DOCSLIB.ORG

Rosid Radiation and the Rapid Rise of Angiosperm-Dominated Forests

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Rosid Radiation and the Rapid Rise of Angiosperm-Dominated Forests Rosid radiation and the rapid rise of angiosperm-dominated forests Hengchang Wanga,b, Michael J. Moorec, Pamela S. Soltisd, Charles D. Belle, Samuel F. Brockingtonb, Roolse Alexandreb, Charles C. Davisf, Maribeth Latvisb,f, Steven R. Manchesterd, and Douglas E. Soltisb,1 aWuhan Botanical Garden, The Chinese Academy of Science, Wuhan, Hubei 430074 China; bDepartment of Botany and dFlorida Museum of Natural History, University of Florida, Gainesville, FL 32611; cBiology Department, Oberlin College, Oberlin, OH 44074-1097; eDepartment of Biological Sciences, University of New Orleans, New Orleans, LA 70148; and fDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138 Communicated by Peter Crane, University of Chicago, Chicago, IL, January 4, 2009 (received for review April 1, 2008) The rosid clade (70,000 species) contains more than one-fourth of all nitrogen-fixing bacteria (nitrogen-fixing clade) and defense mech- angiosperm species and includes most lineages of extant temperate anisms such as glucosinolate production (Brassicales) and cyano- and tropical forest trees. Despite progress in elucidating relationships genic glycosides (2). Many important crops, including legumes within the angiosperms, rosids remain the largest poorly resolved (Fabaceae) and fruit crops (Rosaceae), are rosids. Furthermore, 4 major clade; deep relationships within the rosids are particularly of the 5 published complete angiosperm nuclear genome sequences enigmatic. Based on parsimony and maximum likelihood (ML) anal- are rosids (with 2 other rosids, Manihot and Ricinus, well under- yses of separate and combined 12-gene (10 plastid genes, 2 nuclear; way): Arabidopsis (Brassicaceae), Carica (Caricaceae), Populus >18,000 bp) and plastid inverted repeat (IR; 24 genes and intervening (Salicaceae), and Vitis (Vitaceae, sister to other rosids). The spacers; >25,000 bp) datasets for >100 rosid species, we provide a variation in morphological, chemical, and ecological features and greatly improved understanding of rosid phylogeny. Vitaceae are the importance of rosids as genetic and genomic models require a sister to all other rosids, which in turn form 2 large clades, each with phylogenetic perspective for interpreting large-scale evolutionary a ML bootstrap value of 100%: (i) eurosids I (Fabidae) include the patterns across the clade. Finally, most lineages of extant temperate nitrogen-fixing clade, Celastrales, Huaceae, Zygophyllales, Malpighia- and tropical forest trees are rosids (e.g., Betulaceae, Celtidaceae, les, and Oxalidales; and (ii) eurosids II (Malvidae) include Tapisciaceae, Fabaceae, Fagaceae, Malvaceae, Sapindaceae, and Ulmaceae). In EVOLUTION Brassicales, Malvales, Sapindales, Geraniales, Myrtales, Crossosoma- temperate North America Ϸ71% of the forest tree species are tales, and Picramniaceae. The rosid clade diversified rapidly into these rosids (15). Similarly, rosids often constitute Ͼ50% of tropical tree major lineages, possibly over a period of <15 million years, and species diversity. For example, they comprise 59% of the tree perhaps in as little as 4 to 5 million years. The timing of the inferred species on Barro Colorado Island, Panama (16), 60% of the tree rapid radiation of rosids [108 to 91 million years ago (Mya) and 107–83 flora of Paraguay (17), 60% on Puerto Rico and the Virgin Islands Mya for Fabidae and Malvidae, respectively] corresponds with the (18), and 63% of the tree species of Brazil (19). Analysis of tropical rapid rise of angiosperm-dominated forests and the concomitant forest plots from around the world again suggests a major role of diversification of other clades that inhabit these forests, including rosid trees (20). Half the species richness of