Author
Cássio van den Berg
Other affiliations: University of Brasília, Universidade Católica de Brasília, Royal Botanic Gardens ...read more
Bio: Cássio van den Berg is an academic researcher from State University of Feira de Santana. The author has contributed to research in topics: Molecular phylogenetics & Laeliinae. The author has an hindex of 31, co-authored 133 publications receiving 5559 citations. Previous affiliations of Cássio van den Berg include University of Brasília & Universidade Católica de Brasília.
Topics: Molecular phylogenetics, Laeliinae, Monophyly, Phylogenetic tree, Genus
Papers published on a yearly basis
Papers
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Royal Botanic Garden Edinburgh1, National Institutes of Health2, University of Guelph3, University of Johannesburg4, Royal Botanic Gardens5, Smithsonian Institution6, University of British Columbia7, Natural History Museum8, Korea University9, University of Toronto10, State University of Feira de Santana11, University of Costa Rica12, Columbus State University13, New York Botanical Garden14, University of Wisconsin-Madison15, University of the Andes16, University of Cape Town17, Seoul National University18, Hallym University19, National Autonomous University of Mexico20, Imperial College London21
TL;DR: The 2-locus combination of rbcL+matK 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.
Abstract: 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.
2,255 citations
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TL;DR: A revised classification of Orchidaceae is presented including a list of all 736 currently recognized genera, and three new tribes are recognized within Epidendroideae, which has been much clarified by analyses of multiple plastid DNA regions and the low-copy nuclear gene Xdh.
556 citations
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TL;DR: A proposal for a standardised protocol to barcode all land plants is presented in Taxon, 56, (2), 295-299.
Abstract: Chase, M. W., Cowan, R. S., Hollingsworth, P. M., van den Berg, C., Madrinan, S., Petersen, G., Seberg, O., Jorgsensen, T., Cameron, K. M., Carine, M., Pedersen, N., Hedderson, T. A. J., Conrad, F., Salazar, G. A., Richardson, J. E., Hollingsworth, M. L., Barraclough, T. G., Kelly, L., Wilkinson, M. (2007). A proposal for a standardised protocol to barcode all land plants. Taxon, 56, (2), 295-299.
527 citations
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Empresa Brasileira de Pesquisa Agropecuária1, Universidade Federal de Santa Catarina2, University of São Paulo3, National Institute of Amazonian Research4, Universidade Federal de Minas Gerais5, Federal University of Rio de Janeiro6, Federal University of Rio Grande do Norte7, University of Brasília8, Universidade Federal de Goiás9, Universidade Católica de Brasília10, Pontifícia Universidade Católica do Rio Grande do Sul11, Ludwig Institute for Cancer Research12, State University of Santa Cruz13, Federal University of Ceará14, State University of Campinas15, Sao Paulo State University16, Federal University of Pernambuco17, Pontifícia Universidade Católica do Paraná18, Federal University of Paraná19, Universidade Federal do Rio Grande do Sul20, Federal University of Alagoas21, Federal University of Pará22
TL;DR: The complete genome sequence reveals extensive alternative pathways for energy generation, complex and extensive systems for stress adaptation and motility, and widespread utilization of quorum sensing for control of inducible systems, all of which underpin the versatility and adaptability of the organism.
Abstract: 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) ≈500 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.
299 citations
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Federal University of Bahia1, Royal Botanic Garden Edinburgh2, National Museum of Natural History3, State University of Santa Cruz4, National University of Colombia5, Universidad del Norte, Colombia6, New York Botanical Garden7, Universidade Federal de Santa Catarina8, Federal University of Western Pará9, Federal University of Paraná10, Empresa Brasileira de Pesquisa Agropecuária11, Universidade Federal do Rio Grande do Sul12, Natural History Museum13, State University of Feira de Santana14, University of São Paulo15, Sao Paulo State University16, Royal Botanic Gardens17, Spanish National Research Council18, Del Rosario University19, National Institute of Standards and Technology20, State University of Campinas21, Universidade Federal de São João del-Rei22, Universidade Federal de Minas Gerais23, Missouri Botanical Garden24, Federal University of Rio de Janeiro25, Museu Paraense Emílio Goeldi26, National Institute of Amazonian Research27
TL;DR: A comprehensive dataset of Amazonian seed plant species from published sources that includes falsifiable data based on voucher specimens identified by taxonomic specialists is assembled, providing a valid starting point for macroecological and evolutionary studies aimed at understanding the origin, evolution, and ecology of the exceptional biodiversity ofAmazonian forests.
Abstract: 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.
251 citations
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01 Aug 2000
TL;DR: Assessment of medical technology in the context of commercialization with Bioentrepreneur course, which addresses many issues unique to biomedical products.
Abstract: BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.
4,833 citations
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Conrad L. Schoch1, Keith A. Seifert, Sabine M. Huhndorf2, Vincent Robert3 +157 more•Institutions (59)
TL;DR: Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation.
Abstract: Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.
4,116 citations
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TL;DR: Automatic Barcode Gap Discovery is fast, simple method to split a sequence alignment data set into candidate species that should be complemented with other evidence in an integrative taxonomic approach.
Abstract: Within uncharacterized groups, DNA barcodes, short DNA sequences that are present in a wide range of species, can be used to assign organisms into species. We propose an automatic procedure that sorts the sequences into hypothetical species based on the barcode gap, which can be observed whenever the divergence among organisms belonging to the same species is smaller than divergence among organisms from different species. We use a range of prior intraspecific divergence to infer from the data a model-based one-sided confidence limit for intraspecific divergence. The method, called Automatic Barcode Gap Discovery (ABGD), then detects the barcode gap as the first significant gap beyond this limit and uses it to partition the data. Inference of the limit and gap detection are then recursively applied to previously obtained groups to get finer partitions until there is no further partitioning. Using six published data sets of metazoans, we show that ABGD is computationally efficient and performs well for standard prior maximum intraspecific divergences (a few per cent of divergence for the five data sets), except for one data set where less than three sequences per species were sampled. We further explore the theoretical limitations of ABGD through simulation of explicit speciation and population genetics scenarios. Our results emphasize in particular the sensitivity of the method to the presence of recent speciation events, via (unrealistically) high rates of speciation or large numbers of species. In conclusion, ABGD is fast, simple method to split a sequence alignment data set into candidate species that should be complemented with other evidence in an integrative taxonomic approach.
2,336 citations
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Royal Botanic Garden Edinburgh1, National Institutes of Health2, University of Guelph3, University of Johannesburg4, Royal Botanic Gardens5, Smithsonian Institution6, University of British Columbia7, Natural History Museum8, Korea University9, University of Toronto10, State University of Feira de Santana11, University of Costa Rica12, Columbus State University13, University of Wisconsin-Madison14, New York Botanical Garden15, University of the Andes16, University of Cape Town17, Seoul National University18, Hallym University19, National Autonomous University of Mexico20, Imperial College London21
TL;DR: The 2-locus combination of rbcL+matK 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.
Abstract: 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.
2,255 citations
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TL;DR: The achievements gained through analyses of eDNA from macro-organisms in a conservation context are reviewed, its potential advantages and limitations are discussed, and it is expected the eDNA-based approaches to move from single-marker analyses of species or communities to meta-genomic surveys of entire ecosystems to predict spatial and temporal biodiversity patterns.
1,278 citations