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Phylogenetic Models Linking Speciation and Extinction to Chromosome and Mating System Evolution
Phylogenetic Models Linking Speciation and Extinction to Chromosome and Mating System Evolution by William Allen Freyman A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Integrative Biology and the Designated Emphasis in Computational and Genomic Biology in the Graduate Division of the University of California, Berkeley Committee in charge: Dr. Bruce G. Baldwin, Chair Dr. John P. Huelsenbeck Dr. Brent D. Mishler Dr. Kipling W. Will Fall 2017 Phylogenetic Models Linking Speciation and Extinction to Chromosome and Mating System Evolution Copyright 2017 by William Allen Freyman Abstract Phylogenetic Models Linking Speciation and Extinction to Chromosome and Mating System Evolution by William Allen Freyman Doctor of Philosophy in Integrative Biology and the Designated Emphasis in Computational and Genomic Biology University of California, Berkeley Dr. Bruce G. Baldwin, Chair Key evolutionary transitions have shaped the tree of life by driving the processes of spe- ciation and extinction. This dissertation aims to advance statistical and computational ap- proaches that model the timing and nature of these transitions over evolutionary trees. These methodological developments in phylogenetic comparative biology enable formal, model- based, statistical examinations of the macroevolutionary consequences of trait evolution. Chapter 1 presents computational tools for data mining the large-scale molecular sequence datasets needed for comparative phylogenetic analyses. I describe a novel metric, the miss- ing sequence decisiveness score (MSDS), which assesses the phylogenetic decisiveness of a matrix given the pattern of missing sequence data. In Chapter 2, I introduce a class of phylogenetic models of chromosome number evolution that accommodate both anagenetic and cladogenetic change. -
Proceedings of the Biological Society of Washington
PROC. BIOL. SOC. WASH. 103(1), 1990, pp. 248-253 SIX NEW COMBINATIONS IN BACCHAROIDES MOENCH AND CYANTHILLIUM "SUJME (VERNONIEAE: ASTERACEAE) Harold Robinson Abstract.— ThvQQ species, Vernonia adoensis Schultz-Bip. ex Walp., V. gui- neensis Benth., and V. lasiopus O. HofFm. in Engl., are transferred to the genus Baccharoides Moench, and three species, Conyza cinerea L., C. patula Ait., and Herderia stellulifera Benth. are transferred to the genus Cyanthillium Blume. The present paper provides six new com- tinct from the Western Hemisphere mem- binations of Old World Vemonieae that are bers of that genus. Although generic limits known to belong to the genera Baccharoides were not discussed by Jones, his study placed Moench and Cyanthillium Blume. The ap- the Old World Vernonia in a group on the plicability of these generic names to these opposite side the basic division in the genus species groups was first noted by the author from typical Vernonia in the eastern United almost ten years ago (Robinson et al. 1 980), States. Subsequent studies by Jones (1979b, and it was anticipated that other workers 1981) showed that certain pollen types also more familiar with the paleotropical mem- were restricted to Old World members of bers of the Vernonieae would provide the Vernonia s.l., types that are shared by some necessary combinations. A recent study of Old World members of the tribe tradition- eastern African members of the tribe by Jef- ally placed in other genera. The characters frey (1988) also cites these generic names as noted by Jones have been treated by the synonyms under his Vernonia Group 2 present author as evidence of a basic divi- subgroup C and Vernonia Group 4, al- sion in the Vernonieae between groups that though he retains the broad concept of Ver- have included many genera in each hemi- nonia. -
Poaceae: Bambusoideae) Christopher Dean Tyrrell Iowa State University
