Biol 317 Lecture Notes – Week 4 Summary Caryophyllids
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Full of Beans: a Study on the Alignment of Two Flowering Plants Classification Systems
Full of beans: a study on the alignment of two flowering plants classification systems Yi-Yun Cheng and Bertram Ludäscher School of Information Sciences, University of Illinois at Urbana-Champaign, USA {yiyunyc2,ludaesch}@illinois.edu Abstract. Advancements in technologies such as DNA analysis have given rise to new ways in organizing organisms in biodiversity classification systems. In this paper, we examine the feasibility of aligning two classification systems for flowering plants using a logic-based, Region Connection Calculus (RCC-5) ap- proach. The older “Cronquist system” (1981) classifies plants using their mor- phological features, while the more recent Angiosperm Phylogeny Group IV (APG IV) (2016) system classifies based on many new methods including ge- nome-level analysis. In our approach, we align pairwise concepts X and Y from two taxonomies using five basic set relations: congruence (X=Y), inclusion (X>Y), inverse inclusion (X<Y), overlap (X><Y), and disjointness (X!Y). With some of the RCC-5 relationships among the Fabaceae family (beans family) and the Sapindaceae family (maple family) uncertain, we anticipate that the merging of the two classification systems will lead to numerous merged solutions, so- called possible worlds. Our research demonstrates how logic-based alignment with ambiguities can lead to multiple merged solutions, which would not have been feasible when aligning taxonomies, classifications, or other knowledge or- ganization systems (KOS) manually. We believe that this work can introduce a novel approach for aligning KOS, where merged possible worlds can serve as a minimum viable product for engaging domain experts in the loop. Keywords: taxonomy alignment, KOS alignment, interoperability 1 Introduction With the advent of large-scale technologies and datasets, it has become increasingly difficult to organize information using a stable unitary classification scheme over time. -
Bilirubin: an Animal Pigment in the Zingiberales and Diverse Angiosperm Orders Cary L
Florida International University FIU Digital Commons FIU Electronic Theses and Dissertations University Graduate School 11-5-2010 Bilirubin: an Animal Pigment in the Zingiberales and Diverse Angiosperm Orders Cary L. Pirone Florida International University, [email protected] DOI: 10.25148/etd.FI10122201 Follow this and additional works at: https://digitalcommons.fiu.edu/etd Part of the Biochemistry Commons, and the Botany Commons Recommended Citation Pirone, Cary L., "Bilirubin: an Animal Pigment in the Zingiberales and Diverse Angiosperm Orders" (2010). FIU Electronic Theses and Dissertations. 336. https://digitalcommons.fiu.edu/etd/336 This work is brought to you for free and open access by the University Graduate School at FIU Digital Commons. It has been accepted for inclusion in FIU Electronic Theses and Dissertations by an authorized administrator of FIU Digital Commons. For more information, please contact [email protected]. FLORIDA INTERNATIONAL UNIVERSITY Miami, Florida BILIRUBIN: AN ANIMAL PIGMENT IN THE ZINGIBERALES AND DIVERSE ANGIOSPERM ORDERS A dissertation submitted in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY in BIOLOGY by Cary Lunsford Pirone 2010 To: Dean Kenneth G. Furton College of Arts and Sciences This dissertation, written by Cary Lunsford Pirone, and entitled Bilirubin: An Animal Pigment in the Zingiberales and Diverse Angiosperm Orders, having been approved in respect to style and intellectual content, is referred to you for judgment. We have read this dissertation and recommend that it be approved. ______________________________________ Bradley C. Bennett ______________________________________ Timothy M. Collins ______________________________________ Maureen A. Donnelly ______________________________________ John. T. Landrum ______________________________________ J. Martin Quirke ______________________________________ David W. Lee, Major Professor Date of Defense: November 5, 2010 The dissertation of Cary Lunsford Pirone is approved. -
