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The use and domestication of Theobroma cacao during the mid-Holocene in the upper Amazon


Cacao (Theobroma cacao L.) is an important economic crop, yet studies of its domestication history and early uses are limited. Traditionally, cacao is thought to have been first domesticated in Mesoamerica. However, genomic research shows that T. cacao’s greatest diversity is in the upper Amazon region of northwest South America, pointing to this region as its centre of origin. Here, we report cacao use identified by three independent lines of archaeological evidence—cacao starch grains, absorbed theobromine residues and ancient DNA—dating from approximately 5,300 years ago recovered from the Santa Ana-La Florida (SALF) site in southeast Ecuador. To our knowledge, these findings constitute the earliest evidence of T. cacao use in the Americas and the first unequivocal archaeological example of its pre-Columbian use in South America. They also reveal the upper Amazon region as the oldest centre of cacao domestication yet identified.

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Fig. 1: Locations of the four archaeological sites in Mexico, Central America and South America with the earliest evidence of Theobroma use, as well as the species diversity distributions for the genus Theobroma17,19,58.
Fig. 2: Selected artefacts from SALF that tested positive for T. cacao and Theobroma spp. by aDNA, starch grains and theobromine analyses.
Fig. 3: Starch grains of Theobroma spp. and other economically important plants.
Fig. 4: UPLC-MS/MS chromatograms, multiple reaction monitoring transitions and method parameters.
Fig. 5: Population structure of modern individuals and aDNA mixtures extracted from ceramic residues.

Data availability

NCBI GenBank accession numbers of the Theobroma mitochondrial reference sequences are MF462389, MF462390 and MF462396 to MF462398. Examples of PCR amplified mitochondrial ancient DNA sequences identified as T. cacao sequences are reported in Supplementary Figs. 24. All results on ancient DNA sequences obtained after DNA capture and containing SNPs are reported in Supplementary Information; corresponding SNPs from the collection of modern accessions, used as controls, are reported in the Tropgene database ( Additional data that support the findings of this study are available from the corresponding author on reasonable request.


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S.Z.’s research was funded by a Social Sciences and Humanities Research Council of Canada Doctoral Fellowship and an Honorary Isaak Walton Killam Memorial Scholarship, as well as the Martha Biggar Anders Memorial Award (2008, 2009, 2011), a Graduate Research Scholarship, a Faculty of Graduate Studies Travel Award, a Graduate Studies Scholarship and a Graduate Student Association Professional Development Grant from the University of Calgary. We thank the Universidad San Francisco de Quito, Riobamba and the University of British Columbia, Okanagan for use of laboratory facilities for some of S.Z.’s research. Funding for this project was provided by a Hampton Research Grant (no. F11-00878) from the University of British Columbia. Funding for archaeological excavations at SALF was provided by IRD. This project is supported by Agropolis Fondation under the reference ID 1202-029 through the Investissements d’avenir programme (Labex Agro: no. ANR-10-LABX-0001-01). The Hiseq sequencing activities were made in collaboration with the GeT platform, a partner of the National Infrastructure France Génomique, with thanks for support by the Commissariat aux Grands Investissements (no. ANR-10-INBS-0009). We are grateful to P. Lachenaud for providing genotyping by sequencing data on Guina group, to H. Kucera for assisting with Biochemical analyses, to N. Waber for preparing Fig. 1 and M. Berard for assistance in preparing Figs. 2 and 3. We also thank The United States Department of Agriculture, Agricultural Research Services, Plant Genetic Resources Conservation Unit for generously supplying Theobroma and Herrania pods and the Centro Agronómico Tropical de Investigación y Enseñanza (CATIE—Costa Rica) and the Cocoa Research Center, University of West Indies (CRC, Trinidad and Tobago) for providing Theobroma and Herrania leaves for modern DNA analyses.

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Authors and Affiliations



F.V., M.B., S.Z., T.P., N.G. and C.L. designed the research. F.V., J.H., A.Y. and S.Z. performed excavations at Santa Ana-La Florida. S.Z. designed starch investigation methods and performed starch granule analysis. T.P. and P.S. sampled artefacts for theobromine analysis. N.G. designed mass spectrometry analysis, performed UPLC-MS/MS analyses and processed and analysed mass spectrometry data. L.G. provided general input to the overall project. C.L., C.V., I.L., O.F., X.A., E.G., F.S. and R.L.S., performed aDNA experiments and analyses. H.V. and O.B. performed NGS aDNA sequencing. S.Z., C.L., N.G., T.P., M.B. and F.V. led the writing of the paper with inputs from all other authors.

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Correspondence to Michael Blake.

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Supplementary information

Supplementary Information

Supplementary Notes; Supplementary Figures 1–8; Supplementary Tables 3–9 and 11–16

Reporting Summary.

Supplementary Table 1

Radiocarbon dates from the Santa Ana-La Florida site, Palanda (Zamora-Chinchipe, Ecuador)

Supplementary Table 2

Total SALF samples analysed for starch grains, theobromine and aDNA

Supplementary Table 10

List of aDNA sequences specific to Theobroma and containing SNPs identified by GBS

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Zarrillo, S., Gaikwad, N., Lanaud, C. et al. The use and domestication of Theobroma cacao during the mid-Holocene in the upper Amazon. Nat Ecol Evol 2, 1879–1888 (2018).

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