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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. -
Phytochemical and Antimicrobial Studies of Ludwigia Hyssopifolia (G.Don) Exell Thet Su Hlaing1 Abstract Ludwigia Hyssopifolia (G.Don) Exell
2nd Myanmar Korea Conference Research Journal 433 Phytochemical and Antimicrobial Studies of Ludwigia hyssopifolia (G.Don) Exell Thet Su Hlaing1 Abstract Ludwigia hyssopifolia (G.Don) Exell. is annual herb belongs to the family Onagraceae in the order Myrtales. It is locally known as Taw-lay-hnyin. This plant was collected from Hinthada University Campus, Hinthada Township, Ayeyarwaddy Region. The morphological characters of vegetative and reproductive parts of the fresh specimens were investigated with the help of available literatures. The preliminary phytochemical tests were conducted from the powdered sample of the whole plant. The presence of alkaloid, phenolic compound, flavonoid, terpenoid, starch, reducing sugar, glycoside, saponin, tannin, α-amino acid and carbohydrate were found in the examination. Elemental analysis of powdered sample was examined by using EDXRF spectrometer. Percentage of calcium was higher than the other elements.Antimicrobial activities of various crude extracts were carried out by using paper disc diffusion assay with four test organisms. The methanolic extracts exhibited the highest against on different pathogenic microorganisms. These results showed that Ludwigia hyssopifolia (G.Don) Exell is endowed with many active constituents, minerals and antimicrobial properties that can be found useful in medicinal activities as well as possible application in nutrition and pharmacology. Key words : Ludwigia hyssopifolia (G.Don) Exell, phytochemical tests, antimicrobial activity Introduction Ludwigia hyssopifolia (G.Don) Exell. is commonly known as Taw-lay-hnyin in Myanmar and water primrose in English name. It is one of the traditionally used medicinal plants in Myanmar. It is distributed all over the world, particularly in both temperate and tropical regions of the world (Valkenburg, 2002). -
Universidade Federal Do Recôncavo Da Bahia Centro De Ciências Agrárias, Ambientais E Biológicas
UNIVERSIDADE FEDERAL DO RECÔNCAVO DA BAHIA CENTRO DE CIÊNCIAS AGRÁRIAS, AMBIENTAIS E BIOLÓGICAS CARACTERES IMPORTANTES NA IDENTIFICAÇÃO DE ESPÉCIES DE LUDWIGIA L. (ONAGRACEAE) OCORRENTES NO RECÔNCAVO DA BAHIA, BRASIL NELMA XAVIER MARQUES DE SOUSA Bacharel em Biologia CRUZ DAS ALMAS BAHIA – BRASIL 2017 NELMA XAVIER MARQUES DE SOUSA CARACTERES IMPORTANTES NA IDENTIFICAÇÃO DE ESPÉCIES DE LUDWIGIA L. (ONAGRACEAE) OCORRENTES NO RECÔNCAVO DA BAHIA, BRASIL Trabalho de Conclusão de Curso apresentado à Universidade Federal do Recôncavo da Bahia, como parte das exigências do Curso de Graduação de Bacharelado em Biologia, para obtenção do título de Bacharel em Biologia. CRUZ DAS ALMAS BAHIA - BRASIL 2017 NELMA XAVIER MARQUES DE SOUSA CARACTERES IMPORTANTES NA IDENTIFICAÇÃO DE ESPÉCIES DE LUDWIGIA L. (ONAGRACEAE) OCORRENTES NO RECÔNCAVO DA BAHIA, BRASIL Trabalho de Conclusão de Curso apresentado à Universidade Federal do Recôncavo da Bahia, como parte das exigências do Curso de Graduação de Bacharelado em Biologia, para obtenção do título de Bacharel em Biologia. APROVADA: 03 de Fevereiro de 2017 I Dedicatória Aos meus pais (in memoriam), pela sabedoria de ter colocado a educação em primeiro lugar. “O mundo está nas mãos daqueles que têm a coragem de sonhar e de correr o risco de viver seus sonhos.” Paulo Coelho. II AGRADECIMENTOS Minha gratidão a professora Dra. Lidyanne Aona, por ser uma excelente professora e orientadora. Obrigada pelo suporte, por sempre estar presente, contribuindo muito com minha aprendizagem e ajudando-me em todos os trabalhos, pelo carinho que sempre teve comigo e, principalmente, pela paciência. A professora Dra. Ana Odete Vieira pelos ensinamentos, cooperação e importante contribuição. -