the Neotropical plots amphibians, ants, placental mammals, and ferns. is made up of just 11 families, 4 of which are rosids, with Fabaceae the most important (Moraceae, Meliaceae, and Euphorbiaceae are community assembly ͉ divergence time estimates ͉ phylogeny ͉ other major rosids in the Neotropics); Fabaceae are also the most rapid radiation important family of trees in Africa, but are replaced as number one by another rosid family, Dipterocarpaceae, in Southeast Asia (20). reat progress has been made in elucidating deep-level angio- The important ecological role of many rosid families further argues Gsperm relationships during the past decade. The eudicot clade, Ϸ for greater resolution of rosid phylogeny. with 75% of all angiosperm species, comprises several major Although studies agree on the composition of the rosid clade, subclades: rosids, asterids, Saxifragales, Santalales, and Caryophyl- deep-level relationships within the rosids remain enigmatic. Vita- lales (1–3). Investigations have converged on the branching pattern ceae usually appear as sister to all other rosids, although support for of the basalmost angiosperms, revealing that Amborellaceae, Nym- this placement is generally low (reviewed in refs. 2 and 10). Most phaeales [in the sense of APG II (3) and including Hydatellaceae remaining rosids appear in 2 large subclades (1–3): eurosids I (4)], and Austrobaileyales are successive sisters to all other extant [Fabidae (21)] and eurosids II [Malvidae (21)], with jackknife angiosperms (reviewed in ref. 2). Analyses of complete plastid support of 77% and 95%, respectively. Fabidae include (i) the genome sequences have resolved other problematic deep-level relationships, suggesting that Chloranthaceae and magnoliids are nitrogen-fixing clade (Rosales, Fabales, Cucurbitales, and Fagales); sister to a clade of monocots and eudicots plus Ceratophyllaceae (5, (ii) Zygophyllales; and (iii) a weakly supported clade of Celastrales, 6). Likewise, progress has been made in clarifying relationships Oxalidales, and Malpighiales [COM group (22)]. Malvidae include within the large monocot (7) and asterid (8) clades. Brassicales, Malvales, Sapindales, and Tapisciaceae. Despite these successes, the rosids stand out as the largest and Some rosid clades (Crossosomatales, Geraniales, and Myrtales), least-resolved major clade of angiosperms; basal nodes within the however, do not fall into either Fabidae or Malvidae, and their clade have consistently received low internal support (1, 2, 9, 10). The rosid clade comprises Ϸ70,000 species and 140 families (2, 11). Ϸ Author contributions: P.S.S., S.R.M., and D.E.S. designed research; H.W., M.J.M., C.D.B., Containing more than a quarter of total angiosperm and 39% of S.F.B., R.A., C.C.D., and M.L. performed research; M.J.M., C.D.B., and D.E.S. analyzed data; eudicot species diversity, the rosid clade is broader in circumscrip- and M.J.M., P.S.S., C.D.B., S.R.M., and D.E.S. wrote the paper. tion than the traditional Rosidae or Rosanae (e.g., 12; reviewed in The authors declare no conflict of interest. ref. 2). The oldest fossil flowers conforming to the rosids are from Freely available online through the PNAS open access option. Ϸ the late Santonian to Turonian ( 84–89.5 Mya) (9, 11, 13, 14). Data deposition: The sequences reported in this paper have been deposited in the GenBank Rosids exhibit enormous heterogeneity in habit, habitat, and life database (accession nos. EU002149 to EU002556). form, comprising herbs, shrubs, trees, vines, aquatics, succulents, 1To whom correspondence should be addressed. E-mail: [email protected]fl.edu. and parasites. The rosid clade also contains novel biochemical This article contains supporting information online at www.pnas.org/cgi/content/full/ pathways, such as the machinery necessary for symbiosis with 0813376106/DCSupplemental. www.pnas.org͞cgi͞doi͞10.1073͞pnas.0813376106 PNAS Early Edition ͉ 1of6 Downloaded by guest on September 30, 2021 relationships remain unclear. Myrtales are often resolved as sister to all other rosids, which in turn form 2 large clades, Fabidae and to Fabidae, whereas Crossosomatales and Geraniales appear with an expanded Malvidae, each with a bootstrap value of 100%. Malvidae, but without strong support (1, 2, 10). Furthermore, the The approximately unbiased (AU) topology test indicated that placements of several problematic families—Aphloiaceae, Apo- the sister relationship of Zygophyllales to Malvidae observed in MP danthaceae, Geissolomataceae, Huaceae, Ixerbaceae, Picramni- can be rejected (P Ͻ 0.001) in favor of the ML placement of aceae, and Strasburgeriaceae—also need to be ascertained. Zygophyllales as sister to an expanded Fabidae using both the total Rosid diversification, like angiosperm phylogeny as a whole, is evidence dataset and the 12 targeted genes dataset. characterized by repeating patterns of radiation from deep to shallow levels (2). Lack of resolution at the base of the rosid Divergence Time Estimates. Cross-validation determined a smooth- phylogeny in previous studies suggests an early radiation of crown- ing value of 1,000 for each of the penalized likelihood (PL) analyses. group rosids into major clades. Similar polytomies are evident In general, when the root of the tree was fixed to an age of 125 Mya, within both Fabidae and Malvidae and within clades further nested age estimates were an average of 5–10 million years older than when within Fabidae (i.e., Malpighiales). However, it is unclear whether the root was constrained to a maximum age of 125 Mya (Table 1). the apparent radiations within the rosids are real or merely artifacts Likewise, based on the bootstrap estimates of variation, the 2 due to poorly resolved relationships. Improved analysis of phylog- different methods usually did not fall within
Load more

Recommended publications
  • 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
    [Show full text]
  • Arthur Monrad Johnson Colletion of Botanical Drawings
    http://oac.cdlib.org/findaid/ark:/13030/kt7489r5rb No online items Arthur Monrad Johnson colletion of botanical drawings 1914-1941 Processed by Pat L. Walter. Louise M. Darling Biomedical Library History and Special Collections Division History and Special Collections Division UCLA 12-077 Center for Health Sciences Box 951798 Los Angeles, CA 90095-1798 Phone: 310/825-6940 Fax: 310/825-0465 Email: [email protected] URL: http://www.library.ucla.edu/libraries/biomed/his/ ©2008 The Regents of the University of California. All rights reserved. Arthur Monrad Johnson colletion 48 1 of botanical drawings 1914-1941 Descriptive Summary Title: Arthur Monrad Johnson colletion of botanical drawings, Date (inclusive): 1914-1941 Collection number: 48 Creator: Johnson, Arthur Monrad 1878-1943 Extent: 3 boxes (2.5 linear feet) Repository: University of California, Los Angeles. Library. Louise M. Darling Biomedical Library History and Special Collections Division Los Angeles, California 90095-1490 Abstract: Approximately 1000 botanical drawings, most in pen and black ink on paper, of the structural parts of angiosperms and some gymnosperms, by Arthur Monrad Johnson. Many of the illustrations have been published in the author's scientific publications, such as his "Taxonomy of the Flowering Plants" and articles on the genus Saxifraga. Dr. Johnson was both a respected botanist and an accomplished artist beyond his botanical subjects. Physical location: Collection stored off-site (Southern Regional Library Facility): Advance notice required for access. Language of Material: Collection materials in English Preferred Citation [Identification of item], Arthur Monrad Johnson colletion of botanical drawings (Manuscript collection 48). Louise M. Darling Biomedical Library History and Special Collections Division, University of California, Los Angeles.
