DOCSLIB.ORG

Test Documentation Release Test

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Test Documentation Release Test test Documentation Release test test Dec 06, 2017 Contents 1 Biopython 3 1.1 Tutorial and Cookbook..........................................3 2 Introduction 5 2.1 What is Biopython?...........................................5 2.2 What can I find in the Biopython package................................5 2.3 About these notebooks..........................................6 3 Quick Start 7 3.1 General overview of what Biopython provides.............................7 3.2 Working with sequences.........................................8 3.3 A usage example.............................................8 3.4 Parsing sequence file formats......................................9 3.5 Connecting with biological databases.................................. 11 3.6 What to do next............................................. 11 4 Sequence Objects 13 4.1 Sequences and Alphabets........................................ 13 4.2 Sequences act like strings........................................ 14 4.3 Slicing a sequence............................................ 15 4.4 Turning Seq objects into strings..................................... 16 4.5 Concatenating or adding sequences................................... 16 4.6 Changing case.............................................. 17 4.7 Nucleotide sequences and (reverse) complements............................ 18 4.8 Transcription............................................... 18 4.9 Translation................................................ 19 4.10 Translation Tables............................................ 21 4.11 Comparing Seq objects.......................................... 22 4.12 MutableSeq Objects........................................... 23 4.13 UnknownSeq Objects.......................................... 24 4.14 Working with strings directly...................................... 25 5 Sequence annotation objects 27 5.1 The SeqRecord Object.......................................... 27 5.2 Creating a SeqRecord.......................................... 28 5.3 Feature, location and position objects.................................. 32 5.4 References................................................ 36 i 5.5 The format method............................................ 36 5.6 Slicing a SeqRecord........................................... 36 5.7 Adding SeqRecord objects........................................ 40 5.8 Reverse-complementing SeqRecord objects............................... 41 6 Sequence Input/Output 43 6.1 Parsing or Reading Sequences...................................... 43 6.2 Reading Sequence Files......................................... 44 6.3 Parsing sequences from compressed files................................ 48 6.4 Parsing sequences from the net..................................... 48 6.5 Sequence files as dictionaries...................................... 50 6.6 Writing sequence files.......................................... 56 7 Multiple Sequence Alignment objects 61 7.1 Parsing or Reading Sequence Alignments................................ 61 7.2 Writing Alignments........................................... 73 7.3 Manipulating Alignments........................................ 77 7.4 Alignment Tools............................................. 80 8 BLAST 101 8.1 Running BLAST over the Internet.................................... 102 8.2 Saving blast output............................................ 105 8.3 Running BLAST locally......................................... 105 8.4 Parsing BLAST output.......................................... 107 8.5 The BLAST record class......................................... 108 8.6 Deprecated BLAST parsers....................................... 109 8.7 Bio.Blast.NCBIStandalone........................................ 109 9 BLAST and other sequence search tools (experimental code) 115 9.1 The SearchIO object model....................................... 116 9.2 A note about standards and conventions................................. 129 9.3 Reading search output files........................................ 130 9.4 Dealing with large search output files with indexing.......................... 131 9.5 Writing and converting search output files................................ 131 10 Accessing NCBI’s Entrez databases 133 10.1 Entrez Guidelines............................................ 134 10.2 EInfo: Obtaining information about the Entrez databases........................ 135 10.3 ESearch: Searching the Entrez databases................................ 138 10.4 EPost: Uploading a list of identifiers................................... 139 10.5 ESummary: Retrieving summaries from primary IDs.......................... 139 10.6 EFetch: Downloading full records from Entrez............................. 140 10.7 ELink: Searching for related items in NCBI Entrez........................... 143 10.8 EGQuery: Global Query - counts for search terms........................... 147 10.9 ESpell: Obtaining spelling suggestions................................. 148 10.10 Parsing huge Entrez XML files..................................... 149 10.11 Handling errors.............................................. 150 10.12 Specialized parsers............................................ 153 10.13 Using a proxy.............................................. 162 10.14 Examples................................................. 163 10.15 Using the history and WebEnv...................................... 219 11 Swiss-Prot and ExPASy 225 11.1 Parsing Swiss-Prot files......................................... 