Ethnobotanical and molecular data reveal the complexity of the domestication of chiles (Capsicum annuum L.) in Mexico

C. annuum var. annuum L. is one of the most important crops domesticated in Mesoamerica. Morphological data, chromosomal studies and hybrid fertility indicated that "C. annuum L. was domesticated from wild chiles similar to those still growing today in central Mexico" (Pickersgill 1988). Taking this idea as a working hypothesis, this study uses a combination of ethnobotanical and molecular data to understand the possible process and location of domestication of chiles in Mexico.;The first part documents the utilization of chiles through time in Mesoamerica based on linguistic and archeological evidence, historical accounts and fieldwork. This paper describes the diversity and distribution of both putative wild (C. annuum var. glabriusculum (Dunal) Heiser and Pickersgill) and several varieties of domesticated chiles (C. annuum var. annuum L.) in ancient and modern Mesoamerica. Based on archeological, linguistic and historical data, chiles have been utilized for at least 7,000 years since the first civilizations began in Mesoamerica. It is unknown if chiles were already domesticated at that time but the data strongly suggest that at least wild chiles were extensively utilized in that region. Under these circumstances, the initial domestication of chiles may have occurred many times in the past and may be occurring in the present.;The second part explores the molecular diversity and evolutionary relationships of wild and domesticated chiles in Mexico based on DNA sequences of two low copy nuclear genes (Waxy and G3pdh). Chiles were collected from 10 states in Mexico including populations from home-gardens, milpa, tropical deciduous forests and markets. Molecular analyses of two low-copy nuclear genes indicate similar levels of genetic diversity and complex phylogenetic relationships among 21 domesticated and 54 wild accessions. Two lines of evidence support the hypothesis of multiple domestication origins. Ancestral Recombination Graph analysis identified three Waxy gene lineages and analysis of concatenated genes with the STRUCTURE program identified two groups each of which contained domesticated chiles. The most parsimonious interpretation of this data is that domesticated chiles ( C. annuum L.) in Mexico have multiple origins, although a single domestication cannot be ruled out.