    [Show full text]
  • Alphabetical Lists of the Vascular Plant Families with Their Phylogenetic
    Colligo 2 (1) : 3-10 BOTANIQUE Alphabetical lists of the vascular plant families with their phylogenetic classification numbers Listes alphabétiques des familles de plantes vasculaires avec leurs numéros de classement phylogénétique FRÉDÉRIC DANET* *Mairie de Lyon, Espaces verts, Jardin botanique, Herbier, 69205 Lyon cedex 01, France - [email protected] Citation : Danet F., 2019. Alphabetical lists of the vascular plant families with their phylogenetic classification numbers. Colligo, 2(1) : 3- 10. https://perma.cc/2WFD-A2A7 KEY-WORDS Angiosperms family arrangement Summary: This paper provides, for herbarium cura- Gymnosperms Classification tors, the alphabetical lists of the recognized families Pteridophytes APG system in pteridophytes, gymnosperms and angiosperms Ferns PPG system with their phylogenetic classification numbers. Lycophytes phylogeny Herbarium MOTS-CLÉS Angiospermes rangement des familles Résumé : Cet article produit, pour les conservateurs Gymnospermes Classification d’herbier, les listes alphabétiques des familles recon- Ptéridophytes système APG nues pour les ptéridophytes, les gymnospermes et Fougères système PPG les angiospermes avec leurs numéros de classement Lycophytes phylogénie phylogénétique. Herbier Introduction These alphabetical lists have been established for the systems of A.-L de Jussieu, A.-P. de Can- The organization of herbarium collections con- dolle, Bentham & Hooker, etc. that are still used sists in arranging the specimens logically to in the management of historical herbaria find and reclassify them easily in the appro- whose original classification is voluntarily pre- priate storage units. In the vascular plant col- served. lections, commonly used methods are systema- Recent classification systems based on molecu- tic classification, alphabetical classification, or lar phylogenies have developed, and herbaria combinations of both.
    [Show full text]
  • Medicinal Practices of Sacred Natural Sites: a Socio-Religious Approach for Successful Implementation of Primary
    Medicinal practices of sacred natural sites: a socio-religious approach for successful implementation of primary healthcare services Rajasri Ray and Avik Ray Review Correspondence Abstract Rajasri Ray*, Avik Ray Centre for studies in Ethnobiology, Biodiversity and Background: Sacred groves are model systems that Sustainability (CEiBa), Malda - 732103, West have the potential to contribute to rural healthcare Bengal, India owing to their medicinal floral diversity and strong social acceptance. *Corresponding Author: Rajasri Ray; [email protected] Methods: We examined this idea employing ethnomedicinal plants and their application Ethnobotany Research & Applications documented from sacred groves across India. A total 20:34 (2020) of 65 published documents were shortlisted for the Key words: AYUSH; Ethnomedicine; Medicinal plant; preparation of database and statistical analysis. Sacred grove; Spatial fidelity; Tropical diseases Standard ethnobotanical indices and mapping were used to capture the current trend. Background Results: A total of 1247 species from 152 families Human-nature interaction has been long entwined in has been documented for use against eighteen the history of humanity. Apart from deriving natural categories of diseases common in tropical and sub- resources, humans have a deep rooted tradition of tropical landscapes. Though the reported species venerating nature which is extensively observed are clustered around a few widely distributed across continents (Verschuuren 2010). The tradition families, 71% of them are uniquely represented from has attracted attention of researchers and policy- any single biogeographic region. The use of multiple makers for its impact on local ecological and socio- species in treating an ailment, high use value of the economic dynamics. Ethnomedicine that emanated popular plants, and cross-community similarity in from this tradition, deals health issues with nature- disease treatment reflects rich community wisdom to derived resources.