Iowa State University Capstones, Theses and Retrospective Theses and Dissertations Dissertations 2008 Systematics of the neotropical woody bamboo genus Rhipidocladum (Poaceae: Bambusoideae) Christopher Dean Tyrrell Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/rtd Part of the Botany Commons Recommended Citation Tyrrell, Christopher Dean, "Systematics of the neotropical woody bamboo genus Rhipidocladum (Poaceae: Bambusoideae)" (2008). Retrospective Theses and Dissertations. 15419. https://lib.dr.iastate.edu/rtd/15419 This Thesis is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Retrospective Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Systematics of the neotropical woody bamboo genus Rhipidocladum (Poaceae: Bambusoideae) by Christopher Dean Tyrrell A thesis submitted to the graduate faculty in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE Major: Ecology and Evolutionary Biology Program of Study Committee: Lynn G. Clark, Major Professor Dennis V. Lavrov Robert S. Wallace Iowa State University Ames, Iowa 2008 Copyright © Christopher Dean Tyrrell, 2008. All rights reserved. 1457571 1457571 2008 ii In memory of Thomas D. Tyrrell Festum Asinorum iii TABLE OF CONTENTS ABSTRACT iv CHAPTER 1. GENERAL INTRODUCTION 1 Background and Significance 1 Research Objectives 5 Thesis Organization 6 Literature Cited 6 CHAPTER 2. PHYLOGENY OF THE BAMBOO SUBTRIBE 9 ARTHROSTYLIDIINAE WITH EMPHASIS ON RHIPIDOCLADUM Abstract 9 Introduction 10 Methods and Materials 13 Results 19 Discussion 25 Taxonomic Treatment 26 Literature Cited 31 CHAPTER 3. -
CATALOGUE of the GRASSES of CUBA by A. S. Hitchcock
CATALOGUE OF THE GRASSES OF CUBA By A. S. Hitchcock. INTRODUCTION. The following list of Cuban grasses is based primarily upon the collections at the Estaci6n Central Agron6mica de Cuba, situated at Santiago de las Vegas, a suburb of Habana. The herbarium includes the collections made by the members of the staff, particularly Mr. C. F. Baker, formerly head of the department of botany, and also the Sauvalle Herbarium deposited by the Habana Academy of Sciences, These specimens were examined by the writer during a short stay upon the island in the spring of 1906, and were later kindly loaned by the station authorities for a more critical study at Washington. The Sauvalle Herbarium contains a fairly complete set of the grasses col- lected by Charles Wright, the most important collection thus far obtained from Cuba. In addition to the collections at the Cuba Experiment Station, the National Herbarium furnished important material for study, including collections made by A. H. Curtiss, W. Palmer and J. H. Riley, A. Taylor (from the Isle of Pines), S. M. Tracy, Brother Leon (De la Salle College, Habana), and the writer. The earlier collections of Wright were sent to Grisebach for study. These were reported upon by Grisebach in his work entitled "Cata- logus Plant arum Cubensium," published in 1866, though preliminary reports appeared earlier in the two parts of Plantae Wrightianae. * During the spring of 1907 I had the opportunity of examining the grasses in the herbarium of Grisebach in Gottingen.6 In the present article I have, with few exceptions, accounted for the grasses listed by Grisebach in his catalogue of Cuban plants, and have appended a list of these with references to the pages in the body of this article upon which the species are considered. -
Profile of Nancy A. Moran ‘‘ Always Liked Insects,’’ Says Nancy A
Profile of Nancy A. Moran ‘‘ always liked insects,’’ says Nancy A. bination,’’ she says. ‘‘Why have males Moran, Regent’s Professor of Ecol- and females, and not just reproduce by ogy and Evolutionary Biology at parthenogenesis and have all females?’’ the University of Arizona (Tuc- One of her advisors, William Hamilton, son,I AZ). ‘‘As a little kid, I was known had proposed that sexual reproduction as the girl who collected insects and had was important to create genetic diversity them in jars and things like that.’’ Years to stay one step ahead of coevolving later, this youthful bug collector has be- natural enemies, especially parasites and come a renowned entomologist whose pathogens. ‘‘I became interested in that work crosses over into multiple disci- idea and began looking at it in aphids,’’ plines, including microbiology, ecology, she says, ‘‘which are very useful since and molecular evolution. Moran’s re- they are parthogenetic for part of their search primarily focuses on the ecology life cycle’’ (3). and evolution of aphids and, since 1990, After receiving her Ph.D. in zoology has especially focused on the interaction in 1982, Moran spent the next several and coevolution of these small insects years studying evolutionary ecology in and the symbiotic bacteria that live in- aphids. ‘‘It was less than completely side of them. satisfying in a lot of ways,’’ she admits. ‘‘The whole evolution of insects has ‘‘At that time you were so far from the been in tandem with these bacteria,’’ actual genetic basis of the variation you Moran says. ‘‘We would not see insects were looking at, so you had no handle feeding on plant sap if it weren’t for as to which genes were actually causing symbiosis.’’ Elected to the National Nancy A. -
