DNA barcoding involves sequencing a standard region of DNA as a tool for species identification. However, there has been no agreement on which region(s) should be used for barcoding land plants. To provide a community recommendation on a standard plant barcode, we have compared the performance of 7 leading candidate plastid DNA regions (atpF-atpH spacer, matK gene, rbcL gene, rpoB gene, rpoC1 gene, psbK-psbI spacer, and trnH-psbA spacer). Based on assessments of recoverability, sequence quality, and levels of species discrimination, we recommend the 2-locus combination of rbcL؉matK as the plant barcode. This core 2-locus barcode will provide a universal framework for the routine use of DNA sequence data to identify specimens and contribute toward the discovery of overlooked species of land plants.matK ͉ rbcL ͉ species identification L arge-scale standardized sequencing of the mitochondrial gene CO1 has made DNA barcoding an efficient species identification tool in many animal groups (1). In plants, however, low substitution rates of mitochondrial DNA have led to the search for alternative barcoding regions. From initial investigations of plastid regions (2-4), 7 leading candidates have emerged (5, 6). Four are portions of coding genes (matK, rbcL, rpoB, and rpoC1), and 3 are noncoding spacers (atpF-atpH, trnH-psbA, and psbK-psbI). Different research groups have proposed various combinations of these loci as their preferred plant barcodes, but no consensus has emerged (5-12). This lack of an agreed standard has impeded progress in plant barcoding.Our aim here is to identify a standard DNA barcode for land plants. To achieve this goal, we have pooled data across laboratories including sequence data from 907 samples, representing 445 angiosperm, 38 gymnosperm, and 67 cryptogam species. Using various subsets of these data, we evaluated the 7 candidate loci using criteria in the Consortium for the Barcode of Life's (CBOL) data standards and guidelines for locus selection (http:// www.barcoding.si.edu/protocols.html). Universality: Which loci can be routinely sequenced across the land plants? Sequence quality and coverage: Which loci are most amenable to the production of bidirectional sequences with few or no ambiguous base calls? Discrimination: Which loci enable most species to be distinguished? ResultsUniversality. Direct universality assessments using a single primer pair for each locus in angiosperms resulted in 90%-98% PCR and sequencing success for 6/7 regions. Success for the seventh region, psbK-psbI, was 77% (Fig. 1A). Greater problems were encountered in other land plant groups, with rpoB, matK, atpF-atpH, and psbK-psbI all showing Ͻ50% success in gymnosperms and/or cryptogams based on data compiled from several laboratories (Fig. 1 A).Sequence Quality. Evaluation of sequence quality and coverage from the candidate loci demonstrated that high quality bidirectional sequences were routinely obtained from rbcL, rpoC1, and rpoB (Fig. 1B, x axis). The remaining 4 loci required more manual editing and produced f...

Since the last classification of Orchidaceae in 2003, there has been major progress in the determination of relationships, and we present here a revised classification including a list of all 736 currently recognized genera. A number of generic changes have occurred in Orchideae (Orchidoideae), but the majority of changes have occurred in Epidendroideae. In the latter, almost all of the problematic placements recognized in the previous classification 11 years ago have now been resolved. In Epidendroideae, we have recognized three new tribes (relative to the last classification): Thaieae (monogeneric) for Thaia, which was previously considered to be the only taxon incertae sedis; Xerorchideae (monogeneric) for Xerorchis; and Wullschlaegelieae for achlorophyllous Wullschlaegelia, which had tentatively been placed in Calypsoeae. Another genus, Devogelia, takes the place of Thaia as incertae sedis in Epidendroideae. Gastrodieae are clearly placed among the tribes in the neottioid grade, with Neottieae sister to the remainder of Epidendroideae. Arethuseae are sister to the rest of the higher Epidendroideae, which is unsurprising given their mostly soft pollinia. Tribal relationships within Epidendroideae have been much clarified by analyses of multiple plastid DNA regions and the low-copy nuclear gene Xdh. Four major clades within the remainder of Epidendroideae are recognized: Vandeae/Podochileae/Collabieae, Cymbidieae, Malaxideae and Epidendreae, the last now including Calypsoinae (previously recognized as a tribe on its own) and Agrostophyllinae s.s. Agrostophyllinae and Collabiinae were unplaced subtribes in the 2003 classification. The former are now split between two subtribes, Agrostophyllinae s.s. and Adrorhizinae, the first now included in Epidendreae and the second in Vandeae. Collabiinae, also probably related to Vandeae, are now elevated to a tribe along with Podochileae. Malaxis and relatives are placed in Malaxidinae and included with Dendrobiinae in Malaxideae. The increased resolution and content of larger clades, recognized here as tribes, do not support the 'phylads' in Epidendroideae proposed 22 years ago by Dressler.