    [Show full text]
  • Introduction to Common Native & Invasive Freshwater Plants in Alaska
    Introduction to Common Native & Potential Invasive Freshwater Plants in Alaska Cover photographs by (top to bottom, left to right): Tara Chestnut/Hannah E. Anderson, Jamie Fenneman, Vanessa Morgan, Dana Visalli, Jamie Fenneman, Lynda K. Moore and Denny Lassuy. Introduction to Common Native & Potential Invasive Freshwater Plants in Alaska This document is based on An Aquatic Plant Identification Manual for Washington’s Freshwater Plants, which was modified with permission from the Washington State Department of Ecology, by the Center for Lakes and Reservoirs at Portland State University for Alaska Department of Fish and Game US Fish & Wildlife Service - Coastal Program US Fish & Wildlife Service - Aquatic Invasive Species Program December 2009 TABLE OF CONTENTS TABLE OF CONTENTS Acknowledgments ............................................................................ x Introduction Overview ............................................................................. xvi How to Use This Manual .................................................... xvi Categories of Special Interest Imperiled, Rare and Uncommon Aquatic Species ..................... xx Indigenous Peoples Use of Aquatic Plants .............................. xxi Invasive Aquatic Plants Impacts ................................................................................. xxi Vectors ................................................................................. xxii Prevention Tips .................................................... xxii Early Detection and Reporting
    [Show full text]
  • Actinorhizal Plants of Kumaun Himalaya and Their Ecological
    International Scholars Journals Advances in Agriculture and Agricultural Sciences ISSN 2381-3911 Vol. 6 (7), pp. 001-006, July, 2020. Available online at www.internationalscholarsjournals.org © International Scholars Journals Author(s) retain the copyright of this article. Full Length Research Paper Actinorhizal plants of Kumaun Himalaya and their ecological significance Kiran Bargali Department of Botany, Kumaun University (K.U.) Nainital-263002, Uttarakhand, India. E-mail: [email protected] Accepted 21 June, 2020 Actinorhizal plants are important in having symbiotic association with actinomycete Frankia. Nitrogen (N) fixation by actinorhizal plants is a major source of fixed N in diverse and widespread ecosystems including forests, bogs, swamps, coastal dunes, landslides, glacial deposits, shrublands, prairies and deserts. They play important roles in wild land ecosystem function and are used in land reclamation, range management, forestry, agroforestry and horticulture. In this study, 8 actinorhizal plants of Kumaun Himalayan region have been described. Habit, habitat, distribution and possible ecological significance of these plants are also described. These plants are not only important for the restoration of degraded lands, but also provide good source of timber, fuel wood, fodder, food and medicines, etc. Key words: Actinorhizal, degraded, nitrogen, plantation, reclamation. INTRODUCTION Frankia, a filamentous bacterium (actinomycete), forms In the present study, an attempt has been made to nodule like symbiotic associations with the roots of several identify the actinorhizal plants growing in Kumaun plant species known collectively as "Actinorhizal plant". The Himalayan region. The recent application of plant actinorhizal symbiosis have been reported in numerous nitrogen fixation in ecosystem is a key step to understand plants all over the word except Antartica (Baker and its implications in ecological conservation, and future Schwinterzer, 1990).
    [Show full text]
  • Aquatic Vascular Plant Species Distribution Maps
    Appendix 11.5.1: Aquatic Vascular Plant Species Distribution Maps These distribution maps are for 116 aquatic vascular macrophyte species (Table 1). Aquatic designation follows habitat descriptions in Haines and Vining (1998), and includes submergent, floating and some emergent species. See Appendix 11.4 for list of species. Also included in Appendix 11.4 is the number of HUC-10 watersheds from which each taxon has been recorded, and the county-level distributions. Data are from nine sources, as compiled in the MABP database (plus a few additional records derived from ancilliary information contained in reports from two fisheries surveys in the Upper St. John basin organized by The Nature Conservancy). With the exception of the University of Maine herbarium records, most locations represent point samples (coordinates were provided in data sources or derived by MABP from site descriptions in data sources). The herbarium data are identified only to township. In the species distribution maps, town-level records are indicated by center-points (centroids). Figure 1 on this page shows as polygons the towns where taxon records are identified only at the town level. Data Sources: MABP ID MABP DataSet Name Provider 7 Rare taxa from MNAP lake plant surveys D. Cameron, MNAP 8 Lake plant surveys D. Cameron, MNAP 35 Acadia National Park plant survey C. Greene et al. 63 Lake plant surveys A. Dieffenbacher-Krall 71 Natural Heritage Database (rare plants) MNAP 91 University of Maine herbarium database C. Campbell 183 Natural Heritage Database (delisted species) MNAP 194 Rapid bioassessment surveys D. Cameron, MNAP 207 Invasive aquatic plant records MDEP Maps are in alphabetical order by species name.