Poaceae: Bambusoideae) Lynn G
Aliso: A Journal of Systematic and Evolutionary Botany Volume 23 | Issue 1 Article 26 2007 Phylogenetic Relationships Among the One- Flowered, Determinate Genera of Bambuseae (Poaceae: Bambusoideae) Lynn G. Clark Iowa State University, Ames Soejatmi Dransfield Royal Botanic Gardens, Kew, UK Jimmy Triplett Iowa State University, Ames J. Gabriel Sánchez-Ken Iowa State University, Ames Follow this and additional works at: http://scholarship.claremont.edu/aliso Part of the Botany Commons, and the Ecology and Evolutionary Biology Commons Recommended Citation Clark, Lynn G.; Dransfield, Soejatmi; Triplett, Jimmy; and Sánchez-Ken, J. Gabriel (2007) "Phylogenetic Relationships Among the One-Flowered, Determinate Genera of Bambuseae (Poaceae: Bambusoideae)," Aliso: A Journal of Systematic and Evolutionary Botany: Vol. 23: Iss. 1, Article 26. Available at: http://scholarship.claremont.edu/aliso/vol23/iss1/26 Aliso 23, pp. 315–332 ᭧ 2007, Rancho Santa Ana Botanic Garden PHYLOGENETIC RELATIONSHIPS AMONG THE ONE-FLOWERED, DETERMINATE GENERA OF BAMBUSEAE (POACEAE: BAMBUSOIDEAE) LYNN G. CLARK,1,3 SOEJATMI DRANSFIELD,2 JIMMY TRIPLETT,1 AND J. GABRIEL SA´ NCHEZ-KEN1,4 1Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa 50011-1020, USA; 2Herbarium, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK 3Corresponding author ([email protected]) ABSTRACT Bambuseae (woody bamboos), one of two tribes recognized within Bambusoideae (true bamboos), comprise over 90% of the diversity of the subfamily, yet monophyly of -
150 Years of Research at the United States Department of Agriculture
United States Department of Agriculture Agricultural Research Service 150 Years of Research at June 2013 the United States Department of Agriculture: Plant Introduction and Breeding I Cover photo: The stately building that once housed the U.S. Department of Agriculture in Washington, D.C., ca. 1890. (This photo is preserved in the USDA History Collection, Special Collections, National Agricultural Library.) II United States Department of Agriculture Agricultural Research Service 150 Years of Research at June 2013 the United States Department of Agriculture: Plant Introduction and Breeding R.J. Griesbach Griesbach is Deputy Assistant Administrator, Office of Technology Transfer, USDA, Agricultural Research Service, Beltsville, MD. i Abstract Griesbach, R.J. 2013. 150 Years of Research at the While supplies last, single copies of this publication United States Department of Agriculture: can be obtained at no cost from Robert J. Griesbach, Plant Introduction and Breeding. U.S. Department USDA-ARS, Office of Technology Transfer, 5601 of Agriculture, Agricultural Research Service, Sunnyside Avenue, Room 4-1159, Beltsville, MD Washington, DC. 20705; or by email at [email protected]. The U.S. Department of Agriculture celebrated its Copies of this publication may be purchased in various 150th anniversary in 2012. One of the primary formats (microfiche, photocopy, CD, print on demand) functions of the USDA when it was established in 1862 from the National Technical Information Service, 5285 was “to procure, propagate, and distribute among the people new Port Royal Road, Springfield, VA 22161, (800) 553- and valuable seeds and plants.” The U.S. Government first 6847, www.ntis.gov. became involved in new plant introductions in 1825 when President John Quincy Adams directed U.S. -
Apbvariation in the Functional Properties of Barringtonia Asiatica Extract on Selected Pathogens
