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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. -
(Leguminosae): Nomenclatural Proposals and New Taxa
Great Basin Naturalist Volume 58 Number 1 Article 5 1-30-1998 Astragalus (Leguminosae): nomenclatural proposals and new taxa Stanley L. Welsh Brigham Young University Follow this and additional works at: https://scholarsarchive.byu.edu/gbn Recommended Citation Welsh, Stanley L. (1998) "Astragalus (Leguminosae): nomenclatural proposals and new taxa," Great Basin Naturalist: Vol. 58 : No. 1 , Article 5. Available at: https://scholarsarchive.byu.edu/gbn/vol58/iss1/5 This Article is brought to you for free and open access by the Western North American Naturalist Publications at BYU ScholarsArchive. It has been accepted for inclusion in Great Basin Naturalist by an authorized editor of BYU ScholarsArchive. For more information, please contact [email protected], [email protected]. Great Basin Naturalist 58(1), © 1998, pp. 45-53 ASTRAGALUS (LEGUMINOSAE): NOMENCLATURAL PROPOSALS AND NEW TAXA Stanley L. Welsh! ABSTRACT.-As part of an ongoing summary revision of Astragalus for the Flora North America project, several nomenclatural changes are indicated. Nomenclatural proposals include A. molybdenus val'. shultziorom (Barneby) Welsh, comb. nov.; A. australis var. aboriginorom (Richardson) Welsh, comb. nov.; A. australis var. cattoni (M.E. Jones) Welsh, comb. nov.; A. aU8tralis var. lepagei (Hulten) Welsh, comb. nov; A. australis var. muriei (Hulten) Welsh, comb. nov.; A. subcinereus var. sileranus (M.E. Jones) Welsh, comb. nov.; A. tegetariaides val'. anxius (Meinke & Kaye) Welsh, comb. nov.; A. ampullarioides (Welsh) Welsh, comb. nov.; A. cutlen (Barneby) Welsh, comb. nov.; and A. laccaliticus (M.E. Jones) Welsh, comb. nov. Proposals of new taxa include Astragalus sect. Scytocarpi subsect. Micl'ocymbi Welsh, subsed. nov., and A. sabulosus var. -
Colorado Wildlife Action Plan: Proposed Rare Plant Addendum
Colorado Wildlife Action Plan: Proposed Rare Plant Addendum By Colorado Natural Heritage Program For The Colorado Rare Plant Conservation Initiative June 2011 Colorado Wildlife Action Plan: Proposed Rare Plant Addendum Colorado Rare Plant Conservation Initiative Members David Anderson, Colorado Natural Heritage Program (CNHP) Rob Billerbeck, Colorado Natural Areas Program (CNAP) Leo P. Bruederle, University of Colorado Denver (UCD) Lynn Cleveland, Colorado Federation of Garden Clubs (CFGC) Carol Dawson, Bureau of Land Management (BLM) Michelle DePrenger-Levin, Denver Botanic Gardens (DBG) Brian Elliott, Environmental Consulting Mo Ewing, Colorado Open Lands (COL) Tom Grant, Colorado State University (CSU) Jill Handwerk, Colorado Natural Heritage Program (CNHP) Tim Hogan, University of Colorado Herbarium (COLO) Steve Kettler, U.S. Fish and Wildlife Service (USFWS) Andrew Kratz, U.S. Forest Service (USFS) Sarada Krishnan, Colorado Native Plant Society (CoNPS), Denver Botanic Gardens Brian Kurzel, Colorado Natural Areas Program Eric Lane, Colorado Department of Agriculture (CDA) Paige Lewis, The Nature Conservancy (TNC) Ellen Mayo, U.S. Fish and Wildlife Service Mitchell McGlaughlin, University of Northern Colorado (UNC) Jennifer Neale, Denver Botanic Gardens Betsy Neely, The Nature Conservancy Ann Oliver, The Nature Conservancy Steve Olson, U.S. Forest Service Susan Spackman Panjabi, Colorado Natural Heritage Program Jeff Peterson, Colorado Department of Transportation (CDOT) Josh Pollock, Center for Native Ecosystems (CNE) Nicola Ripley, -
THESE Organisation Du Génome Et Étude Palynologique De Quelques
REPUBLIQUE ALGERIENNE DEMOCRATIQUE ΔϳΑόѧѧѧѧѧѧѧѧѧѧѧѧѧηϟ ΔѧѧѧѧѧѧѧѧѧѧѧϳρέϗϭϣϳΩϟ ΔѧѧѧѧѧѧѧѧѧϳέίΟϟ ΔѧѧѧѧϳέϭϬϣΟϟ ET POPULAIRE ϲѧѧѧѧѧѧѧϣϠόϟ ΙѧѧѧѧѧѧѧΣΑϟ ϭ ϲϟΎѧѧѧѧѧѧѧόϟ ϡѧѧѧѧѧѧѧѧѧѧѧѧѧѧϳϠόΗϟ Γέίϭ MINISTERE DE L’ENSEIGNEMENT SUPÉRIEUR 1 ΔϧϳρϧѧѧѧѧѧѧѧѧѧѧѧѧγϗΔόϣΎΟ ET DE LA RECHERCHE SCIENTIFIQUE UNIVERSITE CONSTANTINE 1 Faculté des Sciences de la Nature et de la Vie Département de Biologie et Ecologie Végétale THESE Présentée en vue de l’obtention du diplôme de DOCTORAT EN SCIENCES Option: Biotechnologies végétales Par KARIM BAZIZ Thème Organisation du génome et étude palynologique de quelques espèces algériennes du genre Astragalus L Soutenue le 12 Février 2015 Devant le jury: Président : Mr D. KHELIFI Professeur à l’université de Constantine 1 Encadrant : Mme N. KHALFALLAH Professeur à l’université de Constantine 1 Co- Encadrant : Mme S. SILJAK-YAKOVLEV Professeur à l’université de Paris Sud Examinateurs : Mme