A revisited history of cacao domestication in pre-Columbian times revealed by archaeogenomic approaches

Abstract

Humans have a long history of transporting and trading plants, contributing to the evolution of domesticated plants. Theobroma cacao originated in the Neotropics from South America. However, little is known about its domestication and use in these regions. In this study, ceramic residues from a large sample of pre-Columbian cultures from South and Central America were analyzed using archaeogenomic and biochemical approaches. Here we show, for the first time, the widespread use of cacao in South America out of its native Amazonian area of origin, extending back 5000 years, likely supported by cultural interactions between the Amazon and the Pacific coast. We observed that strong genetic mixing between geographically distant cacao populations occurred as early as the middle Holocene, in South America, driven by humans, favoring the adaptation of T. cacao to new environments. This complex history of cacao domestication is the basis of today's cacao tree populations and its knowledge can help us better manage their genetic resources.

Figure 1

Geographical localizations of genetic groups and human pre-Columbian cultures associated to the archaeological items analyzed. The eleven genetic groups of the T. cacao species, as previously reported, are indicated at the right top of the figure and their native areas localized in the map with the corresponding colors. Stars represent the area of cultivation of the three old varieties: Criollo (red), Amelonado (light blue) and Nacional (yellow), and with their corresponding wild genetic group, except for Criollo, for which there is no very close wild-type genetic group. The approximate sites of occupation of human pre-Columbian cultures associated to archaeological items investigated in this study are represented on the map by a number and an arrow: (1) Marañon, (2) Valdivia, (3) Machalilla, (4) Bahia/Chorrera, (5) Jama Coaque, (6) La Tolita/Atacames/Nariño, (7) San Augustin, (8) Calima Ilama, (9) Amazonas, (10) Araracuara, (11) Puerto Hormiga, (12) San Jacinto, (13) Barlovento, (14) Zenu, (15) Panama, (16), Maya, (17) Olmec.

Figure 2

Box plots statistical representation of theobromine and caffeine values (pg/sample) observed in several Colombian and Ecuadorian cultures. The points in the graphics represent the individual values, and the numbers in parentheses correspond to the number of samples analyzed per culture. The central box is delimited by the first quartile (value below which 25% of the data falls when arranged in ascending order) and the third quartile (value below which 75% of the data arranged in ascending order lies), and with the median (middle value of the set of values with half of the values less than the median and half the values greater than the median). The ends of the whiskers are calculated using 1.5 times the interquartile space (the distance between the 1st and 3rd quartiles), and with outliers drawn over the upper limit. The dashed lines indicate the threshold at which methylxanthine values are considered positive (700 pg/sample). The number of analyzed archaeological samples per human pre-Columbian culture is indicated in parentheses.

Figure 3

Examples of archaeological ceramic items in which we detected T. cacao ancient DNA presence. Item names and their associated culture: A: P236: sherd from Puerto Hormiga; B: P247: sherd from San Jacinto; C: P175: ceramic item of the Jaen Archaeological site directly collected, Marañon; D: P325: pot, Valdivia phase III; E: P345: pot, Valdivia phase II; F: P348: pot, Machalilla; G: P350: Machalilla; H: P57: effigy vessel of a pregnant woman, Chorrera; I: P137: bottle, Chorrera; J: P306: effigy vessel of an owl, Jama Coaque; K: P307: effigy vessel of mythic being, Jama Coaque; L: P213: vase, Calima Ilama; M: P214: vase, Calima Ilama.

Figure 4

Visualization of the genotype membership proportions of T. cacao genetic groups and wild relatives for each archaeological item. The genetic structure of each archaeological item residues was analyzed individually with the reference collection. The Valdivia phase is indicated at the right and bottom side for each Valdivia sample when determined. The structure of T. cacao ancient DNA sequences from ceramic residues was determined using a Bayesian model-based clustering method, implemented in the STRUCTURE software V2.3.4. The genotype membership proportion was calculated using a set of at least 20 SNP markers, common to the sample and to the reference collection and is indicated by colours corresponding to the genetic groups mentioned at the top right side of the figure. Only archaeological items with unambiguous ancestry values between two groups are reported in this figure. The complete ancestry values are reported for all analyzed items in Supplementary Table 3. The number of SNP used for each Structure analysis is indicated in parentheses.