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Kenneth J. Wurdack 2,4 and Charles C. Davis
American Journal of Botany 96(8): 1551–1570. 2009. M ALPIGHIALES PHYLOGENETICS: GAINING GROUND ON ONE OF THE MOST RECALCITRANT CLADES IN THE ANGIOSPERM TREE OF LIFE 1 Kenneth J. Wurdack 2,4 and Charles C. Davis3,4 2 Department of Botany, Smithsonian Institution, P.O. Box 37012 NMNH MRC-166, Washington, District of Columbia 20013-7012 USA; and 3 Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, Massachusetts 02138 USA The eudicot order Malpighiales contains ~16 000 species and is the most poorly resolved large rosid clade. To clarify phyloge- netic relationships in the order, we used maximum likelihood, Bayesian, and parsimony analyses of DNA sequence data from 13 gene regions, totaling 15 604 bp, and representing all three genomic compartments (i.e., plastid: atpB , matK , ndhF, and rbcL ; mitochondrial: ccmB , cob , matR , nad1B-C , nad6, and rps3; and nuclear: 18S rDNA, PHYC, and newly developed low-copy EMB2765 ). Our sampling of 190 taxa includes representatives from all families of Malpighiales. These data provide greatly in- creased support for the recent additions of Aneulophus , Bhesa , Centroplacus , Ploiarium , and Raffl esiaceae to Malpighiales; sister relations of Phyllanthaceae + Picrodendraceae, monophyly of Hypericaceae, and polyphyly of Clusiaceae. Oxalidales + Huaceae, followed by Celastrales are successive sisters to Malpighiales. Parasitic Raffl esiaceae, which produce the world’ s largest fl owers, are confi rmed as embedded within a paraphyletic Euphorbiaceae. Novel fi ndings show a well-supported placement of Ctenolopho- naceae with Erythroxylaceae + Rhizophoraceae, sister-group relationships of Bhesa + Centroplacus , and the exclusion of Medu- sandra from Malpighiales. New taxonomic circumscriptions include the addition of Bhesa to Centroplacaceae, Medusandra to Peridiscaceae (Saxifragales), Calophyllaceae applied to Clusiaceae subfamily Kielmeyeroideae, Peraceae applied to Euphorbi- aceae subfamily Peroideae, and Huaceae included in Oxalidales. -
2 ANGIOSPERM PHYLOGENY GROUP (APG) SYSTEM History Of
ANGIOSPERM PHYLOGENY GROUP (APG) SYSTEM The Angiosperm Phylogeny Group, or APG, refers to an informal international group of systematic botanists who came together to try to establish a consensus view of the taxonomy of flowering plants (angiosperms) that would reflect new knowledge about their relationships based upon phylogenetic studies. As of 2010, three incremental versions of a classification system have resulted from this collaboration (published in 1998, 2003 and 2009). An important motivation for the group was what they viewed as deficiencies in prior angiosperm classifications, which were not based on monophyletic groups (i.e. groups consisting of all the descendants of a common ancestor). APG publications are increasingly influential, with a number of major herbaria changing the arrangement of their collections to match the latest APG system. Angiosperm classification and the APG Until detailed genetic evidence became available, the classification of flowering plants (also known as angiosperms, Angiospermae, Anthophyta or Magnoliophyta) was based on their morphology (particularly that of the flower) and their biochemistry (what kinds of chemical compound they contained or produced). Classification systems were typically produced by an individual botanist or by a small group. The result was a large number of such systems (see List of systems of plant taxonomy). Different systems and their updates tended to be favoured in different countries; e.g. the Engler system in continental Europe; the Bentham & Hooker system in Britain (particularly influential because it was used by Kew); the Takhtajan system in the former Soviet Union and countries within its sphere of influence; and the Cronquist system in the United States. -
Phylogeny of the Eudicots : a Nearly Complete Familial Analysis Based On