225 11.2 Parsing Prosite records.......................................... 231 ii 11.3 Parsing Prosite documentation records................................. 232 11.4 Parsing Enzyme records......................................... 233 11.5 Accessing the ExPASy server...................................... 234 11.6 Scanning the Prosite database...................................... 244 12 Going 3D: The PDB module 247 12.1 Reading and writing crystal structure files................................ 247 12.2 Structure representation......................................... 250 12.3 Disorder................................................. 256 12.4 Hetero residues.............................................. 258 12.5 Navigating through a Structure object.................................. 258 12.6 Analyzing structures........................................... 555 12.7 Common problems in PDB files..................................... 559 12.8 Accessing the Protein Data Bank.................................... 561 13 Bio.PopGen: Population genetics 563 13.1 GenePop................................................. 563 13.2 Operations on GenePop records..................................... 564 13.3 Coalescent simulation.......................................... 565 14 Phylogenetics with Bio.Phylo 569 14.1 Demo: what is in a tree?......................................... 569 14.2 I/O functions............................................... 572 14.3 View and export trees.......................................... 576 14.4 Using Tree and Clade objects...................................... 581 14.5 Running external applications...................................... 584 14.6 PAML integration............................................ 585 15 Sequence motif analysis using Bio.motifs 587 15.1 Motif objects............................................... 587 15.2 Reading motifs.............................................. 589 15.3 Writing motifs.............................................. 598 15.4 Position-Weight Matrices........................................ 599 15.5 Position-Specific Scoring Matrices................................... 600 15.6 Searching for instances.......................................... 600 15.7 Each motif object has an associated Position-Specific Scoring Matrix................. 602 15.8 Comparing motifs............................................ 604 15.9 De novo motif finding.......................................... 604 16 Cluster analysis 607 16.1 Data representation............................................ 607 16.2 Missing values.............................................. 607 16.3 Random number generator........................................ 608 16.4 Euclidean distance............................................ 609 16.5 City-block distance............................................ 609 16.6 The Pearson correlation coefficient................................... 609 16.7 Absolute Pearson correlation....................................... 609 16.8 Uncentered correlation (cosine of the angle)............................... 610 16.9 Absolute uncentered correlation..................................... 610 16.10 Spearman rank correlation........................................ 611 16.11 Kendall’s 휏 ................................................ 611 16.12 Weighting................................................. 611 16.13 Calculating the distance matrix..................................... 611 16.14 Calculating the cluster centroids..................................... 612 16.15 Calculating the distance between clusters................................ 613 iii 16.16 k-means and k-medians......................................... 615 16.17 k-medoids clustering........................................... 616 16.18 Representing a hierarchical clustering solution............................. 618 16.19 Performing hierarchical clustering.................................... 620 16.20 Calculating the distance matrix..................................... 626 16.21 Calculating
Load more

Recommended publications
  • Native Orchid Society of South Australia
    NATIVE ORCHID SOCIETY of SOUTH AUSTRALIA NATIVE ORCHID SOCIETY OF SOUTH AUSTRALIA JOURNAL Volume 6, No. 10, November, 1982 Registered by Australia Post Publication No. SBH 1344. Price 40c PATRON: Mr T.R.N. Lothian PRESIDENT: Mr J.T. Simmons SECRETARY: Mr E.R. Hargreaves 4 Gothic Avenue 1 Halmon Avenue STONYFELL S.A. 5066 EVERARD PARK SA 5035 Telephone 32 5070 Telephone 293 2471 297 3724 VICE-PRESIDENT: Mr G.J. Nieuwenhoven COMMITTFE: Mr R. Shooter Mr P. Barnes TREASURER: Mr R.T. Robjohns Mrs A. Howe Mr R. Markwick EDITOR: Mr G.J. Nieuwenhoven NEXT MEETING WHEN: Tuesday, 23rd November, 1982 at 8.00 p.m. WHERE St. Matthews Hail, Bridge Street, Kensington. SUBJECT: This is our final meeting for 1982 and will take the form of a Social Evening. We will be showing a few slides to start the evening. Each member is requested to bring a plate. Tea, coffee, etc. will be provided. Plant Display and Commentary as usual, and Christmas raffle. NEW MEMBERS Mr. L. Field Mr. R.N. Pederson Mr. D. Unsworth Mrs. P.A. Biddiss Would all members please return any outstanding library books at the next meeting. FIELD TRIP -- CHANGE OF DATE AND VENUE The Field Trip to Peters Creek scheduled for 27th November, 1982, and announced in the last Journal has been cancelled. The extended dry season has not been conducive to flowering of the rarer moisture- loving Microtis spp., which were to be the objective of the trip. 92 FIELD TRIP - CHANGE OF DATE AND VENUE (Continued) Instead, an alternative trip has been arranged for Saturday afternoon, 4th December, 1982, meeting in Mount Compass at 2.00 p.m.