Vestured Pits in Wood of Onagraceae: Correlations with Ecology, Habit, and Phylogeny1
VESTURED PITS IN WOOD OF Sherwin Carlquist2 and Peter H. Raven3 ONAGRACEAE: CORRELATIONS WITH ECOLOGY, HABIT, AND PHYLOGENY1 ABSTRACT All Onagraceae for which data are available have vestured pits on vessel-to-vessel pit pairs. Vestures may also be present in some species on the vessel side of vessel-to-ray pit pairs. Herbaceous Onagraceae do not have fewer vestures, although woods with lower density (Circaea L. and Oenothera L.) have fewer vestures. Some Onagraceae from drier areas tend to have smaller vessel pits, and on that account may have fewer vestures (Epilobium L. and Megacorax S. Gonz´alez & W. L. Wagner). Pit apertures as seen on the lumen side of vessel walls are elliptical, occasionally oval, throughout the family. Vestures are predominantly attached to pit aperture margins. As seen from the outer surfaces of vessels, vestures may extend across the pit cavities. Vestures are usually absent or smaller on the distal portions of pit borders (except for Ludwigia L., which grows consistently in wet areas). Distinctive vesture patterns were observed in the several species of Lopezia Cav. and in Xylonagra Donn. Sm. & Rose. Vestures spread onto the lumen-facing vessel walls of Ludwigia octovalvis (Jacq.) P. H. Raven. Although the genera are presented here in the sequence of a recent molecular phylogeny of Onagraceae, ecology and growth forms are more important than evolutionary relationships with respect to abundance, degree of grouping, and morphology of vestured pits. Designation of vesture types is not warranted based on the distribution of named types in Onagraceae and descriptive adjectives seem more useful, although more data on vesturing in the family are needed before patterns of diversity and their extent can be fully ascertained. -
An Assessment of Exotic Species in the Tonle Sap Biosphere Reserve
AN ASSESSMENT OF EXOTIC SPECIES IN THE TONLE SAP BIOSPHERE RESERVE AND ASSOCIATED THREATS TO BIODIVERSITY A RESOURCE DOCUMENT FOR THE MANAGEMENT OF INVASIVE ALIEN SPECIES December 2006 Robert van Zalinge (compiler) This publication is a technical output of the UNDP/GEF-funded Tonle Sap Conservation Project Executive Summary Introduction This report is mainly a literature review. It attempts to put together all the available information from recent biological surveys, and environmental and resource use studies in the Tonle Sap Biosphere Reserve (TSBR) in order to assess the status of exotic species and report any information on their abundance, distribution and impact. For those exotic species found in the TSBR, it is examined whether they can be termed as being an invasive alien species (IAS). IAS are exotic species that pose a threat to native ecosystems, economies and/or human health. It is widely believed that IAS are the second most significant threat to biodiversity worldwide, following habitat destruction. In recognition of the threat posed by IAS the Convention on Biological Diversity puts forward the following strategy to all parties in Article 8h: “each contracting party shall as far as possible and as appropriate: prevent the introduction of, control, or eradicate those alien species which threaten ecosystems, habitats or species”. The National Assembly of Cambodia ratified the Convention on Biological Diversity in 1995. After reviewing the status of exotic species in the Tonle Sap from the literature, as well as the results from a survey based on questionnaires distributed among local communities, the main issues are discussed, possible strategies to combat the spread of alien species that are potentially invasive are examined, and recommendations are made to facilitate the implementation of a strategy towards reducing the impact of these species on the TSBR ecosystem. -
