The origins of plant domestication in the upper Madeira River basin in lowland South America

Lead Research Organisation: University of Exeter
Department Name: Archaeology


Plant domestication and the development of agriculture began shortly after 10,000 years ago in the Americas and several other primary centres around the world, and was one of humankind's most pivotal achievements. Recent advances in palaeobotany and molecular genetics have opened new avenues for understanding when, where, how, and why this crucial change first came about. For example, phylogenetic and phylogeographic studies of extant populations can often identify the wild ancestral population and thus the geographic cradle of origin for each domesticate, pointing the archaeologists to a limited area for survey and excavation. A growing body of genetic, biogeographical, and archaeobotanical data has now established Amazonia as one of the most important centres of plant domestication in the world. Recent genetic and biogeographic studies show that the transitional fringe of seasonal forests and savannahs in SW Amazonia, which encompass the upper Madeira River Basin, were probably the cradle of the domestication of several major American crops, including manioc (Manihot esculenta), peanuts (Arachis hypogaea), peach palm (Bactris gasipaes), coca (Erythroxylum coca), chilli peppers (Capsicum baccattum), annatto (Bixa orellana), and tobacco (Nicotina tabacco) (Clement et al. 2010; Piperno and Pearsall 1998). Despite being the most important centre of domestication in lowland South America, until now no interdisciplinary projects have documented the domestication of these important crops in their cradle of origin.
To address this issue, we proposed to organise two workshops and conduct preliminary research activities to plan, write and submit a 3-5 yr international interdisciplinary project integrating molecular genetics, plant biogeography, archaeology, archaeobotany and paleoecology. The main objectives of the project will be to: i) investigate the history of major Amazonian crops including manioc, peach palm, chilli peppers and annatto; ii) reconstruct the context of early agriculture; and iii) investigate the timing and nature of human impact on the environment in the upper Madeira River, SW Amazonia. These objectives build on two previously separate lines of research coordinated by Iriarte and Clement: paleoecology and archaebotany of landscape transformations of the Araucaria forests of southern Brazil (AHRC-Fapesp) and the Purus-Madeira interfluve (ERC), and the origin, dispersal and phylogeography of native Amazonian crops (Fapeam, Fapeam-AIRD, CNPq, Fapesp), respectively.

The project is well-timed to combine state-of-the-art techniques to address the complexity of plant domestication and the development of agriculture. Research on crop origins are benefiting from the refinement of microfossil botanical techniques, in particular starch granules retrieved from the residues of stone tools used to process plants, which are allowing archaeobotanists to document root crops in tropical regions exhibiting poor preservation of macrobotanical remains (visible remains of seeds and fruits) (Piperno 2011). Palaeoecological techniques will help reconstruct the Late Pleistocene through Holocene vegetation history of the upper Madeira River and, in particular, the natural environment and plant associations in which the first crops were domesticated. Particular emphasis will be given to how and when humans began to alter their environments, using fire history to reconstruct the relation between natural- and human-caused processes. Genetic analysis can identify the wild populations from which the first selections were derived to start the domestication of our modern crops, as well as to trace dispersals out of these centres of domestication.

Planned Impact

addressing plant domestication and the origins of agriculture in SW Amazonia is a major research question that cannot be resolved by one discipline alone, but it can be tackled by an interdisciplinary team. This project will represent a methodological breakthrough since this is the first time that this combination of state-of-the-art techniques from molecular genetics (Clement, Rodrigues, Grant, Veasey, Zucchi), archaeology (Neves, Schaan and Michel), archaeobotany (Iriarte), palaeoecology (Mayle, Urrego), and botany (Hopkins) will be integrated to understand plant domestication and the origins of agriculture in Amazonia. Collectively, the results of this research have the potential to make an important contribution to the comparative study of the origin and evolution of agriculture in what was one of the world's most important centres of prehistoric plant domestication.
Over the last decades, Amazonian institutions have concentrated on developing many native crops for modern markets. These crops now need to be prepared for climate change, which is expected to strongly affect central Amazonia. As mentioned above, identification of sources of disease resistance and tolerance of climatic variability will be essential for this preparation. By combining genetics and palaeoecology, it will be possible to identify areas in Amazonia that were once more similar to the types of ecosystems expected in the next 50-100 years of climate change and then identify wild relatives of crops in these areas, which will be expected to have the adaptations necessary for inclusion in improvement programs.
INPA is the major research institution in Amazonia, attracting young researchers from all over Brazil and South America. It provides a lively research environment for young scholars, most of who speak English and will greatly benefit from participating in this international collaboration. This is a strategic effort that will create a Brazil-UK partnership to understand the pre-history of Amazonia in order to build capacity in Amazonia to prepare for changes in ecosystems across the region, and to inform public policy to contribute to biodiversity conservation and human well-being. Furthermore, since archaeobotany is at a very early stage in Amazonia (and Brazil in general), INPA will benefit greatly from the skills and expertise in state-of-the-art archaeobotany and palaeoecology provided by the University of Exeter team, which will then be available to INPA's post-graduate students in Botany, Genetics, Ecology and Agriculture. At the same time, this new collaboration will expand opportunities for future post-graduate studies by students at the Centre for the Archaeology of the Americas, at the University of Exeter.
The University of São Paulo has long-standing partnerships with Amazonian institutions, including INPA and the Federal University of Amazonas. The collaboration among USP, INPA, UFAM and Exeter will also involve students funded by CAPES (at the Centre for the Archaeology of the Americas) and by Fapesp (via a post-doc scholarship) who are establishing collaborations with Neves and Schaan. This proposal will expand the current AHRC-Fapesp project (AH/K004212/1), focussed on southern Brazilian forested landscapes, to Central Amazonia, where INPA, USP and UFAM have on-going work with both plant population domestication and with landscape transformations by both pre-Colombian and modern human populations, financed by Fapeam and CNPq. The focus on palaeoecology in this proposal will provide time depth to the on-going studies of the composition of useful forest species around human settlements, helping to determine when transformations occurred.


