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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. -
The Genus Hauya (Onagraceae) Philip A
Aliso: A Journal of Systematic and Evolutionary Botany Volume 4 | Issue 3 Article 6 1960 The Genus Hauya (Onagraceae) Philip A. Munz Follow this and additional works at: http://scholarship.claremont.edu/aliso Part of the Botany Commons Recommended Citation Munz, Philip A. (1960) "The Genus Hauya (Onagraceae)," Aliso: A Journal of Systematic and Evolutionary Botany: Vol. 4: Iss. 3, Article 6. Available at: http://scholarship.claremont.edu/aliso/vol4/iss3/6 ALISO VoL. 4, No.3, pp. 492-499 APRIL 29, 1960 THE GENUS HAUYA (ONAGRACEAE) PHILIP A. MUNZ The genus Hauya, named in honor of Abbe Rene Just Hai.iy, was described by A. P. de Candolle (Prodromus 3: 36, 1828). The first species described, H. elegans, was based on a drawing by Moc;ifi.o and Sesse, no specimens of the plant being available. The next attention given to the genus was by Hemsley (Diag. Pl. Nov., part 1: 13, 1878 and Bot. Bioi. Centr. Am. 1: 462-3, 1880 and 5: pl. 29). He described two additional species. In this country most of the work on the group has been done by J. Donnell Smith and ]. N. Rose; they published an account (Contr. U.S. Nat. Herb. 16: 288-294, 1913) recognizing eleven species. Hauya arborea (Kellogg) Curran was excluded from the genus by Smith and Rose and used as the type species of a new genus Xylonagra. Certain similarities caused them to keep it in the same tribe Hauyeae. I am in agreement with their disposition. The chief differences between Hauya and Xylonagra as given by them were in size of plant, size of flowers, their number and location, and in the type of seeds. -
State of New York City's Plants 2018
STATE OF NEW YORK CITY’S PLANTS 2018 Daniel Atha & Brian Boom © 2018 The New York Botanical Garden All rights reserved ISBN 978-0-89327-955-4 Center for Conservation Strategy The New York Botanical Garden 2900 Southern Boulevard Bronx, NY 10458 All photos NYBG staff Citation: Atha, D. and B. Boom. 2018. State of New York City’s Plants 2018. Center for Conservation Strategy. The New York Botanical Garden, Bronx, NY. 132 pp. STATE OF NEW YORK CITY’S PLANTS 2018 4 EXECUTIVE SUMMARY 6 INTRODUCTION 10 DOCUMENTING THE CITY’S PLANTS 10 The Flora of New York City 11 Rare Species 14 Focus on Specific Area 16 Botanical Spectacle: Summer Snow 18 CITIZEN SCIENCE 20 THREATS TO THE CITY’S PLANTS 24 NEW YORK STATE PROHIBITED AND REGULATED INVASIVE SPECIES FOUND IN NEW YORK CITY 26 LOOKING AHEAD 27 CONTRIBUTORS AND ACKNOWLEGMENTS 30 LITERATURE CITED 31 APPENDIX Checklist of the Spontaneous Vascular Plants of New York City 32 Ferns and Fern Allies 35 Gymnosperms 36 Nymphaeales and Magnoliids 37 Monocots 67 Dicots 3 EXECUTIVE SUMMARY This report, State of New York City’s Plants 2018, is the first rankings of rare, threatened, endangered, and extinct species of what is envisioned by the Center for Conservation Strategy known from New York City, and based on this compilation of The New York Botanical Garden as annual updates thirteen percent of the City’s flora is imperiled or extinct in New summarizing the status of the spontaneous plant species of the York City. five boroughs of New York City. This year’s report deals with the City’s vascular plants (ferns and fern allies, gymnosperms, We have begun the process of assessing conservation status and flowering plants), but in the future it is planned to phase in at the local level for all species. -
Grijalva Pineda, Alfredo. Flora Útil Etnobotánica De Nicaragua