KEW BULLETIN 55: 257 - 309 (2000) Phylogeny of the eudicots: a nearly complete familial analysis based on rbcL gene sequences 1 V. SAVOLAINENI.2, M. F. FAyl, D. c. ALBACHI.\ A. BACKLUND4, M. VAN DER BANK ,\ K. M. CAMERON1i, S. A. ]e)H;-.;so:--.;7, M. D. LLWOI, j.c. PINTAUDI.R, M. POWELL', M. C. SHEAHAN 1, D. E. SOLTlS~I, P. S. SOLTIS'I, P. WESTONI(), W. M. WHITTEN 11, K.J. WCRDACKI2 & M. W. CHASEl Summary, A phylogenetic analysis of 589 plastid rbcl. gene sequences representing nearly all eudicot families (a total of 308 families; seven photosynthetic and four parasitic families are missing) was performed, and bootstrap re-sampling was used to assess support for clades. Based on these data, the ordinal classification of eudicots is revised following the previous classification of angiosperms by the Angiosperm Phylogeny Group (APG) , Putative additional orders are discussed (e.g. Dilleniales, Escalloniales, VitaiRs) , and several additional families are assigned to orders for future updates of the APG classification. The use of rbcl. alone in such a large matrix was found to be practical in discovering and providing bootstrap support for most orders, Combination of these data with other matrices for the rest of the angiosperms should provide the framework for a complete phylogeny to be used in macro evolutionary studies, !:--':TRODL'CTlON The angiosperms are the first division of organisms to have been re-classified largely on the basis of molecular data analysed phylogenetically (APG 1998). Several large scale molecular phylogenies have been produced for the angiosperms, based on both plastid rbcL (Chase et al. -
Angiosperm Phylogeny Group (APG) System
Angiosperm Phylogeny Group (APG) system The Angiosperm Phylogeny Group, or APG, refers to an informal international group of systematic botanists who came together to try to establish a consensus view of the taxonomy of flowering plants (angiosperms) that would reflect new knowledge about their relationships based upon phylogenetic studies. As of 2010, three incremental versions of a classification system have resulted from this collaboration (published in 1998, 2003 and 2009). An important motivation for the group was what they viewed as deficiencies in prior angiosperm classifications, which were not based on monophyletic groups (i.e. groups consisting of all the descendants of a common ancestor). APG publications are increasingly influential, with a number of major herbaria changing the arrangement of their collections to match the latest APG system. Angiosperm classification and the APG Until detailed genetic evidence became available, the classification of flowering plants (also known as angiosperms, Angiospermae , Anthophyta or Magnoliophyta ) was based on their morphology (particularly that of the flower) and their biochemistry (what kinds of chemical compound they contained or produced). Classification systems were typically produced by an individual botanist or by a small group. The result was a large number of such systems (see List of systems of plant taxonomy). Different systems and their updates tended to be favoured in different countries; e.g. the Engler system in continental Europe; the Bentham & Hooker system in Britain (particularly influential because it was used by Kew); the Takhtajan system in the former Soviet Union and countries within its sphere of influence; and the Cronquist system in the United States. -
Savanna Fire and the Origins of the “Underground Forests” of Africa
SAVANNA FIRE AND THE ORIGINS OF THE “UNDERGROUND FORESTS” OF AFRICA Olivier Maurin1, *, T. Jonathan Davies1, 2, *, John E. Burrows3, 4, Barnabas H. Daru1, Kowiyou Yessoufou1, 5, A. Muthama Muasya6, Michelle van der Bank1 and William J. Bond6, 7 1African Centre for DNA Barcoding, Department of Botany & Plant Biotechnology, University of Johannesburg, PO Box 524 Auckland Park 2006, Johannesburg, Gauteng, South Africa; 2Department of Biology, McGill University, 1205 ave Docteur Penfield, Montreal, QC H3A 0G4, Quebec, Canada; 3Buffelskloof Herbarium, P.O. Box 710, Lydenburg, 1120, South Africa; 4Department of Plant Sciences, University of Pretoria, Private Bag X20 Hatfield 0028, Pretoria, South Africa; 5Department of Environmental Sciences, University of South Africa, Florida campus, Florida 1710, Gauteng, South Africa; 6Department of Biological Sciences and 7South African Environmental Observation Network, University of Cape Town, Rondebosch, 7701, Western Cape, South Africa *These authors contributed equally to the study Author for correspondence: T. Jonathan Davies Tel: +1 514 398 8885 Email: [email protected] Manuscript information: 5272 words (Introduction = 1242 words, Materials and Methods = 1578 words, Results = 548 words, Discussion = 1627 words, Conclusion = 205 words | 6 figures (5 color figures) | 2 Tables | 2 supporting information 1 SUMMARY 1. The origin of fire-adapted lineages is a long-standing question in ecology. Although phylogeny can provide a significant contribution to the ongoing debate, its use has been precluded by the lack of comprehensive DNA data. Here we focus on the ‘underground trees’ (= geoxyles) of southern Africa, one of the most distinctive growth forms characteristic of fire-prone savannas. 