Arbuscular Mycorrhizal Fungi and Dark Septate Fungi in Plants Associated with Aquatic Environments Doi: 10.1590/0102-33062016Abb0296
Arbuscular mycorrhizal fungi and dark septate fungi in plants associated with aquatic environments doi: 10.1590/0102-33062016abb0296 Table S1. Presence of arbuscular mycorrhizal fungi (AMF) and/or dark septate fungi (DSF) in non-flowering plants and angiosperms, according to data from 62 papers. A: arbuscule; V: vesicle; H: intraradical hyphae; % COL: percentage of colonization. MYCORRHIZAL SPECIES AMF STRUCTURES % AMF COL AMF REFERENCES DSF DSF REFERENCES LYCOPODIOPHYTA1 Isoetales Isoetaceae Isoetes coromandelina L. A, V, H 43 38; 39 Isoetes echinospora Durieu A, V, H 1.9-14.5 50 + 50 Isoetes kirkii A. Braun not informed not informed 13 Isoetes lacustris L.* A, V, H 25-50 50; 61 + 50 Lycopodiales Lycopodiaceae Lycopodiella inundata (L.) Holub A, V 0-18 22 + 22 MONILOPHYTA2 Equisetales Equisetaceae Equisetum arvense L. A, V 2-28 15; 19; 52; 60 + 60 Osmundales Osmundaceae Osmunda cinnamomea L. A, V 10 14 Salviniales Marsileaceae Marsilea quadrifolia L.* V, H not informed 19;38 Salviniaceae Azolla pinnata R. Br.* not informed not informed 19 Salvinia cucullata Roxb* not informed 21 4; 19 Salvinia natans Pursh V, H not informed 38 Polipodiales Dryopteridaceae Polystichum lepidocaulon (Hook.) J. Sm. A, V not informed 30 Davalliaceae Davallia mariesii T. Moore ex Baker A not informed 30 Onocleaceae Matteuccia struthiopteris (L.) Tod. A not informed 30 Onoclea sensibilis L. A, V 10-70 14; 60 + 60 Pteridaceae Acrostichum aureum L. A, V, H 27-69 42; 55 Adiantum pedatum L. A not informed 30 Aleuritopteris argentea (S. G. Gmel) Fée A, V not informed 30 Pteris cretica L. A not informed 30 Pteris multifida Poir. -
The Vascular Flora of the Red Hills Forever Wild Tract, Monroe County, Alabama
The Vascular Flora of the Red Hills Forever Wild Tract, Monroe County, Alabama T. Wayne Barger1* and Brian D. Holt1 1Alabama State Lands Division, Natural Heritage Section, Department of Conservation and Natural Resources, Montgomery, AL 36130 *Correspondence: wayne [email protected] Abstract provides public lands for recreational use along with con- servation of vital habitat. Since its inception, the Forever The Red Hills Forever Wild Tract (RHFWT) is a 1785 ha Wild Program, managed by the Alabama Department of property that was acquired in two purchases by the State of Conservation and Natural Resources (AL-DCNR), has pur- Alabama Forever Wild Program in February and Septem- chased approximately 97 500 ha (241 000 acres) of land for ber 2010. The RHFWT is characterized by undulating general recreation, nature preserves, additions to wildlife terrain with steep slopes, loblolly pine plantations, and management areas and state parks. For each Forever Wild mixed hardwood floodplain forests. The property lies tract purchased, a management plan providing guidelines 125 km southwest of Montgomery, AL and is managed by and recommendations for the tract must be in place within the Alabama Department of Conservation and Natural a year of acquisition. The 1785 ha (4412 acre) Red Hills Resources with an emphasis on recreational use and habi- Forever Wild Tract (RHFWT) was acquired in two sepa- tat management. An intensive floristic study of this area rate purchases in February and September 2010, in part was conducted from January 2011 through June 2015. A to provide protected habitat for the federally listed Red total of 533 taxa (527 species) from 323 genera and 120 Hills Salamander (Phaeognathus hubrichti Highton). -
Phytopharmacological Activities of Ludwigia Hyssopifolia (G
