Modern Genetic Techniques and Cacao’s Journey to Mesoamerica


 An example of an RFLP analysis.  Published by: Davidson College

Although cacao has been a topic of interest to both anthropologists and botanists for hundreds of years, much of its biological origins remain a topic of debate. In particular, although it is widely believed that the origin of cacao lies in South America, it is less clear exactly how cacao arrived in Mesoamerica. Modern genetic analyses provide a way to test various hypotheses of ways in which cacao may have made its way north, and can provide evolutionary evidence where anthropological and archeological evidence is lacking.

One popular hypothesis, proposed by Cheesman in 1944, states that cacao was native only to South America, centered in the Upper Amazon. He suggests that although cacao has been grown in Central America and Mexico for upwards of 2000 years, this cacao does not represent a wild population, but rather a domesticated one, brought by humans from its native home in the Amazon (Motamayor). However, over the years this theory has faced some criticism.

Gomez-Pompa et al. argue that the lack of evidence of prehistoric cultivated cacao in South America pokes a hole in this theory. If cacao was not already being grown and domesticated in South America, it improbable, they argue, that a South American traveler would have brought seeds to Mesoamerica with the intent of planting and domesticating cacao there (Gomez-Pompa). They suggest instead that wild cacao was not limited solely to South America, but rather that it was more widely distributed in Latin America, and that it could have been native to parts of Mesoamerica as well.

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Cuatrecasas’ theory of two distinct subspecies, one native to each of Central and South America. Published by: Department of Botany, Smithsonian Institution

This theory, based off 1964 research by Cuatrecasas, relies heavily on the variance in cacao morphology observed between Criollo variety of Central America, and South American Forastero varieties. This diversity in the appearance of the cacao found in these two regions could be seen as evidence of their genetic diversity, and so supporting the idea that the two varieties have been separated for a significant amount of time on an evolutionary timescale (Cautrecasas).

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Sketch from Cuantrecasas, highlighting the morphological differences between different cacao varieties.  Published by: Department of Botany, Smithsonian Institution

But how do we determine which of these two hypotheses reflects reality? This is where modern genomics comes into play. Analyses of microsatellites, mutation-prone segments of DNA, provide good insight into the interrelatedness of different subspecies, due to the high variability in their expression (Genetics Home Reference). Another important tool for the creation of phylogenetic trees are RFLP analyses, in which differences in corresponding genes are identified by differences in their lengths (National Center for Biotechnology Information). A 2002 study published in Nature utilized both of these techniques to analyze the biodiversity and relatedness of samples of unfarmed cacao collected from all over Latin America.

This study found very low levels of genetic diversity among trees sampled in Central America and Mexico. This suggests that these trees do not represent their own wild population, as suggested by Cuantrecasas and Gomez-Pompa, as wild populations consistently show much higher levels of genetic variability (Motamayor). Furthermore, free-growing Criollo trees in Central America were found to be quite closely related to Forastero varieties in South America. This proves that the Criollos of Central America do not constitute their own sub-species, and refutes Cuantrecasas’ hypothesis that the two groups evolved independently.  Instead, this new evidence supports Cheesman’s theory that cacao was brought to Mesoamerica by travelers, where the Maya then began to cultivate it for its beans.

A figure that shows the interrelatedness of different varieties of cacao.  Note that groups A and B cluster closely, showing that the Criollo variety of Mexico and Central America is actually a genetic neighbor of the Forasteros of the Amazon Basin.  Published by: Nature


So, in the absence of sufficient archeological and anthropological evidence, researchers can turn to genomics to make statements about the origins and spread of cacao. Despite objections from the likes of Gomez-Pompa, it appears that Cheesman and others were correct in hypothesizing that cacao was brought from humans to Mesoamerica, where it grew to attain great cultural and economic significance.



Cuatrecasas, J. (1964). Cacao and its allies; a taxonomic revision of the genus Theobroma. Department of Botany, Smithsonian Institution. Retrieved February 19, 2016, from

Gómez-Pompa, A., Flores, J. S., Fernández, M. A., Gomez-Pompa, A., Flores, J. S., & Fernandez, M. A. (1990). The Sacred Cacao Groves of the Maya. Latin American Antiquity, 1(3), 247.

Microsatellite. (2016). In Genetics Home Reference. Retrieved February 19, 2016, from

Motamayor, J. C., Lachenaud, P., Jay Wallace Da Silva E Mota, Loor, R., Kuhn, D. N., Brown, J. S., & Schnell, R. J. (2008). Geographic and Genetic Population Differentiation of the Amazonian Chocolate Tree (Theobroma cacao L). PLoS ONE, 3(10).

Motamayor, J. C., Risterucci, A. M., Lopez, P. A., Ortiz, C. F., Moreno, A., & Lanaud, C. (2002). Cacao domestication I: The origin of the cacao cultivated by the Mayas.Heredity, 89(5), 380-386.

Restriction Fragment Length Polymorphism (RFLP). (2014). In National Center for Biotechnology Information. Retrieved February 19, 2016, from


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