2. We placed geoxyles within the most comprehensive dated phylogeny for the regional flora comprising over 1400 woody species. -
An Update of the Angiosperm Phylogeny Group Classification for the Orders and Families of Flowering Plants: APG II
Blackwell Science, LtdOxford, UKBOJBotanical Journal of the Linnean Society 0024-4074The Linnean Society of London, 2003? 2003 141? Original Article CLASSIFICATION OF ORDERS AND FAMILIES OF FLOWERING PLANTS AGP II Botanical Journal of the Linnean Society, 2003, 141, 399–436. With 1 figure An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II THE ANGIOSPERM PHYLOGENY GROUP* Received June 2002; accepted for publication December 2002 A revised and updated classification for the families of the flowering plants is provided. Newly adopted orders include Austrobaileyales, Canellales, Gunnerales, Crossosomatales and Celastrales. Pertinent literature published since the first APG classification is included, such that many additional families are now placed in the phylogenetic scheme. Among these are Hydnoraceae (Piperales), Nartheciaceae (Dioscoreales), Corsiaceae (Liliales), Triuridaceae (Pan- danales), Hanguanaceae (Commelinales), Bromeliacae, Mayacaceae and Rapateaceae (all Poales), Barbeuiaceae and Gisekiaceae (both Caryophyllales), Geissolomataceae, Strasburgeriaceae and Vitaceae (unplaced to order, but included in the rosids), Zygophyllaceae (unplaced to order, but included in eurosids I), Bonnetiaceae, Ctenolopho- naceae, Elatinaceae, Ixonanthaceae, Lophopyxidaceae, Podostemaceae (Malpighiales), Paracryphiaceae (unplaced in euasterid II), Sladeniaceae, Pentaphylacaceae (Ericales) and Cardiopteridaceae (Aquifoliales). Several major fami- lies are recircumscribed. Salicaceae are expanded -
Angiosperm Phylogeny Based on 18S/26S Rdna Sequence Data: Constructing a Large Data Set Using Next-Generation Sequence Data Author(S): Vitor H
Angiosperm Phylogeny Based on 18S/26S rDNA Sequence Data: Constructing a Large Data Set Using Next-Generation Sequence Data Author(s): Vitor H. Maia, Matthew A. Gitzendanner, Pamela S. Soltis, Gane Ka-Shu Wong, and Douglas E. Soltis Source: International Journal of Plant Sciences, Vol. 175, No. 6 (July/August 2014), pp. 613- 650 Published by: The University of Chicago Press Stable URL: http://www.jstor.org/stable/10.1086/676675 . Accessed: 02/11/2015 13:34 Your use of the JSTOR archive indicates your acceptance of the Terms & Conditions of Use, available at . http://www.jstor.org/page/info/about/policies/terms.jsp . JSTOR is a not-for-profit service that helps scholars, researchers, and students discover, use, and build upon a wide range of content in a trusted digital archive. We use information technology and tools to increase productivity and facilitate new forms of scholarship. For more information about JSTOR, please contact [email protected]. The University of Chicago Press is collaborating with JSTOR to digitize, preserve and extend access to International Journal of Plant Sciences. http://www.jstor.org This content downloaded from 23.235.32.0 on Mon, 2 Nov 2015 13:34:26 PM All use subject to JSTOR Terms and Conditions Int. J. Plant Sci. 175(6):613–650. 2014. ᭧ 2014 by The University of Chicago. All rights reserved. 1058-5893/2014/17506-0001$15.00 DOI: 10.1086/676675 ANGIOSPERM PHYLOGENY BASED ON 18S/26S rDNA SEQUENCE DATA: CONSTRUCTING A LARGE DATA SET USING NEXT-GENERATION SEQUENCE DATA Vitor H. Maia,*,†,‡ Matthew A. -
Phylogenomics and a Posteriori Data Partitioning Resolve the Cretaceous Angiosperm Radiation Malpighiales