    [Show full text]
  • Technical Protocols for Program Outcomes
    Monitoring and Reporting Framework: Technical Protocols for Program Outcomes Melbourne Strategic Assessment © The State of Victoria Department of Environment, Land, Water and Planning 2015 This work is licensed under a Creative Commons Attribution 3.0 Australia licence. You are free to re-use the work under that licence, on the condition that you credit the State of Victoria as author. The licence does not apply to any images, photographs or branding, including the Victorian Coat of Arms, the Victorian Government logo and the Department of Environment, Land, Water and Planning logo. To view a copy of this licence, visit http://creativecommons.org/licenses/by/3.0/au/deed.en ISBN 978-1-74146-577-8 Accessibility If you would like to receive this publication in an alternative format, please telephone the DELWP Customer Service Centre on 136186, email [email protected] or via the National Relay Service on 133 677 www.relayservice.com.au. This document is also available on the internet at www.delwp.vic.gov.au Disclaimer This publication may be of assistance to you but the State of Victoria and its employees do not guarantee that the publication is without flaw of any kind or is wholly appropriate for your particular purposes and therefore disclaims all liability for any error, loss or other consequence which may arise from you relying on any information in this publication. Contents Introduction 5 Context and scope 5 Monitoring Program Outcomes 5 Reporting on Program Outcomes 8 The composition, structure and function of Natural
    [Show full text]
  • Dendrobium Kingianum Bidwill Ex Lindl
    Volume 24: 203–232 ELOPEA Publication date: 19 May 2021 T dx.doi.org/10.7751/telopea14806 Journal of Plant Systematics plantnet.rbgsyd.nsw.gov.au/Telopea • escholarship.usyd.edu.au/journals/index.php/TEL • ISSN 0312-9764 (Print) • ISSN 2200-4025 (Online) A review of Dendrobium kingianum Bidwill ex Lindl. (Orchidaceae) with morphological and molecular- phylogenetic analyses Peter B. Adams1,2, Sheryl D. Lawson2, and Matthew A.M. Renner 3 1The University of Melbourne, School of BioSciences, Parkville 3010, Victoria 2National Herbarium of Victoria, Royal Botanic Gardens Victoria, Birdwood Ave., Melbourne 3004, Victoria 3National Herbarium of New South Wales, Royal Botanic Gardens and Domain Trust, Sydney 2000, New South Wales Author for correspondence: [email protected] Abstract Populations of Dendrobium kingianum Bidwill ex Lindl. from near Newcastle, New South Wales to southern and central west Queensland and encompassing all regions of the distribution were studied using field observations, morphometric analysis and nrITS sequences. A total of 281 individuals were used to construct regional descriptions of D. kingianum and 139 individuals were measured for 19 morphological characters, and similarities and differences among specimens summarised using multivariate statistical methods. Patterns of morphological variation within D. kingianum are consistent with a single variable species that expresses clinal variation, with short-growing plants in the south and taller plants in the northern part of the distribution. The nrITS gene tree suggests two subgroups within D. kingianum subsp. kingianum, one comprising northern, the other southern individuals, which may overlap in the vicinity of Dorrigo, New South Wales. The disjunct D. kingianum subsp. carnarvonense Peter B.