D. SATTA Professeur à l’université de Constantine 1 Mr R. AMIROUCHE Professeur à l’USTHB, FSB Mr M. KAABECHE Professeur à l’université de Sétif 1 ANNEE UNIVERSITAIRE 2014 – 2015 Dédicace Cette thèse représente l’aboutissement du soutien et des encouragements que mes parents m’ont prodigués tout au long de ma scolarité. La patience et l’encouragement de mon épouse qui m’ont aidé à surmonter toutes les difficultés rencontrées au cours de cette thèse. A mon petit garçon ADEM A mon frère MOUNIR et mes deux sœurs NADJET et NASSIMA REMERCIEMENTS A Madame la Professeur NADRA KHALFALLAH, mon encadrant et directeur de thèse. Je vous serai toujours reconnaissant pour vos avis indispensables, vos conseils éclairés et pour votre disponibilité. Vous m'avez fait bénéficier de vos connaissances, de votre immense expérience scientifique et de votre rigueur dans le travail. -
US Fish and Wildlife Service
BARNEBY REED-MUSTARD (S. barnebyi ) CLAY REED-MUSTARD SHRUBBY REED-MUSTARD (S,arguillacea) (S. suffrutescens) .-~ U.S. Fish and Wildlife Service UTAH REED—MUSTARDS: CLAY REED-MUSTARD (SCHOENOCRAMBE ARGILLACEA) BARNEBY REED—MUSTARD (SCHOENOCRAMBE BARNEBYI) SI-IRUBBY REED-MUSTARD (SCHOENOCRAMBE SUFFRUTESCENS) RECOVERY PLAN Prepared by Region 6, U.S. Fish and Wildlife Service Approved: Date: (~19~- Recovery plans delineate reasonable actions which are believed to be required to recover and/or protect the species. Plans are prepared by the U.S. Fish and Wildlife Service, sometimes with the assistance of recovery teams, contractors, State agencies, and others. Objectives will only be attained and funds expended contingent upon appropriations, priorities, and other budgetary constraints. Recovery plans do not necessarily represent the views or the official positions or approvals of any individuals or agencies, other than the U.S. Fish and Wildlife Service, involved in the plan formulation. They represent the official position of the U.S. Fish and Wildlife Service only after they have been signed by the Regional Director or Director as an~roved Approved recovery plans are subject to modification as dictated by new findings, changes in species status, and the completion of recovery tasks. Literature Citation should read as follows: U.S. Fish and Wildlife Service. 1994. Utah reed—mustards: clay reed—mustard (Schoenocrambe argillacea), Barneby reed-mustard (Schoenocrambe barnebyl), shrubby reed—mustard (Schoenacranibe suffrutescens) recovery plan. Denver, Colorado. 22 pp. Additional copies may be purchased from: Fish and Wildlife Reference Service 5430 Grosvenor Lane, Suite 110 Bethesda, Maryland 20814 Telephone: 301/492—6403 or 1—800—582—3421 The fee for the plan varies depending on the number of pages of the plan. -
PCA) Report Name Mosquito Range Site Code S.USCOHP*375
Level 4 Potential Conservation Area (PCA) Report Name Mosquito Range Site Code S.USCOHP*375 IDENTIFIERS Site ID 342 Site Class PCA Site Alias Mosquito Peaks Cirques Macrosite Site Alias Hoosier Ridge Macrosite Site Alias Tenmile Macrosite Site Alias Mosquito Peaks Megasite Network of Conservation Areas (NCA) NCA Site ID NCA Site Code NCA Site Name - No Data County SITE DESCRIPTION Site Description This site incorporates nearly the entire alpine area of the Mosquito Range. The predominant habitats are characterized by alpine meadows, rock outcrops, scree slopes, boulder fields, alpine lakes, willow carrs, snowmelt streamlets, and permanent snow fields. Snow melt flows down the north and south-facing slopes in intermittent drainages from the top of the ridges. The slopes are typified by tufted hairgrass / golden avens (Deschampsia cespitosa / Geum rossii) and kobresia / golden avens (Kobresia myosuroides / Geum rossii) communities, with scattered patches of willows (Salix glauca and Salix brachycarpa) and krummholz Engelmann spruce (Picea engelmannii). Moist areas with mossy ground cover provide the necessary habitat for Penland alpine fen mustard (Eutrema penlandii), which is one of the elements of primary importance in this site. This site supports an extraordinarily high concentration of rare plant species. To date, 20 globally rare plant species and several state rare species have been documented within this site. High elevation outcrops of Leadville Limestone are said to be a predominant factor in setting the stage for such high densities of rare plant species. Many of the rarest plants in this site, including Penland alpine fen mustard, are thought to be restricted to this geologic substrate. -