FLORA ÚTIL ETNOBOTÁNICA DE NICARAGUA. Alfredo Grijalva Pineda. Managua, Nicaragua; Junio del 2006 N 581 G857 Grijalva Pineda, Alfredo Flora útil etnobotánica de Nicaragua / Alfredo Grijalva Pineda. --1a ed.-- Managua : MARENA, 2005. 290 p. : il. ISBN : 99924-903-8-1 1. PLANTAS ÚTILES-INVESTIGACIONES. 2 PLANTAS MEDICINALES 3. TAXONOMÍA VEGETAL Primera edición, 2006, financiada con fondos de la Agencia Española de Cooperación Internacional - AECI, en el marco del Proyecto Integral MARENA/ARAUCARIA Río San Juan, ejecutado por el Gobierno de la República de Nicaragua, a través del Ministerio del Ambiente y los Recursos Naturales - MARENA. Teléfono/Fax: 26391271/ 2331595 Fotografías de portada: Bambusa vulgaris, Melicoccus bijugatus, Gerbera jamesonii, Oxalis debilis (Fotografías de Alfredo Grijalva Pineda). Diseño y Diagramación: Franklin Ruíz M. Esta primera edición cuenta de 500 ejemplares, se terminó de imprimir el 26 de junio del 2006. © MARENA – ARAUCARIA – AECI, 2006 © Grijalva Pineda Alfredo Flora Útil Etnobotánica de Nicaragua Presentación Nicaragua es un país megadiverso, que conserva una gran cantidad de ecosistemas y especies de plantas vasculares de gran valor etnobotánico. Concretamente, éste valor se centra en el conocimiento popular sobre la vegetación y sus usos tradicionales o sea de la relación sociedad – planta, la cual hoy en día se vuelve mas importante, dinámica y necesaria para satisfacer muchas necesidades en el campo y la ciudad, tanto en el ámbito alimenticio, medicinal, industrial, ornamental, habitacional, sumidero de la contaminación del aire, entre otras. El objeto de éste libro titulado “Flora Útil o Etnobotánica”, radica en brindar la información y los conocimientos técnicos - científicos a los investigadores, docentes, estudiantes, ambientalistas y personas interesadas en la protección de la biodiversidad, especialmente las plantas de interés económico para la sociedad, así como, el conocimiento de la vegetación y sus propiedades. -
Levin Et Al. 2004
Systematic Botany (2004), 29(1): pp. 147–164 q Copyright 2004 by the American Society of Plant Taxonomists Paraphyly in Tribe Onagreae: Insights into Phylogenetic Relationships of Onagraceae Based on Nuclear and Chloroplast Sequence Data RACHEL A. LEVIN,1,7 WARREN L. WAGNER,1 PETER C. HOCH,2 WILLIAM J. HAHN,3 AARON RODRIGUEZ,4 DAVID A. BAUM,5 LILIANA KATINAS,6 ELIZABETH A. ZIMMER,1 and KENNETH J. SYTSMA5 1Department of Systematic Biology, Botany, MRC 166, Smithsonian Institution, P. O. Box 37012, Washington, District of Columbia 20013-7012; 2Missouri Botanical Garden, P. O. Box 299, St. Louis, Missouri 63166-0299; 3108 White-Gravenor, Box 571003, Georgetown University, Washington, District of Columbia, 20057-1003; 4Departamento de Botan´‡ca y Zoolog´‡a, Apartado Postal 139, 45101 Zapopan, Jalisco, Mexico; 5Department of Botany, University of Wisconsin, 430 Lincoln Drive, Madison, Wisconsin 53706; 6Departamento Cienti!co de Plantas Vasculares, Museo de Ciencias Naturales, Paseo del Bosque s/n, 1900 La Plata, Provincia de Buenos Aires, Argentina 7Author for correspondence ([email protected]) Communicating Editor: Thomas G. Lammers ABSTRACT. Onagraceae are a family of 17 genera in seven tribes, with the majority of species in tribes Onagreae and Epilobieae. Despite the species-richness of these two tribes, to date no phylogenetic study has been done with suf!cient taxon sampling to examine relationships between and within these tribes. In this study, we used DNA sequence data from one nuclear region (ITS) and two chloroplast regions (trnL-trnF and rps16) to infer phylogenetic relationships among 93 taxa across the family, with concentrated sampling in the large tribe Onagreae. -
Minnesota Biodiversity Atlas Plant List
