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A Phylogenetic Framework for Evolutionary Study of the Nightshades
Särkinen et al. BMC Evolutionary Biology 2013, 13:214 http://www.biomedcentral.com/1471-2148/13/214 RESEARCH ARTICLE Open Access A phylogenetic framework for evolutionary study of the nightshades (Solanaceae): a dated 1000-tip tree Tiina Särkinen1,2*, Lynn Bohs3, Richard G Olmstead4 and Sandra Knapp1 Abstract Background: The Solanaceae is a plant family of great economic importance. Despite a wealth of phylogenetic work on individual clades and a deep knowledge of particular cultivated species such as tomato and potato, a robust evolutionary framework with a dated molecular phylogeny for the family is still lacking. Here we investigate molecular divergence times for Solanaceae using a densely-sampled species-level phylogeny. We also review the fossil record of the family to derive robust calibration points, and estimate a chronogram using an uncorrelated relaxed molecular clock. Results: Our densely-sampled phylogeny shows strong support for all previously identified clades of Solanaceae and strongly supported relationships between the major clades, particularly within Solanum. The Tomato clade is shown to be sister to section Petota, and the Regmandra clade is the first branching member of the Potato clade. The minimum age estimates for major splits within the family provided here correspond well with results from previous studies, indicating splits between tomato & potato around 8 Million years ago (Ma) with a 95% highest posterior density (HPD) 7–10 Ma, Solanum & Capsicum c. 19 Ma (95% HPD 17–21), and Solanum & Nicotiana c. 24 Ma (95% HPD 23–26). Conclusions: Our large time-calibrated phylogeny provides a significant step towards completing a fully sampled species-level phylogeny for Solanaceae, and provides age estimates for the whole family. -
Outline of Angiosperm Phylogeny
Outline of angiosperm phylogeny: orders, families, and representative genera with emphasis on Oregon native plants Priscilla Spears December 2013 The following listing gives an introduction to the phylogenetic classification of the flowering plants that has emerged in recent decades, and which is based on nucleic acid sequences as well as morphological and developmental data. This listing emphasizes temperate families of the Northern Hemisphere and is meant as an overview with examples of Oregon native plants. It includes many exotic genera that are grown in Oregon as ornamentals plus other plants of interest worldwide. The genera that are Oregon natives are printed in a blue font. Genera that are exotics are shown in black, however genera in blue may also contain non-native species. Names separated by a slash are alternatives or else the nomenclature is in flux. When several genera have the same common name, the names are separated by commas. The order of the family names is from the linear listing of families in the APG III report. For further information, see the references on the last page. Basal Angiosperms (ANITA grade) Amborellales Amborellaceae, sole family, the earliest branch of flowering plants, a shrub native to New Caledonia – Amborella Nymphaeales Hydatellaceae – aquatics from Australasia, previously classified as a grass Cabombaceae (water shield – Brasenia, fanwort – Cabomba) Nymphaeaceae (water lilies – Nymphaea; pond lilies – Nuphar) Austrobaileyales Schisandraceae (wild sarsaparilla, star vine – Schisandra; Japanese -
December 2012 Number 1
Calochortiana December 2012 Number 1 December 2012 Number 1 CONTENTS Proceedings of the Fifth South- western Rare and Endangered Plant Conference Calochortiana, a new publication of the Utah Native Plant Society . 3 The Fifth Southwestern Rare and En- dangered Plant Conference, Salt Lake City, Utah, March 2009 . 3 Abstracts of presentations and posters not submitted for the proceedings . 4 Southwestern cienegas: Rare habitats for endangered wetland plants. Robert Sivinski . 17 A new look at ranking plant rarity for conservation purposes, with an em- phasis on the flora of the American Southwest. John R. Spence . 25 The contribution of Cedar Breaks Na- tional Monument to the conservation of vascular plant diversity in Utah. Walter Fertig and Douglas N. Rey- nolds . 