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 OPEN ACCESSDiversity 2010, 2 73 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.

RAPD markers were used to evaluate the genetic variability and structure of seven morphologically defined landraces of pejibaye (Bactris gasipaes Kunth, Palmae) to determine their validity and phylogenetic relationships. Two hundred and twenty plants of four Amazonian and three Central American landraces of var. gasipaes (the domesticate) and 30 plants of var. chichagui (H. Karsten) Henderson (the crop ancestor) maintained at the National Research Institute for Amazonia, Manaus, Amazonas, Brazil, were utilized. Eight RAPD primers yielded 113 markers, with good reproducibility, of which 97 were polymorphic. The four Amazonian landraces had an average heterozygosity of 0.30, with 86% polymorphism, greater than the Central American landraces (0.25; 74.3%) and var. chichagui (0.

Species complexes are common in the Neotropical flora, and the Pagamea guianensis complex is one of the most widespread groups of species in the Amazonian white-sand flora. Previous analyses suggested the occurrence of ten species in this group, but species limits remained unclear due to poor sampling, morphological overlap and low molecular variation. Here we present the most comprehensive population and molecular sampling across the geographical distribution of the P. guianensis complex to date in order to test the monophyly of this group and to clarify species limits. Using a high-throughput DNA sequencing approach, we sequenced 431 loci (>34 M bases) for 179 individuals. We applied phylogenetic and species tree analyses to resolve phylogenetic relationships among the sampled individuals. Species delimitation was inferred based on genomic data, and we tested whether hypothesized species could be differentiated using morphological, ecological and near-infrared spectroscopy data. We confirm the monophyly of the P. guianensis complex and accept 15 distinct and well-supported lineages, here proposed as 14 species and one subspecies. Our findings highlight the importance of multiple lines of evidence from independent datasets in the process of species delimitation and species discovery in species complexes in the Neotropics.

RESUMO -A pupunha (Bactris gasipaes Kunth, Palmae) foi domesticada por seu fruto pelos primeiros povos da Amazônia Ocidental, possuindo um complexo de raças primitivas (landraces) parcialmente caracterizado e mapeado morfologicamente. Ao longo dos Rios Amazonas e Solimões, no Brasil, foram propostas três raças primitivas [Pará (Rio Amazonas), Solimões (baixo e médio Rio Solimões), Putumayo (alto Rio Solimões)], com indicações de que a raça Solimões poderia ser artefato de análise morfométrica. Marcadores RAPDs foram usados para avaliar a hipótese de três raças. Extraiu-se DNA de 30 plantas de cada raça mantida no BAG de Pupunha em Manaus, AM, Brasil. Na amplificação por PCR, 8 primers geraram 80 marcadores, cujas similaridades de Jaccard foram estimadas para agrupamento das plantas com UPGMA. O dendrograma conteve 2 grandes grupos que juntaram-se a uma similaridade de 0,535: o grupo da raça Pará conteve 26 plantas dessa raça, 5 da Putumayo e 1 da Solimões; o grupo do Rio Solimões conteve 29 plantas da raça Solimões, 19 da Putumayo e 1 da Pará. A estrutura do segundo grupo sugere que existe apenas uma raça ao longo do Rio Solimões, pois as plantas amostradas são misturadas em sub-grupos sem ordem aparente. A análise genética não apoia a hipótese de três raças e sugere que a raça Putumayo estendese ao longo do Rio Solimões até Amazônia central. Será necessário juntar dados genéticos com morfológicos para avaliar esta nova hipótese com mais precisão. Palavras-chave: variabilidade genética, biogeografia, ethnobotânica, análise genética Discrimination of Pejibaye (Bactris gasipaes) Landraces in Brazilian Amazonia usingABSTRACT -The pejibaye (Bactris gasipaes Kunth, Palmae) was domesticated for it fruits by the first peoples of western Amazonia. Consequently it exhibits a landrace complex that has been Brazil, three landraces have been proposed [Pará (Amazonas River), Solimões (lower and middle Solimões River), Putumayo (upper Solimões River)], with indications that the Solimões landrace could be an artifact of the morphometric analysis. RAPD markers were used to evaluate the three landrace hypothesis. DNA was extracted from 30 plants of each landrace maintained in the Pejibaye germplasm bank, Manaus, AM, Brazil. During PCR amplification, 8 primers generated 80 markers, Jaccard similarities were estimated, the plants were grouped with UPGMA. The dendrogram 26 plants of this race, 5 of the Putumayo and 1 of the Solimões; the group of the Solimões River contained 29 plants of the Solimões race, 19 of the Putumayo and 1 of the Pará. The structure of the second group suggested that there is only one landrace along the Solimões River, since the plants were mixed in sub-groups without apparent order. This marker-based genetic analysis did not Solimões River to central Amazonia. Genetic and morphological data must now be used to evaluate this new hypothesis.