CONPS Fall Newsletter.Indd
Aquilegia Newsletter of the Colorado Native Plant Society “. dedicated to the appreciation and conservation of the Colorado native flora” Volume 30 Number 4 WORKSHOP EDITION September - October 2006 2006 - 2007 COLORADO NATIVE PLANT SOCIETY WORKSHOP PROGRAM Workshops will be held each month from September through May Microscope Fund along the Front Range. Most workshops will be held in Boulder New microscopes for CONPS workshops are desperately needed! but we are actively seeking members from the West Slope, Fort Learning about plants is much more enjoyable when you can see Collins, Denver and Colorado Springs who would be willing to each trichome, pollinium or involucre. The increase in registra- coordinate one or two workshops a year in those areas. Contact tion fee (from $12 to $20) goes directly to the Microscope Fund. Mary Ellen Ford if you are interested ([email protected] or You can also contribute to the Microscope Fund by mailing con- 303-449-7334). tributions (payable to CONPS) to Mary Ellen Ford. Registration Information Workshops Registration is mail-in only and requires payment at the time of registration. The fee for attending a workshop is $20 per session COLORADO WILDSCAPES: for members only. Non-members must join CONPS to register BRINGING CONSERVATION HOME for a workshop. The registration fee is non-refundable. Leader: Connie Holsinger of Audubon Colorado Location: Foothills Nature Center, Boulder Participation is often limited and registration is processed in the Only Session: September 23, 2006 Time: 9 am to noon order received. If the workshop has already been filled, you will be notified, your check will not be deposited, and you will be Using the beautiful and practical guidebook, Colorado added to the waiting list if that is what you desire. -
KEYSTONE XL PIPELINE PROJECT: Rare Plants and Rare Ecological
KEYSTONE XL PIPELINE PROJECT Rare Plants and Rare Ecological Communities (Condition 8) KXL1399-STCE-EN-RP-0002 Rev C January 2019 Prepared for: TransCanada Keystone Pipeline Limited Partnership A Wholly Owned Subsidiary of TransCanada PipeLines Limited Calgary, Alberta Prepared by: Stantec Consulting Ltd. Calgary, Alberta KEYSTONE XL PIPELINE PROJECT RARE PLANTS AND RARE ECOLOGICAL COMMUNITIES (CONDITION 8) Table of Contents EXECUTIVE SUMMARY ............................................................................................................... I ABBREVIATIONS ....................................................................................................................... III 1.0 INTRODUCTION ............................................................................................................ 1.1 2.0 SURVEY METHODS ..................................................................................................... 2.1 2.1 SUMMARY OF PREVIOUS SURVEYS ......................................................................... 2.1 2.1.1 Previous Rare Plants .................................................................................... 2.1 2.1.2 Previous Rare Ecological Communities ....................................................... 2.2 2.1.3 Other Data Sources ...................................................................................... 2.2 2.2 2017 SURVEYS ............................................................................................................. 2.2 2.2.1 Rare Plants .................................................................................................. -
The Evolutionary Dynamics of Genes and Genomes: Copy Number Variation of the Chalcone Synthase Gene in the Context of Brassicaceae Evolution
The Evolutionary Dynamics of Genes and Genomes: Copy Number Variation of the Chalcone Synthase Gene in the Context of Brassicaceae Evolution Dissertation submitted to the Combined Faculties for Natural Sciences and for Mathematics of the Ruperto-Carola University of Heidelberg, Germany for the degree of Doctor of Natural Sciences presented by Liza Paola Ding born in Mosbach, Baden-Württemberg, Germany Oral examination: 22.12.2014 Referees: Prof. Dr. Marcus A. Koch Prof. Dr. Claudia Erbar Table of contents INTRODUCTION ............................................................................................................. 18 1 THE MUSTARD FAMILY ....................................................................................... 19 2 THE TRIBAL SYSTEM OF THE BRASSICACEAE ........................................... 