ABSTRACTS 117 Systematics Section, BSA / ASPT / IOPB
Systematics Section, BSA / ASPT / IOPB 466 HARDY, CHRISTOPHER R.1,2*, JERROLD I DAVIS1, breeding system. This effectively reproductively isolates the species. ROBERT B. FADEN3, AND DENNIS W. STEVENSON1,2 Previous studies have provided extensive genetic, phylogenetic and 1Bailey Hortorium, Cornell University, Ithaca, NY 14853; 2New York natural selection data which allow for a rare opportunity to now Botanical Garden, Bronx, NY 10458; 3Dept. of Botany, National study and interpret ontogenetic changes as sources of evolutionary Museum of Natural History, Smithsonian Institution, Washington, novelties in floral form. Three populations of M. cardinalis and four DC 20560 populations of M. lewisii (representing both described races) were studied from initiation of floral apex to anthesis using SEM and light Phylogenetics of Cochliostema, Geogenanthus, and microscopy. Allometric analyses were conducted on data derived an undescribed genus (Commelinaceae) using from floral organs. Sympatric populations of the species from morphology and DNA sequence data from 26S, 5S- Yosemite National Park were compared. Calyces of M. lewisii initi- NTS, rbcL, and trnL-F loci ate later than those of M. cardinalis relative to the inner whorls, and sepals are taller and more acute. Relative times of initiation of phylogenetic study was conducted on a group of three small petals, sepals and pistil are similar in both species. Petal shapes dif- genera of neotropical Commelinaceae that exhibit a variety fer between species throughout development. Corolla aperture of unusual floral morphologies and habits. Morphological A shape becomes dorso-ventrally narrow during development of M. characters and DNA sequence data from plastid (rbcL, trnL-F) and lewisii, and laterally narrow in M. -
583–584 Angiosperms 583 *Eudicots and Ceratophyllales
583 583 > 583–584 Angiosperms These schedules are extensively revised, having been prepared with little reference to earlier editions. 583 *Eudicots and Ceratophyllales Subdivisions are added for eudicots and Ceratophyllales together, for eudicots alone Class here angiosperms (flowering plants), core eudicots For monocots, basal angiosperms, Chloranthales, magnoliids, see 584 See Manual at 583–585 vs. 600; also at 583–584; also at 583 vs. 582.13 .176 98 Mangrove swamp ecology Number built according to instructions under 583–588 Class here comprehensive works on mangroves For mangroves of a specific order or family, see the order or family, e.g., mangroves of family Combretaceae 583.73 .2 *Ceratophyllales Class here Ceratophyllaceae Class here hornworts > 583.3–583.9 Eudicots Class comprehensive works in 583 .3 *Ranunculales, Sabiaceae, Proteales, Trochodendrales, Buxales .34 *Ranunculales Including Berberidaceae, Eupteleaceae, Menispermaceae, Ranunculaceae Including aconites, anemones, barberries, buttercups, Christmas roses, clematises, columbines, delphiniums, hellebores, larkspurs, lesser celandine, mandrake, mayapple, mayflower, monkshoods, moonseeds, wolfsbanes For Fumariaceae, Papaveraceae, Pteridophyllaceae, see 583.35 See also 583.9593 for mandrakes of family Solanaceae .35 *Fumariaceae, Papaveraceae, Pteridophyllaceae Including bleeding hearts, bloodroot, celandines, Dutchman’s breeches, fumitories, poppies See also 583.34 for lesser celandine .37 *Sabiaceae * *Add as instructed under 583–588 1 583 Dewey Decimal Classification -
Field Identification of the 50 Most Common Plant Families in Temperate Regions