Boot Lake SNA Plant List Herbarium Scientific Name Minnesota DNR Common Name Status Acer rubrum red maple Acer rubrum var. rubrum red maple Achillea millefolium common yarrow Actaea rubra red baneberry Agalinis tenuifolia var. parviflora slender-leaved false foxglove Agastache foeniculum blue giant hyssop Agrostis scabra rough bentgrass Alnus incana subsp. rugosa speckled alder Ambrosia artemisiifolia common ragweed Amelanchier laevis smooth juneberry Amorpha canescens leadplant Amphicarpaea bracteata hog peanut Andromeda polifolia bog rosemary Andropogon gerardii big bluestem Anemone cylindrica long-headed thimbleweed Anemone quinquefolia var. quinquefolia wood anemone Antennaria neglecta field pussytoes Apios americana groundnut Aquilegia canadensis columbine Arabidopsis lyrata subsp. Lyrata lyre-leaved rock cress Aralia nudicaulis wild sarsaparilla Arisaema triphyllum Jack-in-the-pulpit Aronia melanocarpa black chokeberry Asclepias incarnata var. incarnata swamp milkweed Asclepias syriaca common milkweed Asclepias tuberosa subsp. interior butterflyweed Asparagus officinalis asparagus Athyrium filix-femina lady fern Athyrium filix-femina var. angustum lady fern Berteroa incana hoary alyssum Betula papyrifera paper birch Betula pumila bog birch Bidens frondosa leafy beggarticks Bidens trichosperma showy beggarticks Botrychium dissectum dissected grapefern Bromus inermis smooth brome Calamagrostis canadensis bluejoint Calamagrostis canadensis var. canadensis bluejoint Calla palustris wild calla Caltha palustris common marsh marigold Campanula aparinoides marsh bellflower Campanula rotundifolia harebell Carex brunnescens subsp. sphaerostachya brownish sedge Carex canescens silvery sedge Carex comosa bristly sedge Carex disperma soft-leaved sedge © 2020 MinnesotaSeasons.com. All rights reserved. Page 1 of 8 Boot Lake SNA Plant List Herbarium Scientific Name Minnesota DNR Common Name Status Carex echinata subsp. echinata slender sedge Carex hystericina porcupine sedge Carex lacustris lake sedge Carex lasiocarpa subsp. -
“Hexing Herbs” in Ethnobotanical Perspective: a Historical Review of the Uses of Anticholinergic Solanaceae Plants in Europe
“Hexing Herbs” in Ethnobotanical Perspective: A Historical Review of the Uses of Anticholinergic Solanaceae Plants in Europe KARSTEN FATUR Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia Though not the most frequently used botanical family, the Solanaceae or nightshade family has provided many plants of great importance around the world. Throughout Europe, the “hexing herbs,” plants from this family with anticholinergic alkaloids, have played an especially impor- tant role in the history and formation of traditions pertaining to plant use in many aspects of human life. Represented in Europe by the genera Atropa, Datura, Hyoscyamus, Mandragora,and Scopolia, the alkaloids hyoscyamine/atropine and scopolamine in these plants have allowed them to be used as medicines, poisons, and intoxicants, leading to the creation of a large mythos and extensive cultural valuation. Through a review of the literature, the exact roles that these “hexing herbs” have played in Europe in the past and present are discussed in this paper, ultimately showing the immense importance of these often misunderstood and vilified plants. Key Words: Ethnobotany, Solanaceae, Hexing herbs, Europe, Anticholinergic, Tropane alkaloids. Introduction made them invaluable to humans throughout the ages (Arroo et al. 2007;Boydetal.1984). Used as OVERVIEW inebriants, medicines, poisons, in rituals, and for many cultural inspirations, these plants have played Informally known as the “hexing herbs,” the a crucial role in the shaping of Europe. anticholinergic members of the Solanaceae that are Among these plants, five genera have been long found in Europe likely earned this name through represented in, or are native to, Europe. All are closely association with witches and magic. -
Paleocene–Eocene Palynomorphs from the Chicxulub Impact Crater, Mexico