Journal of Pharmacology & Clinical Research ISSN: 2473-5574 Research Article J of Pharmacol & Clin Res Volume 6 Issue 3 - September 2018 Copyright © All rights are reserved by Isaac John Umaru DOI: 10.19080/JPCR.2018.06.555686 APBVariation in the Functional Properties of Barringtonia Asiatica Extract on Selected Pathogens Isaac John Umaru1,2*, Fasihuddin ABadruddin1, Hauwa AUmaru3, Ezeonu Chukwuma Stephen2 and Ojochenemi Yakubu 1Faculty of Resource Science and Technology, University of Malaysia Sarawak, Kuching, Kota-Samarahan, Malaysia 2Department of Biochemistry, Federal University Wukari Taraba State, Nigeria 3Department of biochemistry, ModiboAdama University of Technology Yola Adamawa state, Nigeria Submission: August 24, 2018; Published: September 10, 2018 *Corresponding author: Isaac John Umaru,Faculty of Resource Science and Technology, University of Malaysia Sarawak, Kuching, Kota-Samarahan Malaysia,Department of Biochemistry Federal university Wukari Taraba State, Email: Abstract Objective: on selected pathogens. The aim of this study is to look at the influence of different concentration from different solvent extract of Barringtonia asiatica Material and Methods: Barringtonia asiatica extracts were evaluated for their functional potential antimicrobial properties. The leaves of Antimicrobial activity against Escherichia coli, salmonella typhi, staphylococcus aureus and Klebsielia pneumonia, were determined by a disc the plant were extracted with n-hexane, dichloromethane, ethyl acetate, chloroform and methanol and then vaporized -
Ornamental Garden Plants of the Guianas Pt. 2
Surinam (Pulle, 1906). 8. Gliricidia Kunth & Endlicher Unarmed, deciduous trees and shrubs. Leaves alternate, petiolate, odd-pinnate, 1- pinnate. Inflorescence an axillary, many-flowered raceme. Flowers papilionaceous; sepals united in a cupuliform, weakly 5-toothed tube; standard petal reflexed; keel incurved, the petals united. Stamens 10; 9 united by the filaments in a tube, 1 free. Fruit dehiscent, flat, narrow; seeds numerous. 1. Gliricidia sepium (Jacquin) Kunth ex Grisebach, Abhandlungen der Akademie der Wissenschaften, Gottingen 7: 52 (1857). MADRE DE CACAO (Surinam); ACACIA DES ANTILLES (French Guiana). Tree to 9 m; branches hairy when young; poisonous. Leaves with 4-8 pairs of leaflets; leaflets elliptical, acuminate, often dark-spotted or -blotched beneath, to 7 x 3 (-4) cm. Inflorescence to 15 cm. Petals pale purplish-pink, c.1.2 cm; standard petal marked with yellow from middle to base. Fruit narrowly oblong, somewhat woody, to 15 x 1.2 cm; seeds up to 11 per fruit. Range: Mexico to South America. Grown as an ornamental in the Botanic Gardens, Georgetown, Guyana (Index Seminum, 1982) and in French Guiana (de Granville, 1985). Grown as a shade tree in Surinam (Ostendorf, 1962). In tropical America this species is often interplanted with coffee and cacao trees to shade them; it is recommended for intensified utilization as a fuelwood for the humid tropics (National Academy of Sciences, 1980; Little, 1983). 9. Pterocarpus Jacquin Unarmed, nearly evergreen trees, sometimes lianas. Leaves alternate, petiolate, odd- pinnate, 1-pinnate; leaflets alternate. Inflorescence an axillary or terminal panicle or raceme. Flowers papilionaceous; sepals united in an unequally 5-toothed tube; standard and wing petals crisped (wavy); keel petals free or nearly so. -
A Glossary of Botanic Terms, with Their Derivation and Accent
A GLOSSARY OF BOTANIC TERMS WITH THEIR DERIVATION AND ACCENT BY BENJAMIN DAYDON JACKSON LONDON DUCKWORTH & CO. PHILADELPHIA: J. B. LIPPINCOTT COMPANY 1900 CONTENTS Pages PREFACE v-xi Plan of the Work ... xii GLOSSARY .... 1-294 Additions during Printing . 295-319 APPENDIX— A. Signs and Abbreviations ..... 322 B. The Pronunciation of Latin and Latinized Words . 322 C. The Use of the Terms "Right" and "Left" . 323 D. Bibliography . .... 324-326 ERRATA ... ... 327 " Every other authout may aspire to praise, the lexicographer can only hope to escape reproach." De Samuel Johnson. PEEFACE Nearly thirty-nine years ago Dr M. C. Cooke published his " Manual,'' which reached a second edition nine years afterwards. Since then no botanic dictionary has been published in Britain, while during the period which has passed since then botany has undergone a momentous change. While systematic botany has been actively prosecuted, the other departments of morphology, physiology and minute anatomy have been energetically pursued by the help of improved appliances and methods of investigation. One result has been a large increase of technical terms, which are only partially accounted for in the various text-books. The time seemed therefore ripe for a new Glossary which should include these terms, and, encouraged by the help of many botanic friends, I have drawn up the present volume. After the work had been partly written, and announced for publication, Mr Crozier's " Dictionary " first came under my notice. I have consequently compared it with my manuscript, and inserted many words which had not come within my knowledge, or had been rejected by me, as will be seen by the acknowledgment in each case. -
