Molecular analyses are providing new elements to decipher the origin, domestication and dispersal of native Amazonian crops in an expanding archaeological context. Solid molecular data are available for manioc (Manihot esculenta), cacao (Theobroma cacao), pineapple (Ananas comosus), peach palm (Bactris gasipaes) and guaraná (Paullinia cupana), while hot peppers (Capsicum spp.), inga (Inga edulis), Brazil nut (Bertholletia excelsa) and cupuassu (Theobroma grandiflorum) are being studied. Emergent patterns include the relationships among domestication, antiquity (terminal Pleistocene to early Holocene), origin in the periphery, ample pre-Columbian dispersal and clear phylogeographic population structure for manioc, pineapple, peach palm and, perhaps, Capsicum peppers. Cacao represents the special case of an Amazonian species possibly brought into domestication in Mesoamerica, but close scrutiny of molecular data suggests that it may also have some incipiently domesticated populations in Amazonia. Another pattern includes the relationships among species with incipiently domesticated populations or very recently domesticated populations, rapid pre- or post-conquest dispersal and lack of phylogeographic population structure, e.g., Brazil nut, cupuassu and guaraná. These patterns contrast the peripheral origin of most species with domesticated populations with the subsequent concentration of their genetic resources in the center of the basin, along the major white water rivers where high pre-conquest population densities developed. Additional molecular genetic analyses on these and other species will allow better examination of these processes and will enable us to relate them to other historical ecological patterns in Amazonia.

Significance: The novelty of the information of this manuscript resides in the addition of species distribution modeling and paleobiolinguistics data, combined with genetic and existing archaeobotanical data, to trace back the geographic origin of a crop, namely domesticated pepper,Capsicum annuum. Furthermore, the utilization of a geographic framework of reference for the four types of data has allowed us to combine these independent data types into a single hypothesis about the origin of this crop. Our results suggest that food crops in Mexico had a multiregional origin with chili pepper originating in central-east Mexico, maize in the Balsas River Basin and common bean in the Lerma–Santiago River Basin, resembling similar finds for the Fertile Crescent and China.

A better knowledge of factors organizing crop genetic diversity in situ increases the efficiency of diversity analyses and conservation strategies, and requires collaboration between social and biological disciplines. Four areas of anthropology may contribute to our understanding of the impact of social factors on crop diversity: ethnobotany, cultural, cognitive and social anthropology. So far, most collaborative studies have been based on ethnobotanical methods, focusing on farmers’ individual motivations and actions, and overlooking the effects of farmer’s social organization per se. After reviewing common shortcomings in studies on sorghum and maize, this article analyzes how social anthropology, through the analysis of intermarriage, residence and seed inheritance practices, can contribute to studies on crop genetic diversity in situ. Crop varieties are thus considered social objects and socially based sampling strategies can be developed. Such an approach is justified because seed exchange is built upon trust and as such seed systems are embedded in a pre-existing social structure and centripetally oriented as a function of farmers’ social identity. The strong analogy between farmers’ cultural differentiation and crop genetic differentiation, both submitted to the same vertical transmission processes, allows proposing a common methodological framework for social anthropology and crop population genetics, where the classical interaction between genetic and environmental factors, G × E, is replaced by a three-way interaction G × E × S, where “S” stands for the social differentiation factors.

Perennial forms of Gossypium hirsutum are classified under seven races. Five Mesoamerican races would have been derived from the wild race ‘yucatanense’ from northern Yucatán. ‘Marie-Galante’, the main race in the Caribbean, would have developed from introgression with G. barbadense. The racial status of coastal populations from the Caribbean has not been clearly defined. We combined Ecological Niche Modeling with an analysis of SSR marker diversity, to elucidate the relationships among cultivated, feral and wild populations of perennial cottons. Out of 954 records of occurrence in Mesoamerica and the Caribbean, 630 were classified into four categories cultivated, feral (disturbed and secondary habitats), wild/feral (protected habitats), and truly wild cotton (TWC) populations. The widely distributed three first categories cannot be differentiated on ecological grounds, indicating they mostly belong to the domesticated pool. In contrast, TWC are restricted to the driest and hottest littoral habitats, in northern Yucatán and in the Caribbean (from Venezuela to Florida), as confirmed by their climatic envelope in the factorial analysis. Extrapolating this TWC climatic model to South America and the Pacific Ocean points towards places where other wild representatives of tetraploid Gossypium species have been encountered. The genetic analysis sample comprised 42 TWC accessions from 12 sites and 68 feral accessions from 18 sites; at nine sites, wild and feral accessions were collected in close vicinity. Principal coordinate analysis, neighbor joining, and STRUCTURE consistently showed a primary divergence between TWC and feral cottons, and a secondary divergence separating ‘Marie-Galante’ from all other feral accessions. This strong genetic structure contrasts strikingly with the absence of geographic differentiation. Our results show that TWC populations of Mesoamerica and the Caribbean constitute a homogenous gene pool. Furthermore, the relatively low genetic divergence between the Mesoamerican and Caribbean domesticated pools supports the hypothesis of domestication of G. hirsutum in northern Yucatán.

Morphological variation was studied in 124 accessions from 61 Passiflora L. species. Twenty-four quantitative descriptors selected for their high variation among subgenera were submitted to a principal component analysis. The first principal component (32% of total variance) was associated with flower length and secondarily with floral cup constriction, the second (27%) with flower width and bract shape, and the third (14%) with peduncle branching, stem width, and leaf length, which relates it to the differentiation of subgenera Astrophea and Deidamioides. The projection of accessions in the resulting tridimensional space consistently separates the four subgenera, as well as supersection Tacsonia of subgenus Passiflora. A neighbor joining analysis, on a selection of 32 qualitative traits and four categorized quantitative variables, clustered species according to their chromosome number and, within subgenus Passiflora, separated supersections Tacsonia (pollinated by the sword-billed hummingbird) and Distephana (pollinated by shorter-billed hummingbirds) from all other, bee-pollinated, species. Thus, the morphological study allows separating the effects of genome evolution from those of more recent and independent coevolutions concerning the pollination syndromes of supersections Tacsonia and Distephana. Within subgenus Decaloba, diverging subclusters are consistent with supersections and particular sections, with the partial exception of supersection Decaloba. Within supersection Tacsonia, subclusters correspond to one or two sections, pointing to overclassification in the current taxonomy. Among the bee-pollinated species of subgenus Passiflora, only supersection Laurifolia is clearly validated. Most of these results are consistent with molecular phylogenetic studies, except for interspecific relations among bee-pollinated species of subgenus Passiflora, which appear particularly difficult to classify.

This chapter covers the morphology and anatomy (stems, leaves, roots, inflorescences, fruits and vegetative propagules) of pineapple, and the...