    [Show full text]
  • Redalyc.Aa from Lomas Formations. a New Orchidaceae Record from The
    Lankesteriana International Journal on Orchidology ISSN: 1409-3871 [email protected] Universidad de Costa Rica Costa Rica Trujillo, Delsy; Delgado Rodríguez, Amalia Aa from lomas formations. A new Orchidaceae record from the desert coast of Peru Lankesteriana International Journal on Orchidology, vol. 11, núm. 1, abril, 2011, pp. 33-38 Universidad de Costa Rica Cartago, Costa Rica Available in: http://www.redalyc.org/articulo.oa?id=44339820005 How to cite Complete issue Scientific Information System More information about this article Network of Scientific Journals from Latin America, the Caribbean, Spain and Portugal Journal's homepage in redalyc.org Non-profit academic project, developed under the open access initiative LANKESTERIANA 11(1): 33—38. 2011. AA FROM LOMAS FORmatIONS. A NEW ORCHIDACEAE RECORD FROM THE DESERT COAST OF PERU DELSY TRUJILLO1,3 and AMALIA DELGADO RODRÍGUEZ2 1 Research Associate, Herbario MOL, Facultad de Ciencias Forestales, Universidad Nacional Agraria La Molina. Av. La Universidad s/n. La Molina. Apartado 12-056 - Lima, Perú. 2 Laboratorio de Dicotiledóneas. Museo de Historia Natural, Universidad Nacional Mayor de San Marcos. Av. Arenales 1256. Jesús María - Lima, Perú. 3 Corresponding author: [email protected] ABSTRACT. Orchid species of the genus Aa have been described as mostly restricted to high elevations zones in the Andes and mountains of Costa Rica. Here, we record populations of Aa weddelliana at lower elevations in lomas formations from the desert coast of Peru; this is the fourth species of Orchidaceae registered in Peruvian lomas. Furthermore, we illustrate and discuss some floral features ofAa weddelliana. RESUMEN. Las especies del género Aa han sido descritas como orquídeas restringidas generalmente a zonas altas de los Andes y montañas de Costa Rica.
    [Show full text]
  • Genomic Diversity Guides Conservation Strategies Among Rare Terrestrial Orchid Species When Taxonomy Remains Uncertain
    Annals of Botany Page 1 of 11 doi:10.1093/aob/mcx022, available online at https://academic.oup.com/aob Genomic diversity guides conservation strategies among rare terrestrial orchid species when taxonomy remains uncertain Collin W. Ahrens1,2,*, Megan A. Supple3, Nicola C. Aitken3, David J. Cantrill1, Justin O. Borevitz3 and Elizabeth A. James1 1Royal Botanic Gardens Victoria, Science Division, Melbourne, Victoria 3004, Australia, 2Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia and 3Australian National University, Research School of Biology, Centre of Excellence in Plant Energy Biology, Canberra, ACT 0200, Australia *For correspondence. E-mail [email protected] Received: 21 January 2017 Editorial decision: 30 January 2017 Accepted: 12 February 2017 Background and Aims Species are often used as the unit for conservation, but may not be suitable for species complexes where taxa are difficult to distinguish. Under such circumstances, it may be more appropriate to consider species groups or populations as evolutionarily significant units (ESUs). A population genomic approach was em- ployed to investigate the diversity within and among closely related species to create a more robust, lineage-specific conservation strategy for a nationally endangered terrestrial orchid and its relatives from south-eastern Australia. Methods Four putative species were sampled from a total of 16 populations in the Victorian Volcanic Plain (VVP) bioregion and one population of a sub-alpine outgroup in south-eastern Australia. Morphological measure- ments were taken in situ along with leaf material for genotyping by sequencing (GBS) and microsatellite analyses. Key Results Species could not be differentiated using morphological measurements.
    [Show full text]
  • Ecology and Ex Situ Conservation of Vanilla Siamensis (Rolfe Ex Downie) in Thailand
    Kent Academic Repository Full text document (pdf) Citation for published version Chaipanich, Vinan Vince (2020) Ecology and Ex Situ Conservation of Vanilla siamensis (Rolfe ex Downie) in Thailand. Doctor of Philosophy (PhD) thesis, University of Kent,. DOI Link to record in KAR https://kar.kent.ac.uk/85312/ Document Version UNSPECIFIED Copyright & reuse Content in the Kent Academic Repository is made available for research purposes. Unless otherwise stated all content is protected by copyright and in the absence of an open licence (eg Creative Commons), permissions for further reuse of content should be sought from the publisher, author or other copyright holder. Versions of research The version in the Kent Academic Repository may differ from the final published version. Users are advised to check http://kar.kent.ac.uk for the status of the paper. Users should always cite the published version of record. Enquiries For any further enquiries regarding the licence status of this document, please contact: [email protected] If you believe this document infringes copyright then please contact the KAR admin team with the take-down information provided at http://kar.kent.ac.uk/contact.html Ecology and Ex Situ Conservation of Vanilla siamensis (Rolfe ex Downie) in Thailand By Vinan Vince Chaipanich November 2020 A thesis submitted to the University of Kent in the School of Anthropology and Conservation, Faculty of Social Sciences for the degree of Doctor of Philosophy Abstract A loss of habitat and climate change raises concerns about change in biodiversity, in particular the sensitive species such as narrowly endemic species. Vanilla siamensis is one such endemic species.