35 Studying the seed bank dynamics of rare plants. Susan Meyer . 46 East meets west: Rare desert Alliums in Arizona. John L. Anderson . 56 Calochortus nuttallii (Sego lily), Spatial patterns of endemic plant spe- state flower of Utah. By Kaye cies of the Colorado Plateau. Crystal Thorne. Krause . 63 Continued on page 2 Copyright 2012 Utah Native Plant Society. All Rights Reserved. Utah Native Plant Society Utah Native Plant Society, PO Box 520041, Salt Lake Copyright 2012 Utah Native Plant Society. All Rights City, Utah, 84152-0041. www.unps.org Reserved. Calochortiana is a publication of the Utah Native Plant Society, a 501(c)(3) not-for-profit organi- Editor: Walter Fertig ([email protected]), zation dedicated to conserving and promoting steward- Editorial Committee: Walter Fertig, Mindy Wheeler, ship of our native plants. Leila Shultz, and Susan Meyer CONTENTS, continued Biogeography of rare plants of the Ash Meadows National Wildlife Refuge, Nevada. -
Phylogeny of the Andean Genus Deprea (Physalideae, Solanaceae): Testing the Generic Circumscription
Phytotaxa 238 (1): 071–081 ISSN 1179-3155 (print edition) www.mapress.com/phytotaxa/ PHYTOTAXA Copyright © 2015 Magnolia Press Article ISSN 1179-3163 (online edition) http://dx.doi.org/10.11646/phytotaxa.238.1.3 Phylogeny of the Andean genus Deprea (Physalideae, Solanaceae): testing the generic circumscription CAROLINA CARRIZO GARCÍA 1, GREG WAHLERT 2, CLARA INÉS OROZCO 3, GLORIA E. BARBOZA 1,4* & LYNN BOHS 2* 1 Instituto Multidisciplinario de Biología Vegetal (CONICET), Av. Velez Sarsfield 1611, Córdoba, Argentina 2 Department of Biology, University of Utah, 201 South Biology, Salt Lake City, USA 84112 3 Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Entrada Calle 53, Bogotá, Colombia; A. A.7495 4 Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de la Torre s/n, Córdoba, Argentina * Corresponding authors: [email protected]; [email protected] Abstract Deprea (Solanaceae) is a small South American genus of 10 species occurring in Andean areas from Venezuela to Bolivia. The circumscription of Deprea has been repeatedly modified in recent years, with new species being described and others transferred into or out of the genus. The relationships of Deprea to other genera of Solanaceae are still poorly understood, although it seems to be closely related to Larnax. A phylogenetic analysis was performed to test the monophyly of Deprea. Sequences from three molecular markers (nuclear ITS and waxy and chloroplast psbA-trnH) were analyzed by parsimony and Bayesian methods. All the species of Deprea and Larnax sampled were intermixed in a strongly supported clade in the consensus trees, and therefore the currently recognized Deprea species do not form a monophyletic group. -
Botanist Interior 43.1
2011 THE MICHIGAN BOTANIST 1 EDWARD G. VOSS (1929 –2012) Anton A. Reznicek and Richard K. Rabeler University of Michigan Herbarium 3600 Varsity Drive Ann Arbor, MI 48108-2228 Edward Groesbec k Voss (Fig. 1), Professor and Curator Emeritus at the Uni - versity of Michigan Department of Ecology and Evolutionary Biology and Uni - versity of Michigan Herbarium, died on February 13, 2012 at his home in Ann Arbor, after a brief illness. He was born on February 22, 1929 in Delaware, Ohio. Ed’s abilities were clear early in his life. He attended Woodward High School in Toledo, Ohio. He received the Achievement Award as the outstanding senior in his 1946 high school class, and was later elected to the Woodward High Hall of Fame. He then graduated with a bachelor’s degree with honors from Denison University (1950); his undergraduate honors thesis, On the classifica - tion of the Hesperiidae , became a significant paper on Lepidoptera (Voss 1952). He completed his education with a master’s in Biology (1951) and a doctoral de - gree in Botany (1954), both from the University of Michigan working with Rogers McVaugh. He was awarded an honorary Doctor of Science from Denison University in 2003. In 1956, he began his long association with the University of Michigan and Michigan’s flora when he was appointed as a research associate at the Herbar - ium, beginning what was expected to be a five-year project to document the flora of Michigan. He joined the Botany faculty in 1960 as assistant professor and was promoted to associate professor (1963), and later, professor (1969). -
