1. Powis, T. G., Cyphers, A., Gaikwad, N. W., Grivetti, L. & Cheong, K. Cacao use and the San Lorenzo Olmec. Proc. Natl Acad. Sci. USA 108, 8595–8600 (2011).

2. Powis, T. G. et al. Oldest chocolate in the New World. Antiquity 81 (2007); https://www.antiquity.ac.uk/projgall/powis314/

3. Henderson, J. S., Joyce, R. A., Hall, G. R., Hurst, W. J. & McGovern, P. E. Chemical and archaeological evidence for the earliest cacao beverages. Proc. Natl Acad. Sci. USA 104, 18937–18940 (2007).

4. Sheets, P. D. The Ceren Site: An Ancient Village Buried by Volcanic Ash in Central America 2nd edn (Wadsworth Publishing, Belmont, 2005).

5. Coe, S. D. & Coe, M. D. The True History of Chocolate 3rd edn (Thames and Hudson, London, 2013).

6. Stuart, D. in Chocolate in Mesoamerica: A Cultural History of Cacao (ed. McNeil, C. L.) 184–201 (Univ. Press of Florida, Gainesville, 2009).

7. Crown, P. L. & Hurst, W. J. Evidence of cacao use in the Prehispanic American Southwest. Proc. Natl Acad. Sci. USA 106, 2110–2113 (2009).

8. Washburn, D. K., Washburn, W. N. & Shipkova, P. A. Cacao consumption during the 8th century at Alkali Ridge, southeastern Utah. J. Arch. Sci. 40, 2007–2013 (2013).

9. Washburn, D. K., Washburn, W. N., Shipkova, P. A. & Pelleymounter, M. A. Chemical analysis of cacao residues in archaeological ceramics from North America: considerations of contamination, sample size and systematic controls. J. Arch. Sci. 50, 191–207 (2014).

10. Grivetti, L. H. & Shapiro, H.-Y. (eds) Chocolate, History, Culture, and Heritage (John Wiley & Sons, Hoboken, 2009).

11. Hurst, W. J., Tarka, S. M. Jr, Powis, T. G., Valdez, F.Jr & Hester, T. R. Cacao usage by the earliest Maya civilization. Nature 418, 289–290 (2002).

12. Powis, T. G., Valdez, F., Hester, T. R., Hurst, W. J. & Tarka, S. M. Spouted vessels and cacao use among the Preclassic Maya. Lat. Am. Antiq. 13, 85–106 (2002).

13. McNeil, C. L. Chocolate in Mesoamerica: A Cultural History of Cacao (Univ. Press of Florida, Gainesville, 2009).

14. Motamayor, J. C. et al. Cacao domestication I: the origin of the cacao cultivated by the Mayas. Heredity 89, 380–386 (2002).

15. Motamayor, J. C. et al. Geographic and genetic population differentiation of the Amazonian chocolate tree (Theobroma cacao L.). PLoS ONE 3, e3311 (2008).

16. Loor Solorzano, R. G. et al. Insight into the wild origin, migration and domestication history of the fine flavour Nacional Theobroma cacao L. variety from Ecuador. PLoS ONE 7, e48438 (2012).

17. Thomas, E. et al. Present spatial diversity patterns of Theobroma cacao L. in the neotropics reflect genetic differentiation in Pleistocene refugia followed by human-influenced dispersal. PLoS ONE 7, e47676 (2012).

18. Valdez, F. in The Handbook of South American Archaeology (eds Silverman, H. & Isbell, W. H.) 865–888 (Springer, New York, 2008).

19. Cuatrecasas, J. Cacao and its allies, a taxonomic revision of the genus.Theobroma. Contr. US Natl Herb. 35, 379–614 (1964).

20. Walker, T. in Chocolate: History, Culture, and Heritage (eds Grivetti, L. E. & Shapiro, H.-Y.) 543–558 (John Wiley & Sons, Hoboken, 2009).

21. Bletter, N. & Daly, D. C. in Chocolate in Mesoamerica: A Cultural History of Cacao (ed. McNeil, C. L.) 31–68 (Univ. Press of Florida, Gainesville, 2009).

22. Valdez, F., Guffroy, J., de Saulieu, G., Hurtado, J. & Yepes, A. Découverte d’un site cérémoniel formatif sur le versant oriental des Andes. C. R. Palevol. 4, 369–374 (2005).

23. Zarrillo, S. Human Adaptation, Food Production, and Cultural Interaction During the Formative Period in Highland Ecuador. PhD dissertation, Univ. Calgary (2012).

24. Lanaud, C., Loor, R. G., Zarrilo, S. & Valdez, F. Origen de la domesticacion del cacao y su uso temprano en el Ecuador. Nuestro Patrimonio 12, 12–14 (2012).

25. Zarrillo, S. & Valdez, F. in Arqueologia Amazonica: las Civilizaciones Ocultas del Bosque Tropical (ed. Valdez, F.) 147–171 (Abya-Yala, Ecuador, 2013).

26. Reichert, E. T. The Differentiation and Specificity of Starches in Relation to Genera, Species, Etc. (Carnegie Institution of Washington, Washington DC, 1913).

27. Schmieder, R. L. & Keeney, G. Characterization and quantification of starch in cocoa beans and chocolate products. J. Food. Sci. 45, 555–557 (1980).