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Description The project just started last year. We have only carried out fieldwork and we are just starting the laboratory analysis of the samples.
Exploitation Route The domestication of plants is a major interdisciplinary topic that goes beyond archaeology and paleoecology to involve botany, genetics and plant breeder to mention a few.
Sectors Agriculture, Food and Drink,Education,Environment

Description Domesticated Amazon: relationships between people, plants and landscapes
Amount R$ 1 (BRL)
Funding ID 435985/2018-3 
Organisation National Council for Scientific and Technological Development (CNPq) 
Sector Public
Country Brazil
Start 02/2019 
End 02/2020
Description INPA Doctoral funding
Amount R$ 1 (BRL)
Organisation National Institute of Amazonian Research 
Sector Public
Country Brazil
Start 07/2017 
End 08/2020
Description Relações entre pessoas, plantas e paisagens no Amazonas sob uma ótica interdisciplinar
Amount R$ 1 (BRL)
Funding ID 062.00148/2020 
Organisation Universal Photonics 
Sector Private
Country United States
Start 01/2020 
End 01/2022
Description A living archaeology in the Amazonian rainforest: first use of tree DNA and chronological profiling to reconstruct prehistoric human rainforest disturbance 
Organisation Max Planck Society
Country Germany 
Sector Charity/Non Profit 
PI Contribution Development and discussion of topic for future research
Collaborator Contribution Development and discussion of topic for future research
Impact ongoing
Start Year 2017
Description Amazonas Federal University, Doriane Picanco Rodrigues 
Organisation Federal University of Amazonas
Country Brazil 
Sector Academic/University 
PI Contribution University of Exeter will provide the archaeological and paleoecological expertise.
Collaborator Contribution The Department of Genetics at the Amazonas Federal University will provide the molecular biology expertise as well as their genetic labs for the analysis of data.
Impact We have not started to process any data at the moment, so no outcomes are available at the moment
Start Year 2015
Description Elizabeth A. Vasey, University of Sao Paulo 
Organisation Universidade de São Paulo
Country Brazil 
Sector Academic/University 
PI Contribution University of Exeter will provide the archaeological and paleoecological expertise.
Collaborator Contribution The Department of Genetics at the University of Sao Paulo will provide the molecular biology expertise as well as their genetic labs for the analysis of data.
Impact We have not started to process any data at the moment, so no outcomes are available at the moment
Start Year 2015
Description Historical genomics of long-term people-palm interactions in the Neotropics 
Organisation Institute of Development Research (IRD)
Department IRD Centre de Montpelier
Country France 
Sector Academic/University 
PI Contribution Research discussions
Collaborator Contribution Methodological and theoretical expertise
Impact research development
Start Year 2019
Description INPA, Manaus Brazil 
Organisation National Center for Scientific Research (Centre National de la Recherche Scientifique CNRS)
Department IN2P3-Lyon
Country France 
Sector Academic/University 
PI Contribution University of Exeter is providing with the archaeological and paleoecological expertise to this project including the labs for processing phytolith, pollen and charcoal analysis.
Collaborator Contribution INPA, the Brazilian National Institute for Amazonian Research is our main partner in this Newton Fund initiative. INPA is providing with their molecular biology and ethnobiology expertise.
Impact We are just starting the first field season of data collection this coming July 2016, therefore at the moment there are not outputs.
Start Year 2015