene, increased fire activity across ecosystems ranging from fire-adapted to fire-intolerant forests is attributed to the apex of pre-Columbian activity. These data suggest human-caused ignitions during the late Holocene are the driving factor of regional scale fire activity in the Bolivian lowlands. After ca. 650 cal yr BP, there is an increase in biomass burning and fire frequency synchronous with the expansion of Moraceae/Urticaceae pollen (>50%) at Laguna Chaplin. This occurs during the time-transgressive southward expansion of the rainforest boundary, during the apex of pre-Columbian activity in the region. The increase in biomass burning at Laguna Chaplin is reflected at other sites in the region with known human occupation histories. The presence of Zea mays ca. 970 to 170 cal yr BP indicates maize cultivation is practiced in the immediate vicinity surrounding Laguna Chaplin. The simultaneous increase in fire activity with the expansion of the less flammable humid rainforest vegetation suggests human fire management practices. These data are interpreted as the use of frequent, low severity, human-caused fires to clear the croplands from encroaching rainforest vegetation. Despite evidence of pre-Columbian fire management during the late Holocene, vegetation and fire data indicate the extent of human-landscape modification and fire management at Laguna Chaplin, is not enough to inhibit the climate-driven regional forest expansion of the savanna-rainforest ecotonal boundary to its most southern extent in the last 50,000 years. This study demonstrates the utility of applying a multi-proxy, high-resolution paleoecological method to disentangle climate and pre-Columbian disturbance in the Bolivian Amazon.