28. Pagán Jiménez, J. R. Almidones: Guía de Material Comparativo Moderno del Ecuador Para los Estudios Paleoetnobotánicos en el Neotrópico (Aspha, Buenos Aires, 2015).

29. Hammerstone, J. F., Romanczyk, L. J. & Martin Aitken, W. Purine alkaloid distribution with Herrania and Theobroma. Phytochemistry 35, 1237–1240 (1994).

30. Pääbo, S. et al. Genetic analyses from ancient DNA. Annu. Rev. Genet. 38, 645–679 (2004).

31. Parducci, L. et al. Molecular- and pollen-based vegetation analysis in lake sediments from central Scandinavia. Mol. Ecol. 22, 3511–3524 (2013).

32. Willerslev, E. et al. Fifty thousand years of Arctic vegetation and megafaunal diet. Nature 506, 47–51 (2014).

33. Carpenter, M. L. et al. Pulling out the 1%: whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries. Am. J. Hum. Genet. 93, 852–864 (2013).

34. Argout, X. et al. The genome of Theobroma cacao. Nat. Genet. 43, 101–108 (2011).

35. Pritchard, J. K., Stephens, M. & Donnelly, P. Inference of population structure using multilocus genotype data. Genetics 155, 945–959 (2000).

36. Hansen, A., Willerslev, E., Wiuf, C., Mourier, T. & Arctander, P. Statistical evidence for miscoding lesions in ancient DNA templates. Mol. Biol. Evol. 18, 262–265 (2001).

37. Silva, P. & Oliveira-Cardoso, A. Historico das introduçoes de cacaueiro (Theobroma cacao L.) no Reconcavo da Bahia, Brasil. Revista Theobroma 10, 135–140 (1980).

38. Mackensen, A. K., Brey, T., Bock, C. & Luna, S. Spondylus crassisquama Lamarck, 1819 as a microecosystem and the effects of associated macrofauna on its shell integrity: isles of biodiversity or sleeping with the enemy? Mar. Biodivers. 42, 443–451 (2012).

39. Piperno, D. R. & Pearsall, D. M. The Origins of Agriculture in the Lowland Neotropics (Academic Press, New York, 1998).

40. Hilbert, L. et al. Evidence for mid-Holocene rice domestication in the Americas. Nat. Ecol. Evol. 1, 1693–1698 (2017).

41. Biehl, B. Veränderungen der subcellulären struktur in keimblättern von kakaosamen (Theobroma cacao L.) während der fermentation und troeknung. Z. Lebensm. Unters. Forch. 153, 137–150 (1973).

42. Redgwell, R. J. & Hansen, C. E. Isolation and characterisation of cell wall polysaccharides from cocoa (Theobroma cacao L.) beans. Planta 210, 823–830 (2000).

43. King, A., Powis, T. G., Cheong, K. & Gaikwad, N. Cautionary tales on the identification of caffeinated beverages in North America. J. Archaeol. Sci. 85, 30–40 (2017).

44. Kufer, J. & McNeil, C. L. in Chocolate in Mesoamerica: A Cultural History of Cacao (ed. McNeil, C. L.) 384–407 (Univ. Press of Florida, Gainesville, 2009).

45. Cieslak, M. et al. Origin and history of mitochondrial DNA lineages in domestic horses. PLoS ONE 5, e15311 (2010).

46. Pääbo, S. Ancient DNA: extraction, characterization, molecular cloning, and enzymatic amplification. Proc. Natl Acad. Sci. USA 86, 1939–1943 (1989).

47. Dabney, J., Meyer, M. & Pääbo, S. in DNA Repair, Mutagenesis, and Other Responses to DNA Damage (eds Friedberg, E. C., Elledge, S. J., Lehmann, A. R., Lindahl, T. & Muzi-Falconi, M.) 19–26 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, 2013).

48. Argout, X. et al. Towards the understanding of the cocoa transcriptome: production and analysis of an exhaustive dataset of ESTs of Theobroma cacao L. generated from various tissues and under various conditions. BMC Genomics 9, 512 (2008).

49. Ye, J. et al. Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction. BMC Bioinform. 13, 134 (2012).

50. Waterhouse, A. M., Procter, J. B., Martin, D. M. A., Clamp, M. & Barton, G .J. Jalview version 2—a multiple sequence alignment editor and analysis workbench. Bioinformatics 25, 1189–1191 (2009).

51. Ewing, B., Hillier, L., Wendl, M. C. & Green, P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8, 175–185 (1998).

52. Hamelin, C., Sempere, G., Jouffe, V. & Ruiz, M. TropGeneDB, the multi-tropical crop information system updated and extended. Nucleic Acids Res. 41, D1172–D1175 (2013).

53. Argout, X. et al. The cacao Criollo genomev2.0: an improved version of the genome for genetic and functional genomic studies. BMC Genomics 18, 730 (2017).

54. Haak, W. et al. Massive migration from the steppe was a source for Indo-European languages in Europe. Nature 522, 207–211 (2015).

55. Cruz-Dávalos, D. I. et al. Experimental conditions improving in-solution target enrichment for ancient DNA. Mol. Ecol. Resour. 17, 508–522 (2017).

56. Li, H. & Durbin, R. Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics 26, 589–595 (2010).

57. Jónsson, H., Ginolhac, A., Schubert, M., Johnson, P. L. F. & Orlando, L. mapDamage 2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics 29, 1682–1684 (2013).