Recent debates on the number of plant species in the vast lowland rain forests of the Amazon have been based largely on model estimates, neglecting published checklists based on verified voucher data. Here we collate taxonomically verified checklists to present a list of seed plant species from lowland Amazon rain forests. Our list comprises 14,003 species, of which 6,727 are trees. These figures are similar to estimates derived from nonparametric ecological models, but they contrast strongly with predictions of much higher tree diversity derived from parametric models. Based on the known proportion of tree species in neotropical lowland rain forest communities as measured in complete plot censuses, and on overall estimates of seed plant diversity in Brazil and in the neotropics in general, it is more likely that tree diversity in the Amazon is closer to the lower estimates derived from nonparametric models. Much remains unknown about Amazonian plant diversity, but this taxonomically verified dataset provides a valid starting point for macroecological and evolutionary studies aimed at understanding the origin, evolution, and ecology of the exceptional biodiversity of Amazonian forests.Amazonia | floristics | rain forests | seed plants | species diversity

With more than 56,000 species (excluding fungi), Brazil has one of the richest floras in the worldnearly 19% of the world flora. Our knowledge of the diversity and status of nonvascular plants in Brazil is still fragmentary, although localized studies on algae have revealed loss of species resulting from environmental pollution. Emphasis on local floral surveys, rather than wider taxonomic studies, has obscured estimates of national totals for most taxonomic groups. Knowledge of angiosperms, especially monocotyledons (of which 45% of the species are endemic), is more complete than most. For this group figures are more reliable, with some distribution patterns, endemism levels, and centers of diversity identified. Much, however, still awaits discovery. Coordinated efforts to catalog Brazil's flora are in progress and include projects such as the conservation priority-setting workshops of the Brazilian Ministry of the Environment, which have identified key conservation areas in the major biomes; development of threatened species lists for plants; and the assembly of type data on species of northeastern Brazil through the Darwin Initiative-all of which greatly assist in increasing our knowledge. These initiatives also underline the urgent need to expand the numbers and geographic spread of projects on plant systematics and taxonomy in Brazil, a measure that demands adequate provision of funding and training programs for plant specialists. Finally, Brazil's environmental agency (IBAMA) could play a proactive role in opening protected areas under its jurisdiction, thereby facilitating botanical research by university departments and research institutes. Biodiversidad y Conservación de Plantas en BrasilResumen: Con más de 56,00 especies (excluyendo hongos), Brasil tiene una de las floras más ricas del mundo-casi 19% de la flora mundial. Nuestro conocimiento de la diversidad y del estatus de plantas no vasculares aun es muy incompleto, aunque estudios sobre algas han revelado la pérdida de especies debido a la contaminación ambiental. Elénfasis en estudios florísticos locales, en lugar de estudio taxonómicos más amplios, ha enmascarado a las estimaciones de totales nacionales en casi todos los grupos taxonómicos. El conocimiento sobre angiospermas, especialmente monocotiledóneas (de las cuales 45% de las especies son endémicas), es el más completo. Las cifras para este grupo son más confiables, y se han identificado algunos patrones de distribución, niveles de endemismo y centros de diversidad. Sin embargo, falta mucho por descubrir. Están en progreso esfuerzos coordinados para catalogar la flora de Brasil e incluyen proyectos-que contribuyen enormemente al incremento de nuestro conocimiento -como talleres de definición de prioridades organizados por el Ministerio del Ambiente, que ha identificadoáreas clave para la conservación en los principales biomas; desarrollo de listas de especies de plantas amenazadas; y la organización de datos sobre especies tipo del noreste de Brasil por medio de la Iniciativa Darwin. Sin emb...

We reconstructed phylogenetic relationships in Leguminosae subfam. Mimosoideae tribe Ingeae using 135 sequences from the nuclear (ITS) and 119 from the plastid (trnL–F) genome, representing 23 of the 36 currently recognized genera in the tribe with newly generated sequences of Blanchetiodendron, Guinetia, Macrosamanea, Thailentadopsis and Viguieranthus and an extensive sampling of Calliandra. Only two of the five Neotropical generic alliances of Barneby & Grimes (1996) were supported as monophyletic. Calliandra is resolved as monophyletic with the inclusion of Guinetia. The five previously proposed sections within Calliandra were not supported by our study. Nevertheless, based on these results, a new infrageneric classification is proposed for Calliandra, and the African species of the genus are assigned to a new genus, Afrocalliandra. Three new sections are proposed for Calliandra: (1) sect. Tsugoideae based on C. ser. Tsugoideae, with four species from northwestern South America; (2) sect. Septentrionales, with six species distributed in dry areas from the United States to Mexico and (3) sect. Monticola, which consists of species restricted to the Espinhaço range of Brazil; these latter species form a clade with low levels of sequence variation, a potential indicator of the recent diversification of this group.

