Domestication of cocoa in pre-Columbian times: history revisited by archaeogenomics

Results & impact 7 March 2024
For the first time, an international scientific team* coordinated by CIRAD has shown that the use and domestication of cocoa and its wild relatives in South America date back more than 5000 years outside of the Amazon, its area of origin, and 1500 years before its domestication in Central America. They have published in Nature Scientific Report their results mainly based on the analysis of ancient DNA and methylxanthines collected in residues from 352 archaeological ceramic items.
Reserve at the Guayaquil MAAC Museum (Ecuador), from which some of the ceramics analysed for this research project were taken © C. Lanaud, CIRAD
Reserve at the Guayaquil MAAC Museum (Ecuador), from which some of the ceramics analysed for this research project were taken © C. Lanaud, CIRAD

Reserve at the Guayaquil MAAC Museum (Ecuador), from which some of the ceramics analysed for this research project were taken © C. Lanaud, CIRAD

The history of plant domestication is strongly linked to human migrations and trade. The circulation of plants began in South America in the middle of the Holocene.

For early botanists like Vavilov, as well as in popular culture, Mesoamerica and Central America are considered the cradle of cocoa, which was domesticated by the Olmec and Mayan populations who are supposed to have introduced cocoa to Central America from a small number of plants native to the Amazon. However, little information exists on its domestication in South America, and particularly along the Pacific coast where many human cultures flourished for over 5000 years, such as those of the Valdivia in Ecuador and Puerto Hormiga in Colombia.

To clarify the history of cocoa domestication in South and Central America, CIRAD set up a scientific team, involving 16 institutions from seven different countries. “This multidisciplinary team, which includes archaeologists, anthropologists, geneticists and biochemists, analysed the ancient DNA and biochemical compounds present in the food residues of 352 archaeological ceramic items” reveals Claire Lanaud, a geneticist at CIRAD who initiated the project. “These items belong to 19 human cultures mainly spread along the Pacific coast of Ecuador and Colombia, but also from the Amazon regions of Colombia, Peru and Central America.

Based on bioinformatics and pan-genomic studies, carried out in particular by Xavier Argout, a research scientist at CIRAD, as well as on genetic studies, the researchers have shown that the use and domestication of cocoa (T. cacao) and its wild relative species date back more than 5000 years, outside its area of origin in the Amazon, or 1500 years before its domestication in Central America. Moreover, the genetic ancestry of cocoa, present in ceramics, has shown remarkable diversity, with the mixture of several genetic groups of the T. cocoa species, originating from geographically distant Amazon regions. “This testifies to the intensive exchanges which took place, several millennia ago, between the populations of the coast and the Amazon” says Francisco Valdez, an archaeologist at IRD. This genetic mixing undoubtedly fostered the adaptation of cocoa trees to their new environment.

These results largely call into question the hypotheses formulated so far on the domestication of the oldest cocoa varieties. They present a more complex model of T. cacao domestication than expected, and highlight the crucial role of the oldest human cultures in this domestication.

*This multidisciplinary work was initiated by a team from CIRAD (AGAP Institut). It involved the participation of 16 institutions from seven different countries, including four French institutions: CIRAD, the National Museum of Natural History, IRD and the University of Montpellier. Its funding was mainly provided by a MUSE project (Montpellier University of Excellence) as well as by Valrhona.


A revisited history of cocoa domestication in pre‐Columbian times revealed by archaeogenomic approaches. Claire Lanaud, Hélène Vignes, José Utge, Gilles Valette, Bénédicte Rhoné, Mariella Garcia Caputi, Natalia Angarita, Olivier Fouet, Nilesh Gaikwad, Sonia Zarrillo, Terry G. Powis, Ann Cyphers, Francisco Valdez, S. Quirino Olivera Nunez, Camilla Speller, Michael Blake, Fred Jr. Valde, Scott Raymond, Sarah M. Rowe, Guy S. Duke, Francisco Romano, Rey Gaston Loor Solórzano & Xavier Argout. Scientific reports.   


CIRAD is France's agricultural research and international cooperation organization for the sustainable development of tropical and Mediterranean regions. With its partners, it co-constructs knowledge and solutions for resilient agricultures in a more sustainable and inclusive world. It mobilizes science, innovation and training to achieve sustainable development goals. It puts its expertise at the service of everyone, from producers to public policymakers, to promote the protection of biodiversity, agro-ecological transitions, the sustainability of food systems, health (of plants, animals and ecosystems), the sustainable development of rural areas and their resilience in the face of climate change. Present on every continent in some 50 countries, CIRAD draws on the skills of its 1800 employees, including 1240 scientists, and on a global network of 200 partners. It supports France's scientific diplomacy. 

The IRD is a multi-disciplinary French public research organization which, for 80 years, has been committed to equitable partnerships with developing countries and French overseas territories.  As a player on the international development agenda, its priorities are in line with the Sustainable Development Goals (SDGs).  Together, scientists and the Institute's partners propose concrete solutions to the global challenges facing societies and the planet. This win-win relationship makes science and innovation major levers for development.