Vascular Plants and a Brief History of the Kiowa and Rita Blanca National Grasslands
United States Department of Agriculture Vascular Plants and a Brief Forest Service Rocky Mountain History of the Kiowa and Rita Research Station General Technical Report Blanca National Grasslands RMRS-GTR-233 December 2009 Donald L. Hazlett, Michael H. Schiebout, and Paulette L. Ford Hazlett, Donald L.; Schiebout, Michael H.; and Ford, Paulette L. 2009. Vascular plants and a brief history of the Kiowa and Rita Blanca National Grasslands. Gen. Tech. Rep. RMRS- GTR-233. Fort Collins, CO: U.S. Department of Agriculture, Forest Service, Rocky Mountain Research Station. 44 p. Abstract Administered by the USDA Forest Service, the Kiowa and Rita Blanca National Grasslands occupy 230,000 acres of public land extending from northeastern New Mexico into the panhandles of Oklahoma and Texas. A mosaic of topographic features including canyons, plateaus, rolling grasslands and outcrops supports a diverse flora. Eight hundred twenty six (826) species of vascular plant species representing 81 plant families are known to occur on or near these public lands. This report includes a history of the area; ethnobotanical information; an introductory overview of the area including its climate, geology, vegetation, habitats, fauna, and ecological history; and a plant survey and information about the rare, poisonous, and exotic species from the area. A vascular plant checklist of 816 vascular plant taxa in the appendix includes scientific and common names, habitat types, and general distribution data for each species. This list is based on extensive plant collections and available herbarium collections. Authors Donald L. Hazlett is an ethnobotanist, Director of New World Plants and People consulting, and a research associate at the Denver Botanic Gardens, Denver, CO. -
Volume 4 Number 1 Oregon State University February I998 , ,.;
Volume 4 Number 1 Oregon State University February I998 Clay Gautier Checklist: Asteraceac by Rhoda Love by Scon Sundherg und Kenton L. Chambers We are pleased to announce the completion of the Clay Gaulier is fhe newatmember of the &gon checklist of Oregon composites (Astmceae)by the AtlasEoject Leaders group. Hehas volunteered with Oregon Vascular mant CbecklktProject. The Scott Sundberg and o& since 1996. 44Clayhas been Asteraceae checklist was written by Eenton.chambers instrumental in deveIoping an ektmnic version of the and Scott Sundberg andis currently being reviewed by OregonPlant Aflas that willbe fully intmmfive and Checklist project members. It is a pomon of thc Oregon accessibIeto the public via tb Iaremeff' says Scott. va.scular 61At Checklist, which iQpreparatoryto a new Clay, who commuIes'ta~0SUhmF&gene,brings a Flora of Oregon. The Asteraceae Checklist includes special combination of skills tbfhis task: underpdLta@ accepted names of all Oregon tam [species, subspecies Ad graduate workcinec~logyand 12 years of experience and varieties) growing outside of cultivation, as well as as a proEssional software'developer. common m,plant origin (native or introduced) and Clay was born in San Francis~oin the niid-B%es comments on taxonomic problems and hybridization. and grew np in California and Nevada. He says, "My Each recod iq backed up by annotated herbarium wife, Gail Baker, and I both went tb Redwood High specimens or by reference to a published monograph or School in Marin Countv when I was a freshman, but we revision. The, ,.; accepted. namcs.will.be mssslerenced to didn't mypcq~y~~+l ~:~?,l$er in B&.o@gPli; . -
A Molecular Phylogeny of the Solanaceae