    [Show full text]
  • (Orchidaceae). Plant Syst
    J. Orchid Soc. India, 30: 1-10, 2016 ISSN 0971-5371 DEVELOPMENT OF MALLLEEE AND FEMALLLE GAMETOPHYTES IN HABENARIA OVVVALIFOLIA WIGHT (ORCHIDAAACCCEEEAAAE) M R GURUDEVAAA Department of Botany, Visveswarapura College of Science, K.R. Road, Bengaluru - 560 004, Karnataka, India Abstract The anther in Habenaria ovalifolia Wight was dithecous and tetrasporangiate. Its wall development confirmed to the monocotyledonous type. Each archesporial cell developed into a block of sporogenous cells and finally organized into pollen massulae. The anther wall was 4-5 layered. The endothecial cells developed ring-like tangential thickening on their inner walls. Tapetal cells were uninucleate and showed dual origin. The microspore tetrads were linear, tetrahedral, decussate and isobilateral. The pollens were shed at 2-celled stage. The ovules were anatropous, bitegmic and tenuinucellate. The inner integument alone formed the micropyle. The development of embryo sac was monosporic and G-1a type. The mature embryo sac contained an egg apparatus, secondary nucleus and three antipodal cells. Double fertilization occurred normally. Introduction species. THE ORCHIDACEAE, one of the largest families of Materials and Methods angiosperms is the most evolved amongst the Habenaria ovalifolia Wight is a terrestrial herb with monocotyledons. The orchid embryology is interesting, ellipsoidal underground tubers. There are about 4-6 as these plants exhibit great diversity in the oblong or obovate, acute, entire leaves cluster below development of male and female gametophyte. The the middle of the stem (Fig. 1). The inflorescence is a first embryological study in the family was made by many flowered raceme. The flowers are green, Muller in 1847. Since then several investigations have bracteate and pedicellate (Fig.
    [Show full text]
  • Diversity and Distribution of Vascular Epiphytic Flora in Sub-Temperate Forests of Darjeeling Himalaya, India
    Annual Research & Review in Biology 35(5): 63-81, 2020; Article no.ARRB.57913 ISSN: 2347-565X, NLM ID: 101632869 Diversity and Distribution of Vascular Epiphytic Flora in Sub-temperate Forests of Darjeeling Himalaya, India Preshina Rai1 and Saurav Moktan1* 1Department of Botany, University of Calcutta, 35, B.C. Road, Kolkata, 700 019, West Bengal, India. Authors’ contributions This work was carried out in collaboration between both authors. Author PR conducted field study, collected data and prepared initial draft including literature searches. Author SM provided taxonomic expertise with identification and data analysis. Both authors read and approved the final manuscript. Article Information DOI: 10.9734/ARRB/2020/v35i530226 Editor(s): (1) Dr. Rishee K. Kalaria, Navsari Agricultural University, India. Reviewers: (1) Sameh Cherif, University of Carthage, Tunisia. (2) Ricardo Moreno-González, University of Göttingen, Germany. (3) Nelson Túlio Lage Pena, Universidade Federal de Viçosa, Brazil. Complete Peer review History: http://www.sdiarticle4.com/review-history/57913 Received 06 April 2020 Accepted 11 June 2020 Original Research Article Published 22 June 2020 ABSTRACT Aims: This communication deals with the diversity and distribution including host species distribution of vascular epiphytes also reflecting its phenological observations. Study Design: Random field survey was carried out in the study site to identify and record the taxa. Host species was identified and vascular epiphytes were noted. Study Site and Duration: The study was conducted in the sub-temperate forests of Darjeeling Himalaya which is a part of the eastern Himalaya hotspot. The zone extends between 1200 to 1850 m amsl representing the amalgamation of both sub-tropical and temperate vegetation.