Field identification of the 50 most common plant families in temperate regions (including agricultural, horticultural, and wild species) by Lena Struwe [email protected] © 2016, All rights reserved. Note: Listed characteristics are the most common characteristics; there might be exceptions in rare or tropical species. This compendium is available for free download without cost for non- commercial uses at http://www.rci.rutgers.edu/~struwe/. The author welcomes updates and corrections. 1 Overall phylogeny – living land plants Bryophytes Mosses, liverworts, hornworts Lycophytes Clubmosses, etc. Ferns and Fern Allies Ferns, horsetails, moonworts, etc. Gymnosperms Conifers, pines, cycads and cedars, etc. Magnoliids Monocots Fabids Ranunculales Rosids Malvids Caryophyllales Ericales Lamiids The treatment for flowering plants follows the APG IV (2016) Campanulids classification. Not all branches are shown. © Lena Struwe 2016, All rights reserved. 2 Included families (alphabetical list): Amaranthaceae Geraniaceae Amaryllidaceae Iridaceae Anacardiaceae Juglandaceae Apiaceae Juncaceae Apocynaceae Lamiaceae Araceae Lauraceae Araliaceae Liliaceae Asphodelaceae Magnoliaceae Asteraceae Malvaceae Betulaceae Moraceae Boraginaceae Myrtaceae Brassicaceae Oleaceae Bromeliaceae Orchidaceae Cactaceae Orobanchaceae Campanulaceae Pinaceae Caprifoliaceae Plantaginaceae Caryophyllaceae Poaceae Convolvulaceae Polygonaceae Cucurbitaceae Ranunculaceae Cupressaceae Rosaceae Cyperaceae Rubiaceae Equisetaceae Rutaceae Ericaceae Salicaceae Euphorbiaceae Scrophulariaceae -
Phylogenetic Signal of the Nuclear Gene Ga20ox1 in Seed Plants: the Relationship Between Monocots and Eudicots
American Research Journal of Biosciences ISSN-2379-7959 Volume 3, Issue 1, 8 Pages Research Article Open Access Phylogenetic Signal of the Nuclear Gene GA20ox1 in Seed Plants: The Relationship Between Monocots and Eudicots Lilian Oliveira Machado, Suziane Alves Barcelos, Deise Sarzi Shröder, *Valdir Marcos Stefenon *Universidade Federal do Pampa - UNIPAMPA,[email protected] Nucleus of Genomics and Molecular Ecology, Interdisciplinary Center of Biotechnological Research, Av. Antonio Trilha 1847, 97300-000, São Gabriel, RS, Brazil Abstract:Received Date: May 17, 2017 Accepted Date: May 31, 2017 Published Date: June 02, 2017 This study investigated the phylogenetic signal of the nuclear gene GA20ox1 in seed plants focusing in the relationship between Monocots and Eudicots. Sequences were obtained from GenBank and analyzed using the maximum likelihood and the maximum parsimony approaches. A maximum likelihood tree was built using sequences of the rbcL plastid gene in order to enable comparison of the results. The GA20ox1 gene presents neutral evolution, levels of homoplasy equivalent to that observed in chloroplast sequences and generated well-resolved phylogenetic relationships. The relationship between Mocots and Eudicots based on the GA20ox1 gene was clear resolved, revealing the evolution of both groups. All these characteristics taken together make the GA20ox1 gene a promissory marker to corroborate as well as to complement and resolve phylogeneticKeywords: relationships among species within one to several genera. IntroductionNuclear gene, flowering plants, systematics, gibberellin, phylogeny The large amount of DNA sequences generated in the last decades for an increasing number of different species has enabled to refine the phylogenetic relationships among flowering plants and enabled the generation of better-resolved classifications for this group (APG 2009, Babineau et al. -
Whole-Genome Microsynteny-Based Phylogeny of Angiosperms Tao