22 3 CHALCONE SYNTHASE ........................................................................................ 23 PART 1: TROUBLE WITH THE OUTGROUP............................................................ 27 4 MATERIAL AND METHODS ................................................................................. 28 4.1 Experimental set-up ......................................................................................................................... 28 4.1.1 Plant material and data composition .............................................................................................. 28 4.1.2 DNA extraction and PCR amplification ........................................................................................ -
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. -
Annotated Checklist of Vascular Flora, Bryce
National Park Service U.S. Department of the Interior Natural Resource Program Center Annotated Checklist of Vascular Flora Bryce Canyon National Park Natural Resource Technical Report NPS/NCPN/NRTR–2009/153 ON THE COVER Matted prickly-phlox (Leptodactylon caespitosum), Bryce Canyon National Park, Utah. Photograph by Walter Fertig. Annotated Checklist of Vascular Flora Bryce Canyon National Park Natural Resource Technical Report NPS/NCPN/NRTR–2009/153 Author Walter Fertig Moenave Botanical Consulting 1117 W. Grand Canyon Dr. Kanab, UT 84741 Sarah Topp Northern Colorado Plateau Network P.O. Box 848 Moab, UT 84532 Editing and Design Alice Wondrak Biel Northern Colorado Plateau Network P.O. Box 848 Moab, UT 84532 January 2009 U.S. Department of the Interior National Park Service Natural Resource Program Center Fort Collins, Colorado The Natural Resource Publication series addresses natural resource topics that are of interest and applicability to a broad readership in the National Park Service and to others in the management of natural resources, including the scientifi c community, the public, and the NPS conservation and environmental constituencies. Manuscripts are peer-reviewed to ensure that the information is scientifi cally credible, technically accurate, appropriately written for the intended audience, and is designed and published in a professional manner. The Natural Resource Technical Report series is used to disseminate the peer-reviewed results of scientifi c studies in the physical, biological, and social sciences for both the advancement of science and the achievement of the National Park Service’s mission. The reports provide contributors with a forum for displaying comprehensive data that are often deleted from journals because of page limitations. -
Sensitive and Rare Plant Species Inventory in the Salt River and Wyoming Ranges, Bridger-Teton National Forest
Sensitive and Rare Plant Species Inventory in the Salt River and Wyoming Ranges, Bridger-Teton National Forest Prepared for Bridger-Teton National Forest P.O. Box 1888 Jackson, WY 83001 by Bonnie Heidel Wyoming Natural Diversity Database University of Wyoming Dept 3381, 1000 E. University Avenue University of Wyoming Laramie, WY 21 February 2012 Cooperative Agreement No. 07-CS-11040300-019 ABSTRACT Three sensitive and two other Wyoming species of concern were inventoried in the Wyoming and Salt River Ranges at over 20 locations. The results provided a significant set of trend data for Payson’s milkvetch (Astragalus paysonii), expanded the known distribution of Robbin’s milkvetch (Astragalus robbinsii var. minor), and relocated and expanded the local distributions of three calciphilic species at select sites as a springboard for expanded surveys. Results to date are presented with the rest of species’ information for sensitive species program reference. This report is submitted as an interim report representing the format of a final report. Tentative priorities for 2012 work include new Payson’s milkvetch surveys in major recent wildfires, and expanded Rockcress draba (Draba globosa) surveys, both intended to fill key gaps in status information that contribute to maintenance of sensitive plant resources and information on the Forest. ACKNOWLEDGEMENTS All 2011 field surveys of Payson’s milkvetch (Astragalus paysonii) were conducted by Klara Varga. These and the rest of 2011 surveys built on the 2010 work of Hollis Marriott and the earlier work of she and Walter Fertig as lead botanists of Wyoming Natural Diversity Database. This project was initially coordinated by Faith Ryan (Bridger-Teton National Forest), with the current coordination and consultation of Gary Hanvey and Tyler Johnson.