    [Show full text]
  • Review Article Organic Compounds: Contents and Their Role in Improving Seed Germination and Protocorm Development in Orchids
    Hindawi International Journal of Agronomy Volume 2020, Article ID 2795108, 12 pages https://doi.org/10.1155/2020/2795108 Review Article Organic Compounds: Contents and Their Role in Improving Seed Germination and Protocorm Development in Orchids Edy Setiti Wida Utami and Sucipto Hariyanto Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya 60115, Indonesia Correspondence should be addressed to Sucipto Hariyanto; [email protected] Received 26 January 2020; Revised 9 May 2020; Accepted 23 May 2020; Published 11 June 2020 Academic Editor: Isabel Marques Copyright © 2020 Edy Setiti Wida Utami and Sucipto Hariyanto. ,is is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. In nature, orchid seed germination is obligatory following infection by mycorrhizal fungi, which supplies the developing embryo with water, carbohydrates, vitamins, and minerals, causing the seeds to germinate relatively slowly and at a low germination rate. ,e nonsymbiotic germination of orchid seeds found in 1922 is applicable to in vitro propagation. ,e success of seed germination in vitro is influenced by supplementation with organic compounds. Here, we review the scientific literature in terms of the contents and role of organic supplements in promoting seed germination, protocorm development, and seedling growth in orchids. We systematically collected information from scientific literature databases including Scopus, Google Scholar, and ProQuest, as well as published books and conference proceedings. Various organic compounds, i.e., coconut water (CW), peptone (P), banana homogenate (BH), potato homogenate (PH), chitosan (CHT), tomato juice (TJ), and yeast extract (YE), can promote seed germination and growth and development of various orchids.
    [Show full text]
  • Cryopreservation of Plbs of Brassidium Fly Away Using Encapsulation-Dehydration Technique
    © 2015 Journal compilation ISSN 1684-3908 (print edition) http://biology.num.edu.mn Mongolian Journal of Biological http://mjbs.100zero.org/ Sciences MJBS Volume 13(1-2), 2015 ISSN 2225-4994 (online edition) http://dx.doi.org/10.22353/mjbs.2015.13.03 Original Ar cle Cryopreservation of PLBs of Brassidium Fly Away Using Encapsulation-Dehydration Technique Arulvilee Rajasegar1,2, Ranjetta Poobathy1, Xavier Rathinam2, Yungeree Oyunbileg 3 and Sreeramanan Subramaniam1* 1School of Biological Sciences, Universiti Sains Malaysia (USM), Georgetown, 11800, Penang, Malaysia 2AIMST University, Semeling, 11800, Kedah, Malaysia. 3Institute of General and Experimental Biology, Mongolian Academy of Sciences, Peace avenue-54B, Ulaanbaatar 13330, Mongolia. Abstract Key words: In vitro grown protocorm-like bodies (PLBs) of Brassidium Fly Away orchid hybrid Encapsulation- were cryopreserved using encapsulation- dehydration technique. The viability of the dehydration, PLBs, cryopreserved cells was determined by 2,3,5-triphenyltetrazolium chloride (TTC) cryopreservation assay. For the preculture treatment, the PLBs were excised into two standard sizes of 1-2 and 4-5 mm and were precultured on half-strength Murashige and Skoog (MS) semi solid medium supplemented with diff erent concentrations of sucrose (0, 0.2, Article information: 0.4, 0.6, 0.8 and 1.0M). The PLBs size 4-5 mm and 0.6 M sucrose concentration Received: 29 Dec. 2013 was selected based on highest viability obtained in TTC assay. The PLBs were Accepted: 27 Mar. 2015 encapsulated for 30 minutes using 3% (w/v) liquid sodium alginate medium Published: 27 Nov. 2015 supplemented with 0.4M sucrose and 0.1M calcium chloride and osmoprotected in 0.75M sucrose solution for 24 hours at 25°C.