Phylogenomics and a posteriori data partitioning resolve the Cretaceous angiosperm radiation Malpighiales Zhenxiang Xia, Brad R. Ruhfela,b, Hanno Schaefera,c, André M. Amorimd, M. Sugumarane, Kenneth J. Wurdackf, Peter K. Endressg, Merran L. Matthewsg, Peter F. Stevensh, Sarah Mathewsi,1, and Charles C. Davisa,1 aDepartment of Organismic and Evolutionary Biology, Harvard University Herbaria, Cambridge, MA 02138; bDepartment of Biological Sciences, Eastern Kentucky University, Richmond, KY 40475; cBiodiversitaet der Pflanzen, Technische Universitaet Muenchen, D-85354 Freising, Germany; dDepartamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, 45.662-900, Bahia, Brazil; eRimba Ilmu Botanic Garden, Institute of Biological Sciences, University of Malaya, 50603 Kuala Lumpur, Malaysia; fDepartment of Botany, Smithsonian Institution, Washington, DC 20013; gInstitute of Systematic Botany, University of Zurich, CH-8008 Zurich, Switzerland; hDepartment of Biology, University of Missouri, St. Louis, MO 63166; and iArnold Arboretum, Harvard University, Boston, MA 02131 Edited by Robert K. Jansen, University of Texas, Austin, TX, and accepted by the Editorial Board September 11, 2012 (received for review April 6, 2012) The angiosperm order Malpighiales includes ∼16,000 species and mental, and genomic investigations of flowering plants, but also constitutes up to 40% of the understory tree diversity in tropical rain for crop improvement. forests. Despite remarkable progress in angiosperm systematics dur- Despite substantial progress -
Systematic Affinities of Rhizophoraceae And
American Journal of Botany 87(4): 547-564. 2000. SYSTEMATIC AFFINITIES OF RHIZOPHORACEAE AND ANISOPHYLLEACEAE, AND INTERGENERIC RELATIONSHIPS WITHIN RHIZOPHORACEAE, BASED ON CHLOROPLAST DNA, NUCLEAR RIBOSOMAL DNA, AND MORPHOLOGY1 ANDREA E. SCHWARZBACH23 AND ROBERT E. RICKLEFS3-4 'University of Missouri St. Louis, Department of Biology, 8001 Natural Bridge Road, St. Louis, Missouri 63121-4499 USA; and "Smithsonian Tropical Research Institute, Unit 0948, APO AA 34002-0948 A cladistic analysis of sequences from the chloroplast gene rbcL was used to determine the systematic affinities of Rhizophoraceae and Anisophylleaceae. This analysis rejects close relationships of Rhizophoraceae with Celastraceae or Elaeocarpaceae, suggested previously, and identifies Erythroxylaceae as sister group within the Malpighiales, supported by several morphological and anatomical characters. Our molecular results also indicate that Anisophylleaceae are nested within Cucurbitales. Although this placement is novel, this affinity is also well supported by shared morphological characters. Tribal and generic relationships within Rhizophoraceae are evaluated with a combination of six molecular data sets (rbcL, atpB-rbcL intergenic spacer, trnL-trnF intergenic spacer, ITS1, ITS2, and 5.8S) and a morphological data set. These rela- tionships are compared with results from previous morphological cladistic analyses. Against the background of the molecular results, we briefly discuss the evolution of morphological characters traditionally used for tribal subdivision as well as characters presumably significant for adaptation to mangrove habitats, namely, aerial stilt roots and vivipary. Key words: Anisophylleaceae; atpB-rbcL spacer; cpDNA; Erythroxylaceae; ITS; mangroves; nrDNA; rbcL; Rhizo- phoraceae; trnL-trnF spacer; vivipary. The Rhizophoraceae comprise 15 genera and —140 species, mainly in the genera Cassipourea and Dactylo- species (Table 1). -
Original Article a Novel Phylogenetic Regionalization of Phytogeographic
1 Article type: Original Article A novel phylogenetic regionalization of phytogeographic zones of southern Africa reveals their hidden evolutionary affinities Barnabas H. Daru1,2,*, Michelle van der Bank1, Olivier Maurin1, Kowiyou Yessoufou1,3, Hanno Schaefer4, Jasper A. Slingsby5,6, and T. Jonathan Davies1,7 1African Centre for DNA Barcoding, University of Johannesburg, APK Campus, PO Box 524, Auckland Park, 2006, Johannesburg, South Africa 2Department of Plant Science, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa 3Department of Environmental Sciences, University of South Africa, Florida Campus, Florida 1710, South Africa 4Technische Universität München, Plant Biodiversity Research, Emil-Ramann Strasse 2, 85354 Freising, Germany 5Fynbos Node, South African Environmental Observation Network, Private Bag X7, 7735, Rhodes Drive, Newlands, South Africa 6Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch 7701, South Africa 7Department of Biology, McGill University, Montreal, QC H3A 0G4, Canada *Correspondence: Barnabas H. Daru, Department of Plant Science, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa. Journal of Biogeography 2 Email: [email protected] Running header: Phylogenetic regionalization of vegetation types Manuscript information: 266 words in the Abstract, 5060 words in manuscript, 78 literature citations, 22 text pages, 4 figures, 1 table, 4 supplemental figures, and 3 supplemental tables. Total word count (inclusive of abstract, text and references) = 7407. Journal of Biogeography 3 Abstract Aim: Whilst existing bioregional classification schemes often consider the compositional affinities within regional biotas, they do not typically incorporate phylogenetic information explicitly. Because phylogeny captures information on the evolutionary history of taxa, it provides a powerful tool for delineating biogeographic boundaries and for establishing relationships among them. -
ANGIOSPERMS: the Flowering Plants
AMBORELLALES Amborella trichopoda: (1) 2:6 6:58 Cabomb- MAGNOLIIDS MAGNOLIIDS An isolated species. aceae 5:13 ANGIOSPERMS: The flowering plants Evidence suggests it Water lilies, Widespread 22:200 Canellaceae Yerba is sister to all other Barclaya S & E Asia, 5:3615 mansa 5:6 Water lilies Trees Himant- 5:11 50:2500 Trees, Aromatic Nymphaeaceae N & S Am 2:75 Piperaceae Saururaceae 5-8:480 A chart of flowering plant families flowering plants. (2) Degeneri- andraceae Sweetshrub Lauraceae shrubs, lianas trees: (Sub)trop E As, N Am Cosmopolitan, Magnoliaceae Trees 1:2 Shrubs, trees Siparunaceae Am, Gtr Afr Pepper, Pepper elder, Birthwort, Pipe- (3) freshwater aceae Cinnamon, Bay, Monimiaceae Herbs NYMPHAEALES Trees and shrubs Fiji 1:2 SE Asia, Calycanthaceae Trop Am, W Afr White cinn- Betel pepper,Kava,Cubeb vine, Snake-root This chart depicts a phylogeny of all existing flowering plants. The disks represent 1:12 Austr Aromatic Avocado, Camphor, (Sub)tropics, amon 1:1 (1) & (2) aquatics with Magnolia,Champak, N Am, E As, Sassafras: Trees, Austr, S Am, Shrubs, herbs, Aristolochiaceae families of plants. Groups of related families are indicated by a hierarchy of regions. Amborell- Annual, Tulip tree NE Austr shrubs, trees, small trees and lianas Herbs, shrubs,vines Lactori- aceae tufted aquatics diverse flower structure. few lianas shrubs, parasitic SE Asia 4-7:60-90 Root 1:1 daceae Some of these groups are named. Insets below explain how to interpret the chart New (3) many characters 2: 227 129:2220 vines: (Sub)trop, Winteraceae Pantropical, parasites Widespread, Juan Fern- and describe the information associated with each family. -
Contents / Contenu
Contents / Contenu Barcoding natural history collections with special attention to type Abramson and Petrova 903 material: challenge to taxonomy, nomenclature, and species distribution patterns. Case study of Palearctic voles and lemmings DNA barcoding and the molecular clock in animals Adamowicz et al. 903 Entomological surveillance using DNA barcoding identify presence of Adeniran et al. 903 Lutzomyia verrucarum sandfly (Diptera: Psychodidae) in leishmaniasis endemic community in Mexico Barcoding of Anurans: an Indian initiative Aggarwal et al. 904 Species delimitation of the genus Latrodectus (Araneae: Theridiidae) by Aguilera et al. 904 DNA barcode and morphological evidence Bangladesh Barcode of Life (BdBOL) Ahmed 904 DNA barcoding of freshwater fishes of Bangladesh Ahmed et al. 904 DNA barcoding of freshwater fishes of Kainji Lake, Nigeria Akinwande et al. 905 Comparing mini-barcoding methodology and hair-morphology to species Alberts et al. 905 identification of fecal samples from Neotropical felids Combining molecular and chemical data for species discrimination within Alberts and Meyer 905 the South African Erythroxylaceae (coca) family For personal use only. Diversity and species distributions of Glyceriformia (Annelida, Polychaeta) Allotey et al. 905 in shelf areas off western Africa Metabarcoding plants from lake sediments: where are we and where are we Alsos et al. 906 going Building a comprehensive barcode reference library of the Norwegian Alvestad et al. 906 Echinodermata through NorBOL: an ongoing effort Genome Downloaded