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Chromobacterium violaceum is one of millions of species of free-living microorganisms that populate the soil and water in the extant areas of tropical biodiversity around the world. Its complete genome sequence reveals (i) extensive alternative pathways for energy generation, (ii) Ϸ500 ORFs for transport-related proteins, (iii) complex and extensive systems for stress adaptation and motility, and (iv) widespread utilization of quorum sensing for control of inducible systems, all of which underpin the versatility and adaptability of the organism. The genome also contains extensive but incomplete arrays of ORFs coding for proteins associated with mammalian pathogenicity, possibly involved in the occasional but often fatal cases of human C. violaceum infection. There is, in addition, a series of previously unknown but important enzymes and secondary metabolites including paraquat-inducible proteins, drug and heavy-metal-resistance proteins, multiple chitinases, and proteins for the detoxification of xenobiotics that may have biotechnological applications.T he genomes of soil-and water-borne free-living bacteria have received relatively little attention thus far in comparison to pathogenic and extremophilic organisms, yet they provide fundamental insights into environmental adaptation strategies and represent a rich source of genes with biotechnological potential and medical utility. A particularly interesting organism of this kind is Chromobacterium violaceum, a Gram-negative ␤-proteobacterium first described at the end of the 19th century (1), which dominates a variety of ecosystems in tropical and subtropical regions. This bacterium has been found to be highly abundant in the water and borders of the Negro river, a major component of the Brazilian Amazon (2) and as a result has been studied in Brazil over the last three decades. These, in general, have focused on the most notable product of the bacterium, the violacein pigment, which has already been introduced as a therapeutic compound for dermatological purposes (3). Violacein also exhibits antimicrobial activity against the important tropical pathogens Mycobacterium tuberculosis (4), Trypanosoma cruzi (5), and Leishmania sp. (6) and is reported to have other bactericidal (2, 7-10), antiviral (11), and anticancer (12, 13) activities.Some other aspects of the biotechnological potential of C. violaceum have also begun to be explored, including the synthesis of poly(3-hydroxyvaleric acid) homopolyester and other shortchain polyhydroxyalkanoates, which might represent alternatives to plastics derived from petrochemicals (14, 15), the hydrolysis of plastic films (16), and the solubilization of gold through a mercury-free process, thereby avoiding environmental contamination (17, 18). These studies, however, have been based on knowledge of only a tiny fraction of the genetic constitution of the organism. In addition, the more basic issues of the mechanisms and strategies underlying the adaptability of C. violaceum, including its observed but infrequent infection of h...

Habenaria is a large genus of terrestrial orchids distributed throughout the tropical and subtropical regions of the world. The integrity and monophyly of this genus have been under discussion for many years, and at one time or another, several genera have been either included in a broadly defined Habenaria or segregated from it. In this study, the phylogenetic relationships of the Neotropical members of the genus and selected groups of African Habenaria were investigated using DNA sequences from the nuclear internal transcribed spacer (ITS) region and the plastid matK gene sampled from 151 taxa of Habenaria from the Neotropics (ca. 51% of the total) as well as 20 species of Habenaria and Bonatea from the Old World. Bayesian and parsimony trees were congruent with each other, and in all analyses, the Neotropical species formed a highly supported group. African species of Habenaria in sections Dolichostachyae, Podandria, Diphyllae, Ceratopetalae and Bilabrellae, and the Neotropical clade formed a highly supported "core Habenaria clade", which includes the type species of the genus from the New World. The topology of the trees indicates an African origin for the Neotropical clade and the low sequence divergence among the Neotropical species suggests a recent radiation of the genus in the New World. Species of Bonatea and Habenaria sections Chlorinae and Multipartitae formed a well-supported clade that was sister to the "core Habenaria clade". The Neotropical clade consists of at least 21 well-supported subgroups, but all Neotropical sections of the current sectional classification are paraphyletic or polyphyletic and will need extensive revision and recircumscription. Most of the Neotropical subgroups formed morphologically uniform assemblage of species, but some cases of morphological divergence within subgroups and convergence between subgroups indicated that morphology alone can be misleading for inferring relationships within the genus. The genera Bertauxia, Kusibabella and Habenella, segregated from New World Habenaria, are not monophyletic and a revision of the sectional classification rather than a generic division seems most appropriate. Our results do not support an extensive generic fragmentation of Habenaria as previously suggested and will provide a framework for revising the infrageneric classification and investigating the patterns of morphological evolution and geographical distribution of the genus in the New World.