Peach palm (Bactris gasipaes Kunth) is a Neotropical palm domesticated by Native Americans. Its domestication resulted in a set of landraces (var. gasipaes), some with very starchy fruit used for fermentation, others with an equilibrium of starch and oil used as snacks. Which of the three wild types (var. chichagui) was involved and where the domestication process began are unclear, with three hypotheses under discussion: an origin in southwestern Amazonia; or in northwestern South America; or multiple origins. We reevaluate one of the wild types, defining it as the incipient domesticate, and then evaluate these hypotheses using the Brazilian peach palm Core Collection and selected herbaria samples to: (1) model the potential distributions of wild and domesticated populations; (2) identify the probable origin of domestication with a phylogeographic analysis of chloroplast DNA sequences; and (3) determine the dispersal routes after domestication using spatial analysis of genetic diversity based on 17 nuclear microsatellite loci. The two very small-fruited wild types have distinct distributions in the northern Andes region and across southern Amazonia, both under moderately humid climates, while the incipient domesticate, partly sympatric with the southern wild type, is also found along the Equatorial Andes, in a more humid climatic envelope, more similar to that of the domesticated landraces. Two distribution models for Last Glacial Maximum conditions (CCSM4, MIROC) also suggest distinct distributions for the two wild populations. The chloroplast DNA phylogeographic network confirms the area of sympatry of the incipient domesticate and the southern wild type in southwestern Amazonia as the origin of domestication. The spatial patterns of genetic diversity confirm the proposal of two dispersals, one along the Ucayali River, into western Amazonia, northwestern South America and finally Central America; the other along the Madeira River into central and then eastern Amazonia. The first dispersal resulted in very starchy fruit for fermentation, while the second may have been later and resulted in snack fruits. Further explorations of southwestern Amazonia are essential for more precise identification of the earliest events, both with new archeological methods and genetic analyses with larger samples.

Most native Amazonian crops were domesticated in the periphery of the basin. The upper Madeira River basin is an important part of this periphery where several important crops were domesticated and others are suspected to have been domesticated or arrived early. Some of these crops have been reasonably well studied, such as manioc, peanut, peach palm, coca and tobacco, while others are not as well known, such as the hot peppers Capsicum baccatum and C. frutescens, and still others need confirmation, such as cocoyam and annatto. We review the information available for manioc, peach palm, Capsicum, peanut, annatto and cocoyam. The state-of-the-art for Capsicum frutescens, annatto and cocoyam is insufficient to conclude definitively that they were domesticated in the upper Madeira, while all the others have at least one of their origins or centers of diversity in the upper Madeira. Keywords: Amazonian crops. Center of domestication. Crop domestication. Southwestern AmazoniaResumo: A maioria dos cultivos nativos da Amazônia foi domesticada na periferia da bacia. A bacia do alto rio Madeira é uma parte importante dessa periferia, onde se suspeita que vários cultivos importantes foram domesticados, alguns são confirmados e outros possivelmente chegaram há muito tempo na região. Alguns destes cultivos foram razoavelmente bem estudados, tais como mandioca, amendoim, pupunha, coca e tabaco, enquanto outros não são tão bem conhecidos, como as pimentas Capsicum baccatum e C. frutescens, e ainda outros precisam de confirmação, como taioba e urucum. Revisamos as informações disponíveis para a mandioca, pupunha, Capsicum, amendoim, urucum e taioba. O estado da arte de Capsicum frutescens, urucum e taioba é insuficiente para concluir definitivamente que eles foram domesticados no alto rio Madeira, enquanto todos os outros têm pelo menos uma das suas origens ou centros de diversidade na região.

Various pre-Columbian and post-European conquest events in the history of Amazonian occupation may explain the absence of clearer patterns of genetic structure. However, the wide distribution of the most common chloroplast haplotype agrees with an early dispersal of manioc across Brazilian Amazonia. Furthermore, differences in genetic structure and in the spatial distribution of genetic diversity suggest that bitter and sweet manioc had distinct dispersal histories. Knowledge about how prehistoric and contemporary Amazonian peoples manage their crops is valuable for the maintenance and conservation of the impressive diversity of their native crops.

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