    [Show full text]
  • Ailanthus Excelsa Roxb
    Ailanthus excelsa Roxb. Simaroubaceae maharukh LOCAL NAMES Arabic (ailanthus,neem hindi); English (ailanthus,coramandel ailanto,tree- of-heaven); Gujarati (aduso,ardusi,bhutrakho); Hindi (maharuk,ardu,ardusi,arua,horanim maruk,aduso,mahanim,mahrukh,maruf,pedu,Pee vepachettu,pir nim); Nepali (maharukh); Sanskrit (madala); Tamil (periamaram,peru,perumaran,pimaram,pinari); Trade name (maharukh) BOTANIC DESCRIPTION Ailanthus excelsa is a large deciduous tree, 18-25 m tall; trunk straight, 60-80 cm in diameter; bark light grey and smooth, becoming grey-brown and rough on large trees, aromatic, slightly bitter. Leaves alternate, pinnately compound, large, 30-60 cm or more in length; leaflets 8-14 or more pairs, long stalked, ovate or broadly lance shaped from very unequal base, 6-10 cm long, 3-5 cm wide, often curved, long pointed, hairy gland; edges coarsely toothed and often lobed. Flower clusters droop at leaf bases, shorter than leaves, much branched; flowers many, mostly male and female on different trees, short stalked, greenish-yellow; calyx 5 lobed; 5 narrow petals spreading 6 mm across; stamens 10; on other flowers, 2-5 separate pistils, each with elliptical ovary, 1 ovule, and slender style. Fruit a 1-seeded samara, lance shaped, flat, pointed at ends, 5 cm long, 1 cm wide, copper red, strongly veined, twisted at the base The generic name ‘Ailanthus’ comes from ‘ailanthos’ (tree of heaven), the Indonesian name for Ailanthus moluccana. BIOLOGY The flowers appear in large open clusters among the leaves towards the end of the cold season. Male, female and bisexual flowers are intermingled on the same tree. The fruits ripen just before the onset of the monsoon.
    [Show full text]
  • Plant Conservation Alliance®S Alien Plant Working Group Tree of Heaven Ailanthus Altissima (Mill.) Swingle Quassia Family (Sima
    FACT SHEET: TREE OF HEAVEN Tree of Heaven Ailanthus altissima (Mill.) Swingle Quassia family (Simaroubaceae) NATIVE RANGE Central China DESCRIPTION Tree-of-heaven, also known as ailanthus, Chinese sumac, and stinking shumac, is a rapidly growing, deciduous tree in the mostly tropical quassia family (Simaroubaceae). Mature trees can reach 80 feet or more in height. Ailanthus has smooth stems with pale gray bark, and twigs which are light chestnut brown, especially in the dormant season. Its large compound leaves, 1-4 feet in length, are composed of 11-25 smaller leaflets and alternate along the stems. Each leaflet has one to several glandular teeth near the base. In late spring, clusters of small, yellow-green flowers appear near the tips of branches. Seeds are produced on female trees in late summer to early fall, in flat, twisted, papery structures called samaras, which may remain on the trees for long periods of time. The wood of ailanthus is soft, weak, coarse-grained, and creamy white to light brown in color. All parts of the tree, especially the flowers, have a strong, offensive odor, which some have likened to peanuts or cashews. NOTE: Correct identification of ailanthus is essential. Several native shrubs, like sumacs, and trees, like ash, black walnut and pecan, can be confused with ailanthus. Staghorn sumac (Rhus typhina), native to the eastern U.S., is distinguished from ailanthus by its fuzzy, reddish-brown branches and leaf stems, erect, red, fuzzy fruits, and leaflets with toothed margins. ECOLOGICAL THREAT Tree-of-heaven is a prolific seed producer, grows rapidly, and can overrun native vegetation.