Palynology ISSN: (Print) (Online) Journal homepage: https://www.tandfonline.com/loi/tpal20 Paleocene–Eocene palynomorphs from the Chicxulub impact crater, Mexico. Part 2: angiosperm pollen Vann Smith , Sophie Warny , David M. Jarzen , Thomas Demchuk , Vivi Vajda & Sean P.S. Gulick To cite this article: Vann Smith , Sophie Warny , David M. Jarzen , Thomas Demchuk , Vivi Vajda & Sean P.S. Gulick (2020) Paleocene–Eocene palynomorphs from the Chicxulub impact crater, Mexico. Part 2: angiosperm pollen, Palynology, 44:3, 489-519, DOI: 10.1080/01916122.2019.1705417 To link to this article: https://doi.org/10.1080/01916122.2019.1705417 View supplementary material Accepted author version posted online: 17 Dec 2019. Published online: 23 Jan 2020. Submit your article to this journal Article views: 138 View related articles View Crossmark data Full Terms & Conditions of access and use can be found at https://www.tandfonline.com/action/journalInformation?journalCode=tpal20 PALYNOLOGY 2020, VOL. 44, NO. 3, 489–519 https://doi.org/10.1080/01916122.2019.1705417 Paleocene–Eocene palynomorphs from the Chicxulub impact crater, Mexico. Part 2: angiosperm pollen Vann Smitha,b , Sophie Warnya,b, David M. Jarzenc, Thomas Demchuka, Vivi Vajdad and Sean P.S. Gulicke aDepartment of Geology and Geophysics, LSU, Baton Rouge, LA, USA; bMuseum of Natural Science, LSU, Baton Rouge, LA, USA; cCleveland Museum of Natural History, Cleveland, OH, USA; dSwedish Museum of Natural History, Stockholm, Sweden; eInstitute for Geophysics and Department of Geological Sciences, Jackson School of Geosciences, University of Texas at Austin, TX, USA ABSTRACT KEYWORDS At the end of the Cretaceous Period, an asteroid collided with the Earth and formed the Chicxulub Mexico; Paleocene; impact structure on the Yucatan Platform. -
UC Berkeley UC Berkeley Electronic Theses and Dissertations
UC Berkeley UC Berkeley Electronic Theses and Dissertations Title Phylogenetic Models Linking Speciation and Extinction to Chromosome and Mating System Evolution Permalink https://escholarship.org/uc/item/29n8r0nm Author Freyman, William Allen Publication Date 2017 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California 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. -
Research on Spontaneous and Subspontaneous Flora of Botanical Garden "Vasile Fati" Jibou
Volume 19(2), 176- 189, 2015 JOURNAL of Horticulture, Forestry and Biotechnology www.journal-hfb.usab-tm.ro Research on spontaneous and subspontaneous flora of Botanical Garden "Vasile Fati" Jibou Szatmari P-M*.1,, Căprar M. 1 1) Biological Research Center, Botanical Garden “Vasile Fati” Jibou, Wesselényi Miklós Street, No. 16, 455200 Jibou, Romania; *Corresponding author. Email: [email protected] Abstract The research presented in this paper had the purpose of Key words inventory and knowledge of spontaneous and subspontaneous plant species of Botanical Garden "Vasile Fati" Jibou, Salaj, Romania. Following systematic Jibou Botanical Garden, investigations undertaken in the botanical garden a large number of spontaneous flora, spontaneous taxons were found from the Romanian flora (650 species of adventive and vascular plants and 20 species of moss). Also were inventoried 38 species of subspontaneous plants, adventive plants, permanently established in Romania and 176 vascular plant floristic analysis, Romania species that have migrated from culture and multiply by themselves throughout the garden. In the garden greenhouses were found 183 subspontaneous species and weeds, both from the Romanian flora as well as tropical plants introduced by accident. Thus the total number of wild species rises to 1055, a large number compared to the occupied area. Some rare spontaneous plants and endemic to the Romanian flora (Galium abaujense, Cephalaria radiata, Crocus banaticus) were found. Cultivated species that once migrated from culture, accommodated to environmental conditions and conquered new territories; standing out is the Cyrtomium falcatum fern, once escaped from the greenhouses it continues to develop on their outer walls. Jibou Botanical Garden is the second largest exotic species can adapt and breed further without any botanical garden in Romania, after "Anastasie Fătu" care [11]. -