Whole-genome microsynteny-based phylogeny of angiosperms Tao Zhao ( [email protected] ) Ghent University Jiayu Xue Institute of Botany, Jiangsu Province and Chinese Academy of Sciences Arthur Zwaenepoel Ghent University Shu-min Kao Ghent University Zhen Li Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium. M. Schranz Wageningen University https://orcid.org/0000-0001-6777-6565 Yves Van de Peer Ghent University https://orcid.org/0000-0003-4327-3730 Article Keywords: Synteny network, gene order, matrix representation, phylogeny, angiosperms, maximum- likelihood Posted Date: August 17th, 2020 DOI: https://doi.org/10.21203/rs.3.rs-51378/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License 1 Whole-genome microsynteny-based phylogeny of angiosperms 2 3 Tao Zhao1,2,3, Jia-Yu Xue4, Arthur Zwaenepoel1,2, Shu-Min Kao1,2, Zhen Li1,2, M. Eric 4 Schranz5, Yves Van de Peer1,2,6,7 5 6 1Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 7 Belgium. 8 2Center for Plant Systems Biology, VIB, Ghent, Belgium. 9 3State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory 10 of Apple, College of Horticulture, Northwest A & F University, Yangling, 712100, 11 China. 12 4Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 13 China. 14 5Biosystematics Group, Wageningen University and Research, Wageningen, The 15 Netherlands. 16 6Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics 17 and Microbiology, University of Pretoria, Pretoria, South Africa. 18 7College of Horticulture, Nanjing Agricultural University, Nanjing, China. -
From Cacti to Carnivores: Improved Phylotranscriptomic Sampling And
Article Type: Special Issue Article RESEARCH ARTICLE INVITED SPECIAL ARTICLE For the Special Issue: Using and Navigating the Plant Tree of Life Short Title: Walker et al.—Phylotranscriptomic analysis of Caryophyllales From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales Joseph F. Walker1,13, Ya Yang2, Tao Feng3, Alfonso Timoneda3, Jessica Mikenas4,5, Vera Hutchison4, Caroline Edwards4, Ning Wang1, Sonia Ahluwalia1, Julia Olivieri4,6, Nathanael Walker-Hale7, Lucas C. Majure8, Raúl Puente8, Gudrun Kadereit9,10, Maximilian Lauterbach9,10, Urs Eggli11, Hilda Flores-Olvera12, Helga Ochoterena12, Samuel F. Brockington3, Michael J. Moore,4 and Stephen A. Smith1,13 Manuscript received 13 October 2017; revision accepted 4 January 2018. 1 Department of Ecology & Evolutionary Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI 48109-1048 USA 2 Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, 1445 Gortner Avenue, St. Paul, MN 55108 USA 3 Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK 4 Department of Biology, Oberlin College, Science Center K111, 119 Woodland Street, Oberlin, OH 44074-1097 USA 5 Current address: USGS Canyonlands Research Station, Southwest Biological Science Center, 2290 S West Resource Blvd, Moab, UT 84532 USA 6 Institute of Computational and Mathematical Engineering (ICME), Stanford University, 475 Author Manuscript Via Ortega, Suite B060, Stanford, CA, 94305-4042 USA This is the author manuscript accepted for publication and has undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record. -
Caryophyllales) J
Plant Biology ISSN 1435-8603 RESEARCH PAPER Crassulacean acid metabolism in the Basellaceae (Caryophyllales) J. A. M. Holtum1,2 , L. P. Hancock3, E. J. Edwards3,4 & K. Winter2 1 College of Science and Engineering, James Cook University, Townsville, Qld, Australia 2 Smithsonian Tropical Research Institute, Panama City, Panama 3 Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, USA 4 Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA Keywords ABSTRACT Anredera baselloides;C4 photosynthesis; Caryophyllales; facultative CAM; portullugo. • C4 and crassulacean acid metabolism (CAM) have evolved in the order Caryophyllales many times but neither C4 nor CAM have been recorded for the Basellaceae, a small Correspondence family in the CAM-rich sub-order Portulacineae. J. A. M. Holtum, College of Science and • 24 h gas exchange and day–night changes in titratable acidity were measured in leaves Engineering, James Cook University, of Anredera baselloides exposed to wet–dry–wet cycles. Townsville, Qld 4811, Australia. • While net CO2 uptake was restricted to the light period in well-watered plants, net E-mail: [email protected] CO2 fixation in the dark, accompanied by significant nocturnal increases in leaf acid- ity, developed in droughted plants. Plants reverted to solely C3 photosynthesis upon Editor rewatering. R. Leegood • The reversible induction of nocturnal net CO2 uptake by drought stress indicates that this species is able to exhibit CAM in a facultative manner. This is the first report of Received: 19 October 2017; Accepted: 22 CAM in a member of the Basellaceae. January 2018 doi:10.1111/plb.12698 close and the carbon is converted to carbohydrate (Holtum & INTRODUCTION Osmond 1981; Holtum et al. -