    [Show full text]
  • Plant Life Magill’S Encyclopedia of Science
    MAGILLS ENCYCLOPEDIA OF SCIENCE PLANT LIFE MAGILLS ENCYCLOPEDIA OF SCIENCE PLANT LIFE Volume 4 Sustainable Forestry–Zygomycetes Indexes Editor Bryan D. Ness, Ph.D. Pacific Union College, Department of Biology Project Editor Christina J. Moose Salem Press, Inc. Pasadena, California Hackensack, New Jersey Editor in Chief: Dawn P. Dawson Managing Editor: Christina J. Moose Photograph Editor: Philip Bader Manuscript Editor: Elizabeth Ferry Slocum Production Editor: Joyce I. Buchea Assistant Editor: Andrea E. Miller Page Design and Graphics: James Hutson Research Supervisor: Jeffry Jensen Layout: William Zimmerman Acquisitions Editor: Mark Rehn Illustrator: Kimberly L. Dawson Kurnizki Copyright © 2003, by Salem Press, Inc. All rights in this book are reserved. No part of this work may be used or reproduced in any manner what- soever or transmitted in any form or by any means, electronic or mechanical, including photocopy,recording, or any information storage and retrieval system, without written permission from the copyright owner except in the case of brief quotations embodied in critical articles and reviews. For information address the publisher, Salem Press, Inc., P.O. Box 50062, Pasadena, California 91115. Some of the updated and revised essays in this work originally appeared in Magill’s Survey of Science: Life Science (1991), Magill’s Survey of Science: Life Science, Supplement (1998), Natural Resources (1998), Encyclopedia of Genetics (1999), Encyclopedia of Environmental Issues (2000), World Geography (2001), and Earth Science (2001). ∞ The paper used in these volumes conforms to the American National Standard for Permanence of Paper for Printed Library Materials, Z39.48-1992 (R1997). Library of Congress Cataloging-in-Publication Data Magill’s encyclopedia of science : plant life / edited by Bryan D.
    [Show full text]
  • Integrating Local Knowledge with Tree Diversity Analyses to Optimize On
    Agroforest Syst (2019) 93:755–770 https://doi.org/10.1007/s10457-017-0172-8 Integrating local knowledge with tree diversity analyses to optimize on-farm tree species composition for ecosystem service delivery in coffee agroforestry systems of Uganda Hannington Bukomeko . Laurence Jassogne . Susan Balaba Tumwebaze . Gerald Eilu . Philippe Vaast Received: 16 December 2016 / Accepted: 5 December 2017 / Published online: 8 December 2017 Ó The Author(s) 2017. This article is an open access publication Abstract Coffee agroforestry systems deliver of importance to their livelihoods (‘Needs rank’) and ecosystem services (ES) critical for rural livelihoods ranked trees according to suitability for providing ES. like food but also disservices that constrain livelihoods Using Bradley Terry modeling, we grouped trees into like fostering coffee-pests. Since such ES are tree- ‘ES groups’ according to suitability for providing based, maximizing ES and limiting constraints different ES and ranked ‘ES groups’ according to tree requires knowledge on optimizing on-farm tree com- diversity (‘Diversity rank’). Tree-suitability for pro- position especially trees adapted to local conditions. viding ES and importance of ES to farmers varied with The study was in three sites along a rainfall gradient in rainfall regime but tree diversity did not match Central Uganda where we: assessed tree diversity in farmers’ needs for ES. We propose the FaD–FaN coffee agroforestry; ranked tree suitability for provid- (matching farm tree diversity to farmers’ needs) ing ES according to farmers’ knowledge; and then approach for optimizing tree species composition with proposed an approach for optimizing on-farm tree respect to tree-suitability for farmers’ priority ES.
    [Show full text]
  • 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.
    [Show full text]