NEW EPIPACTIS (ORCHIDACEAE) SPECIES for the ROMANIAN FLORA 1 2 3 Corina, ARDELEAN , A., ARDELEAN , B., BOCEANU 1 -Association P.P.V.N.C
Research Journal of Agricultural Science, 50 (1), 2018 NEW EPIPACTIS (ORCHIDACEAE) SPECIES FOR THE ROMANIAN FLORA 1 2 3 Corina, ARDELEAN , A., ARDELEAN , B., BOCEANU 1 -Association P.P.V.N.C. Excelsior, Arad [email protected] 2- myNature Association, Timişoara 3 – Neptun 19, sc. A, apt. 6, Brasov Abstract. Four Epipactis species are recorded as new taxa for the Romanian Flora: Epipactis nordeniorum Robatsch, E. tallosii A.Molnár & Robatsch, E. exilis P.Delforge and E. pontica Taubenheim. With this contribution, not only the number of Epipactis species in Romania is increased to fourteen, but also we fill in gaps in geographical distribution of Epipactis species at European level. For each investigated taxon, we provide information about the habitat type, associated plant species, and population size . Key words: Epipactis nordeniorum, E. tallosii, E. exilis, E. pontica, Romania, new occurrence records. INTRODUCTION This paper presents four new species of Epipactis taxa as a new species for Romanian flora. Genus Epipactis is a very difficult taxonomic group and only few papers dealing with this taxon in Romania were published during the last decade. Comparing data from the most recent Romanian Floras (SÂRBU, I., ET AL., 2013, CIOCÂRLAN V., 2009) and other publications until now in Romania Epipactis genus is represented by ten species: E. albensis Novakova et Rydlo, E. atrorubens (Hoffm.) Besser, E. helleborine (L.) Crantz, E. greuteri H.Baumann & Künkele, E. guegelii K. Robatsch, E. leptochila (Godfery) Godfery, E. microphylla (Ehrh.) Sw., E. palustris (L.) Crantz, E. persica (Soo) Nannfeldt, E. purpurata J.E. Smith. Relative recently, Wuscherpfennig (2008) clarified the status of two of the Epipactis species which occur in Danube Delta: E. -
Wildflowers of Bombay Hook National Wildlife Refuge 2591 Whitehall Neck Road Smyrna, Delaware 19977 302-653-9345 a Preliminary
Wildflowers of Bombay Hook National Wildlife Refuge 2591 Whitehall Neck Road Smyrna, Delaware 19977 302-653-9345 A Preliminary List Compiled by: Norman E. Holgersen, Wildlife Biologist January, 1974 Updated: December, 1995 Wildflowers of the Bombay Hook National Wildlife Refuge Arrowhead Family (Alismataceae) Arrowhead Sagittaria latifolia Water-plantain Alisma subcordatum Frog’s - bit Family (Hydrocharitaceae) American frogbit Limnobium spongia Arum Family (Araceae) Jack-in-the-pulpit Arisaema triphyllum Skunk cabbage Symplocarpus foetidus Arrow arum Peltandra virginica Yellow-eyed Grass Family (Xyridaceae) Yellow-eyed grass Xyris iridifolia Spiderwort Family (Commelinaceae) Asiatic dayflower Commelina communis Pickerelweed Family (Pontederiaceae) Mud-plantain Heteranthera reniformis Pickerelweed Pontederia cordata Lily Family (Liliaceae) Perfoliate bellwort Uvularia perfoliata Star-of-Bethlehem Ornithogalum umbellatum Trout-lily Erythronium americanum Turk’s-cap lily Lilium superbum Day-Lilly Hermerocallis fulva Field garlic Allium vineale False Solomon’s seal Smilacina racemosa Canada mayflower Maianthemum canadense Iris Family (Iridaceae) Larger blue flag Iris versicolor Orchid Family (Orchidaceae) Nodding ladies’-tresses Spiranthes cernua Slender ladies’-tresses Spiranthes lacera Ladies’-tresses Spiranthes sp. Rattlesnake-plantain Goodyera pubescens Showy orchis Orchis spectabilis Crane-fly orchid Tipularia discolor Lizard’s-tail Family (Saururaceae) Lizard’s-tail Saururus cernuus Buckwheat Family (Polygonaceae) Virginia knotweed