Seney National Wildlife Refuge • Common Name(Order
Seney National Wildlife Refuge Flora • Common Name(Order Family Genus species) Monocotyledons • Arum, Green Arrow (Arales Araceae Peltranda virginica) • Arethusa (Orchidales Orchidaceae Arethusa bulbosa) • Arrowhead, Grassy (Alismatales Alismataceae Sagittaria graminea) • Bentgrass, Redtop (Poales Poaceae/Graminae Agrostis gigantea) • Bluegrass, Fowl (Poales Poaceae/Graminae Poa palustris) • Bluegrass, Kentucky (Poales Poaceae/Graminae Poa pratensis) • Brome, Smooth (Poales Poaceae/Graminae Bromus inermis) • Bulrush, Hardstem (Cyperales Cyperaceae Scirpus acutus) • Bulrush, Three-square (Cyperales Cyperaceae Scirpus americanus) • Bur-reed, Common (Typhales Sparganiaceae Sparganium eurycarpum) • Bur-reed, Eastern (Typhales Sparganiaceae Sparganium americanum) • Bur-reed, Floating (Typhales Sparganiaceae Sparganium angustifolium) • Bur-reed, Floating-leaf (Typhales Sparganiaceae Sparganium fluctuans) • Bur-reed, Least (Typhales Sparganiaceae Sparganium minimum) • Canarygrass, Reed (Poales Poaceae/Graminae Phalaris arundinaceae) • Cattail, Common (Typhales Typaceae Typha latifolia) • Cattail, Common Hybrid (Typhales Typaceae Typha x glauca) • Cattail, Narrow-leaved (Typhales Typaceae Typha angustifolia) • Celery, Wild (Hydrocharitales Hydrocharitaceae Vallisneria americana) • Chives (Liliales Liliaceae Allium schoenoprasum) • Coral-root, Spotted (Orchidales Orchidaceae Corallorhiza maculata) • Cordgrass (Poales Poaceae/Graminae Spartina pectinata) • Cottongrass, Tall (Cyperales Cyperaceae Eriophorum angustifolium) • Cottongrass, Tawny (Cyperales -
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. -
Molecular Systematics of the Genus Uvularia and Selected Liliales Based Upon Matk and Rbcl Gene Sequence Data
Plant Species Biol, 13 : 129-146, 1998 PLANT SPECIES BIOLOGY > by the Society for the Study of Species Biology Molecular Systematics of the Genus Uvularia and Selected Liliales Based upon matK and rbcL Gene Sequence Data KAZUHIKO HAYASHI1' 2), SEIJI YOSHIDA3", HIDETOSHI KATO41, FREDERICK H. UTECH51, DENNIS F. WHIGHAM61 and SHOICHI KAWANO11 1) Department of Botany, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan 21 Biology Laboratory, Osaka Gakuin University, Suita, Osaka 564-8511, Japan 31 Taishi Senior High School, Taishi, Ibo, Hyogo 671-1532, Japan 41 Makino Herbarium, Department of Biology, Faculty of Science, Tokyo Meteropolitan University, Hachioji, Tokyo 192-0397, Japan 5) Carnegie Museum of Natural History, Pittsburgh, PA 15213, U.S.A. 61 Smithsonian Environmental Research Center, Edgewater, MD 21037, U.S.A. Abstract To elucidate the affinity and phylogeny of the endemic North American genus Uvularia, two chloroplast genes, matK and rbcL, were sequenced for all five species of the genus {Uvularia floridana, U. grandifolia, U. per- foliata, U. puberula, and U. sessilifolia) and four selected members of the Liliales (Erythronium japonicum, Disporum sessile, Medeola virginiana, and Clintonia borealis). Sequence data of both matK and rbcL genes support an Uvularia which consist of two clades, section Oakesiella and section Uvularia. Though sessile-leaved and associated with sec- tion Oakesiella, U. puberula exhibits several intermediate characteristics between the sections. However, the overall molecular results correspond to an earlier sub-grouping based upon gross morphology, karyology and ecological life history traits. These two cpDNA genes, notably matK tree, proved to be informative in reaffirming relationships with- in Uvularia.