T/Iieuicanauseum
>t/iieuicanAuseum PUBLISHED BY THE AMERICAN MUSEUM OF NATURAL HISTORY CENTRAL PARK WEST AT 79TH STREET, NEW YORK 24, N.Y. NUMBER 1723 APRIL 29, 1955 Studies of Peruvian Birds. No. 66 The Swallows (Hirundinidae) BY JOHN T. ZIMMER I am again indebted to Dr. William H. Phelps of Caracas, Mr. James Bond and Mr. Rodolphe de Schauensee of the Academy of Natural Sciences of Philadelphia, Mr. James Greenway of the Museum of Comparative Zoology, Cambridge, and to Dr. Allan R. Phillips of Tucson, Arizona, for the loan of critical material used in the following studies. Names of colors are capitalized when direct comparison has been made with Ridgway's "Color standards and color nomenclature." Progne chalybea chalybea (Gmelin) [Hirundo] chalybea GMELIN, 1789, Systema naturae, vol. 1, pt. 2, p. 1026- based on Hirundo cayanensis Brisson, Ornithologie, vol. 2, p. 495, pl. 46, fig. 1, and Daubenton, Planches enlumin6es, pl. 545, fig. 2; Cayenne. Progne leucogaster BAIRD, 1865 (May), Smithsonian Misc. Coll., no. 181, p. 280-various localities in Mexico, Guatemala, [El] Salvador, Costa Rica, Pa- namA, and Colombia; type in U. S. Natl. Mus. from Cajab6n, Guatemala. Puerto Indiana, 3 c, 2 9 ; Morropon, 4 c, 2 9. Compared with 118 additional skins from central Brazil north to the three Guianas and Trinidad, to the eastward, and Mexico and Texas, to the westward, with all intermediate countries except British Hon- duras represented in the series. A random sample of 15 males and 11 females from throughout the range shows the males to have the wing 124-138 mm. (average, 131.7); tail, 58-66 (62.5); females, wing, 121- 132 (130); tail, 54-65 (61). -
Recommendation of Native Species for the Reforestation of Degraded Land Using Live Staking in Antioquia and Caldas’ Departments (Colombia)
UNIVERSITÀ DEGLI STUDI DI PADOVA Department of Land, Environment Agriculture and Forestry Second Cycle Degree (MSc) in Forest Science Recommendation of native species for the reforestation of degraded land using live staking in Antioquia and Caldas’ Departments (Colombia) Supervisor Prof. Lorenzo Marini Co-supervisor Prof. Jaime Polanía Vorenberg Submitted by Alicia Pardo Moy Student N. 1218558 2019/2020 Summary Although Colombia is one of the countries with the greatest biodiversity in the world, it has many degraded areas due to agricultural and mining practices that have been carried out in recent decades. The high Andean forests are especially vulnerable to this type of soil erosion. The corporate purpose of ‘Reforestadora El Guásimo S.A.S.’ is to use wood from its plantations, but it also follows the parameters of the Forest Stewardship Council (FSC). For this reason, it carries out reforestation activities and programs and, very particularly, it is interested in carrying out ecological restoration processes in some critical sites. The study area is located between 2000 and 2750 masl and is considered a low Andean humid forest (bmh-MB). The average annual precipitation rate is 2057 mm and the average temperature is around 11 ºC. The soil has a sandy loam texture with low pH, which limits the amount of nutrients it can absorb. FAO (2014) suggests that around 10 genera are enough for a proper restoration. After a bibliographic revision, the genera chosen were Alchornea, Billia, Ficus, Inga, Meriania, Miconia, Ocotea, Protium, Prunus, Psidium, Symplocos, Tibouchina, and Weinmannia. Two inventories from 2013 and 2019, helped to determine different biodiversity indexes to check the survival of different species and to suggest the adequate characteristics of the individuals for a successful vegetative stakes reforestation.