    [Show full text]
  • Lankesteriana IV
    LANKESTERIANA 7(1-2): 229-239. 2007. DENSITY INDUCED RATES OF POLLINARIA REMOVAL AND DEPOSITION IN THE PURPLE ENAMEL-ORCHID, ELYTHRANTHERA BRUNONIS (ENDL.) A.S. GEORGE 1,10 2 3 RAYMOND L. TREMBLAY , RICHARD M. BATEMAN , ANDREW P. B ROWN , 4 5 6 7 MARC HACHADOURIAN , MICHAEL J. HUTCHINGS , SHELAGH KELL , HAROLD KOOPOWITZ , 8 9 CARLOS LEHNEBACH & DENNIS WIGHAM 1 Department of Biology, 100 Carr. 908, University of Puerto Rico – Humacao campus, Humacao, Puerto Rico, 00791-4300, USA 2 Natural History Museum, Cromwell Road, London SW7 5BD, UK 3 Department of Environment and Conservation, Species and Communities Branch, Locked Bag 104 Bentley Delivery Centre WA 6893, Australia 4 New York Botanic Garden, 112 Alpine Terrace, Hilldale, NJ 00642, USA 5 School of Life Sciences, University of Sussex, Falmer, Brighton, Sussex, BN1 9QG, UK 6 IUCN/SSC Orchid Specialist Group Secretariat, 36 Broad Street, Lyme Regis, Dorset, DT7 3QF, UK 7 University of California, Ecology and Evolutionary Biology, Irvine, CA 92697, USA 8 Massey University, Allan Wilson Center for Molecular Ecology and Evolution 9 Smithsonian Institution, Smithsonian Environmental Research Center, Box 28, Edgewater, MD 21037, USA 10 Author for correspondence: [email protected] RESUMEN. La distribución y densidad de los individuos dentro de las poblaciones de plantas pueden afectar el éxito reproductivo de sus integrantes. Luego de describir la filogenia de las orquideas del grupo de las Caladeniideas y su biología reproductiva, evaluamos el efecto de la densidad en el éxito reproductivo de la orquídea terrestre Elythranthera brunonis, endémica de Australia del Oeste. El éxito reproductivo de esta orquídea, medido como la deposición y remoción de polinios, fue evaluado.
    [Show full text]
  • Floristic Composition of a Neotropical Inselberg from Espírito Santo State, Brazil: an Important Area for Conservation
    13 1 2043 the journal of biodiversity data 11 February 2017 Check List LISTS OF SPECIES Check List 13(1): 2043, 11 February 2017 doi: https://doi.org/10.15560/13.1.2043 ISSN 1809-127X © 2017 Check List and Authors Floristic composition of a Neotropical inselberg from Espírito Santo state, Brazil: an important area for conservation Dayvid Rodrigues Couto1, 6, Talitha Mayumi Francisco2, Vitor da Cunha Manhães1, Henrique Machado Dias4 & Miriam Cristina Alvarez Pereira5 1 Universidade Federal do Rio de Janeiro, Museu Nacional, Programa de Pós-Graduação em Botânica, Quinta da Boa Vista, CEP 20940-040, Rio de Janeiro, RJ, Brazil 2 Universidade Estadual do Norte Fluminense Darcy Ribeiro, Laboratório de Ciências Ambientais, Programa de Pós-Graduação em Ecologia e Recursos Naturais, Av. Alberto Lamego, 2000, CEP 29013-600, Campos dos Goytacazes, RJ, Brazil 4 Universidade Federal do Espírito Santo (CCA/UFES), Centro de Ciências Agrárias, Departamento de Ciências Florestais e da Madeira, Av. Governador Lindemberg, 316, CEP 28550-000, Jerônimo Monteiro, ES, Brazil 5 Universidade Federal do Espírito Santo (CCA/UFES), Centro de Ciências Agrárias, Alto Guararema, s/no, CEP 29500-000, Alegre, ES, Brazil 6 Corresponding author. E-mail: [email protected] Abstract: Our study on granitic and gneissic rock outcrops environmental filters (e.g., total or partial absence of soil, on Pedra dos Pontões in Espírito Santo state contributes to low water retention, nutrient scarcity, difficulty in affixing the knowledge of the vascular flora of inselbergs in south- roots, exposure to wind and heat) that allow these areas eastern Brazil. We registered 211 species distributed among to support a highly specialized flora with sometimes high 51 families and 130 genera.
    [Show full text]