TAXON 57 (4) • November 2008: 1159–1181 Olmstead & al. • Molecular phylogeny of Solanaceae MOLECULAR PHYLOGENETICS A molecular phylogeny of the Solanaceae Richard G. Olmstead1*, Lynn Bohs2, Hala Abdel Migid1,3, Eugenio Santiago-Valentin1,4, Vicente F. Garcia1,5 & Sarah M. Collier1,6 1 Department of Biology, University of Washington, Seattle, Washington 98195, U.S.A. *olmstead@ u.washington.edu (author for correspondence) 2 Department of Biology, University of Utah, Salt Lake City, Utah 84112, U.S.A. 3 Present address: Botany Department, Faculty of Science, Mansoura University, Mansoura, Egypt 4 Present address: Jardin Botanico de Puerto Rico, Universidad de Puerto Rico, Apartado Postal 364984, San Juan 00936, Puerto Rico 5 Present address: Department of Integrative Biology, 3060 Valley Life Sciences Building, University of California, Berkeley, California 94720, U.S.A. 6 Present address: Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14853, U.S.A. A phylogeny of Solanaceae is presented based on the chloroplast DNA regions ndhF and trnLF. With 89 genera and 190 species included, this represents a nearly comprehensive genus-level sampling and provides a framework phylogeny for the entire family that helps integrate many previously-published phylogenetic studies within So- lanaceae. The four genera comprising the family Goetzeaceae and the monotypic families Duckeodendraceae, Nolanaceae, and Sclerophylaceae, often recognized in traditional classifications, are shown to be included in Solanaceae. The current results corroborate previous studies that identify a monophyletic subfamily Solanoideae and the more inclusive “x = 12” clade, which includes Nicotiana and the Australian tribe Anthocercideae. These results also provide greater resolution among lineages within Solanoideae, confirming Jaltomata as sister to Solanum and identifying a clade comprised primarily of tribes Capsiceae (Capsicum and Lycianthes) and Physaleae. -
Ajo Peak to Tinajas Altas: a Flora of Southwestern Arizona. Part 20
Felger, R.S. and S. Rutman. 2016. Ajo Peak to Tinajas Altas: A Flora of Southwestern Arizona. Part 20. Eudicots: Solanaceae to Zygophyllaceae. Phytoneuron 2016-52: 1–66. Published 4 August 2016. ISSN 2153 733X AJO PEAK TO TINAJAS ALTAS: A FLORA OF SOUTHWESTERN ARIZONA PART 20. EUDICOTS: SOLANACEAE TO ZYGOPHYLLACEAE RICHARD STEPHEN FELGER Herbarium, University of Arizona Tucson, Arizona 85721 & International Sonoran Desert Alliance PO Box 687 Ajo, Arizona 85321 *Author for correspondence: [email protected] SUSAN RUTMAN 90 West 10th Street Ajo, Arizona 85321 [email protected] ABSTRACT A floristic account is provided for Solanaceae, Talinaceae, Tamaricaceae, Urticaceae, Verbenaceae, and Zygophyllaceae as part of the vascular plant flora of the contiguous protected areas of Organ Pipe Cactus National Monument, Cabeza Prieta National Wildlife Refuge, and the Tinajas Altas Region in southwestern Arizona—the heart of the Sonoran Desert. This account includes 40 taxa, of which about 10 taxa are represented by fossil specimens from packrat middens. This is the twentieth contribution for this flora, published in Phytoneuron and also posted open access on the website of the University of Arizona Herbarium: <http//cals.arizona.edu/herbarium/content/flora-sw-arizona>. Six eudicot families are included in this contribution (Table 1): Solanaceae (9 genera, 21 species), Talinaceae (1 species), Tamaricaceae (1 genus, 2 species), Urticaceae (2 genera, 2 species), Verbenaceae (4 genera, 7 species), and Zygophyllaceae (4 genera, 7 species). The flora area covers 5141 km 2 (1985 mi 2) of contiguous protected areas in the heart of the Sonoran Desert (Figure 1). The first article in this series includes maps and brief descriptions of the physical, biological, ecological, floristic, and deep history of the flora area (Felger et al. -
(Trnf) Pseudogenes Defines a Distinctive Clade in Solanaceae Péter Poczai* and Jaakko Hyvönen
Poczai and Hyvönen SpringerPlus 2013, 2:459 http://www.springerplus.com/content/2/1/459 a SpringerOpen Journal SHORT REPORT Open Access Discovery of novel plastid phenylalanine (trnF) pseudogenes defines a distinctive clade in Solanaceae Péter Poczai* and Jaakko Hyvönen Abstract Background: The plastome of embryophytes is known for its high degree of conservation in size, structure, gene content and linear order of genes. The duplication of entire tRNA genes or their arrangement in a tandem array composed by multiple pseudogene copies is extremely rare in the plastome. Pseudogene repeats of the trnF gene have rarely been described from the chloroplast genome of angiosperms. Findings: We report the discovery of duplicated copies of the original phenylalanine (trnFGAA) gene in Solanaceae that are specific to a larger clade within the Solanoideae subfamily. The pseudogene copies are composed of several highly structured motifs that are partial residues or entire parts of the anticodon, T- and D-domains of the original trnF gene. Conclusions: The Pseudosolanoid clade consists of 29 genera and includes many economically important plants such as potato, tomato, eggplant and pepper. Keywords: Chloroplast DNA (cpDNA); Gene duplications; Phylogeny; Plastome evolution; Tandem repeats; trnL-trnF; Solanaceae Findings of this region. If this is ignored, it will easily lead to situa- The plastid trnT-trnF region has been widely applied to tions where basic requirement of homology of the charac- resolve phylogeny of embryophytes (Quandt and Stech ters used for phylogenetic analyses is compromised. This 2004; Zhao et al. 2011) and to address various questions of might lead to false hypotheses of phylogeny, especially population genetics since the development of universal when they are based on the analyses of only this region. -
Flora of North Central Texas Flora of North Central Texas
SHINNERS & MAHLER’S FLOR A OF NORTH CENTRAL TEXAS GEORGE M. DIGGSIGGS,, JJR.. BBARNEY L. LIPSCOMBIPSCOMB ROBERT J. O’KENNON D VEGETATIONAL AREAS OF TEXAS MODIFIED FROM CHECKLIST OF THE VASCULAR PLANTS OF TEXAS (HATCH ET AL. 1990). NEARLY IDENTICAL MAPS HAVE BEEN USED IN NUMEROUS WORKS ON TEXAS INCLUDING GOULD (1962) AND CORRELL AND JOHNSTON (1970). 1 PINEYWOODS 2 GULF PRAIRIES AND MARSHEs 3 POST OAK SAVANNAH 4 BLACKLAND PRAIRIES 5 CROSS TIMBERS AND PRAIRIES 6 SOUTH TEXAS PLAINS 7 EDWARDS PLATEAU 8 ROLLING PLAINS 9 HIGH PLAINS 10 TRANS-PECOS, MOUNTAINS AND BASINS D VEGETATIONAL AREAS OF NORTH CENTRAL TEXAS D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D SHINNERS & MAHLER’S ILLUSTRATED FLORA OF NORTH CENTRAL TEXAS Shinners & Mahler’s ILLUSTRATED FLORA OF NORTH CENTRAL TEXAS IS PUBLISHED WITH THE SUPPORT OF: MAJOR BENEFACTORS: NEW DOROTHEA L. LEONHARDT FOUNDATION (ANDREA C. HARKINS) BASS FOUNDATION ROBERT J. O’KENNON RUTH ANDERSSON MAY MARY G. PALKO AMON G. CARTER FOUNDATION MARGRET M. RIMMER MIKE AND EVA SANDLIN INSTITUTIONAL SUPPORT: AUSTIN COLLEGE BOTANICAL RESEARCH INSTITUTE OF TEXAS SID RICHARDSON CAREER DEVELOPMENT FUND OF AUSTIN COLLEGE OTHER CONTRIBUTORS: PEG AND BEN KEITH FRIENDS OF HAGERMAN NAT IONAL WILDLIFE REFUGE SUMMERLEE FOUNDATION JOHN D. -
Solanaceae – Nightshade (Tomato) Family
SOLANACEAE – NIGHTSHADE (TOMATO) FAMILY Plant: herbs, woody vines, shrubs and trees Stem: Root: Leaves: simple (rarely pinnate) and alternate except sometimes on the upper stem opposite; no stipules Flowers: perfect; often showy; mostly (4)5 sepals, often persistent and partially fused; mostly (4)5 petals, sometimes tubular; stamens usually 5 (rarely 2 or 4) and alternate to corolla lobes; ovary superior, 1 style, stigma usually lobed Fruit: capsule (2-chambered) or berry, usually many seeds, often oily Other: large family; some poisonous; others include – peppers, tomato, potato, eggplant, tobacco and many ornamentals such as Petunia; Dicotyledons Group Genera: 95+ genera; locally Datura, Solanum (nightshade) WARNING – family descriptions are only a layman’s guide and should not be used as definitive Flower Morphology in the Solanaceae (Nightshade or Tomato Family) Examples of some common genera Gray Five Eyes [Ground Saracha] Chamaesaracha coniodes (Moric. Garden Petunia ex Dunal) Britton Petunia ×atkinsiana D. Don ex Loud. Bittersweet [Deadly] Nightshade [axillaris × integrifolia] (Introduced) Solanum dulcamara L. var. dulcamara Jimsonweed [Thorn Apple] Datura stramonium L. (Introduced). Clammy Groundcherry Physalis heterophylla Nees var. Garden Egg Plant heterophylla Solanum melongena L. (Introduced) Christmas Berry [Carolina Desert-Thorn] Chinese Lantern [Plains Purple Ground Cherry] Sticky Nightshade Lycium carolinianum Walter Quincula lobata (Torr.) Raf. Solanum sisymbriifolium Lam. var. carolinianum SOLANACEAE – NIGHTSHADE (TOMATO) FAMILY Gray Five Eyes [Ground Saracha]; Chamaesaracha coniodes (Moric. ex Dunal) Britton Jimsonweed [Thorn Apple]; Datura stramonium L. (Introduced). Christmas Berry [Carolina Desert-Thorn]; Lycium carolinianum Walter var. carolinianum Garden Petunia; Petunia ×atkinsiana D. Don ex Loud. [axillaris × integrifolia] (Introduced) Cutleaf Groundcherry; Physalis angulata L. Coastal [Narrow Leaf] Groundcherry; Physalis angustifolia Nutt.