Deepak V. S. et al. /Asian Journal of Research in Chemistry and Pharmaceutical Sciences. 7(2), 2019, 781-789. Review Article ISSN: 2349 – 7106 Asian Journal of Research in Chemistry and Pharmaceutical Sciences Journal home page: www.ajrcps.com PHYTOPHARMACOLOGICAL ACTIVITIES OF LUDWIGIA HYSSOPIFOLIA (G. DON) EXELL: A REVIEW V. S. Deepak*1, A. Suresh 1, C. K. Amritha 1, P. Prajitha 1, Hiba Faslu 1 1* Department of Pharmacology, Devaki Amma Memorial College of Pharmacy, Malappuram, Kerala, India. ABSTRACT Ludwigia hyssopifolia (G. Don) Exell, commonly known as the water primrose is a broad leaf weed which is extensively grown in Bangladesh, Ceylon and in all parts of India. In the traditional system of medicine, Ludwigia hyssopifolia have been recommended for the treatment of diarrhoea, dysentery, flatulence, jaundice, spitting of blood, leucorrhoea. The plant has also been suggested to possess astringent, anthelmintic, carminative and diuretic actions. Previous phytochemical investigation of plant revealed the presence of flavonoids like vitexin, isovitexin, orietin, Isorietin, alkaloid like piperine and the plant sterol like β-sitosterol. The present review highlights the taxonomical, botanical, phytoconstituents, pharmacological discussion on Ludwigia hyssopifolia . KEYWORDS Ludwigia hyssopifolia (G. Don) Exell, Onagraceae, Traditional use, Phytochemical constituents, Pharmacological activity and Bioactivity. INTRODUCTON People have been using medicinal plants for various Author for Correspondence: therapeutic purposes since prehistoric period. The knowledge about the traditional use of medicinal plants has always explored the search for new Deepak V S, therapeutic cures. The traditional systems of Department of Pharmacology, treatments with medicinal plants are often cheaper, locally available, simple medicinal preparations Devaki Amma Memorial College of Pharmacy, which bring out beneficial results 1. -
Wingleaf Primrose-Willow (Ludwigia Decurrens) Ecological Risk Screening Summary
Wingleaf Primrose-willow (Ludwigia decurrens) Ecological Risk Screening Summary U.S. Fish and Wildlife Service, May 2021 Revised, June 2021 Web Version, 7/21/2021 Organism Type: Plant Overall Risk Assessment Category: High Photo: Clarence A. Rechenthin, USDA NRCS East Texas PMC. Public domain. Available: https://plants.sc.egov.usda.gov/ImageLibrary/original/lude4_002_php.jpg (June 2021). 1 Native Range and Status in the United States Native Range From Ramamoorthy and Zardini (1987): “[…] from southeastern United States where it is widely distributed from southern Missouri, southern Ohio, and northern Virginia (one collection from southern Wisconsin), south to the 1 Gulf of Mexico and from central Texas and central Oklahoma, east to the Atlantic coast, reappearing in southern Mexico (Chiapas, Tabasco, and Veracruz) and extending south to northeastern Argentina, and east from central Minas Gerais in Brazil west to western Ecuador. Abundant in all countries of Central America except Belize; rare in the West Indies; common in Surinam, Guyana, Venezuela, Colombia, and Ecuador; scattered in Peru and Brazil; more common in Paraguay and northeastern Argentina.” From POWO (2021): “Native to: Alabama, Argentina Northeast, Argentina Northwest, Bolivia, Brazil North, Brazil Northeast, Brazil South, Brazil Southeast, Brazil West-Central, Colombia, Costa Rica, Cuba, Ecuador, French Guiana, Guatemala, Guyana, Honduras, Illinois, Kentucky, Mexico Southeast, Mexico Southwest, Nicaragua, Panamá, Paraguay, Peru, South Carolina, Suriname, Tennessee, Trinidad- Tobago, Uruguay, Venezuela, Windward Is. [a “Botanical Country” including the Lesser Antillean islands of Dominica, Martinique, St. Lucia, St. Vincent and the Grenadines, Barbados, and Grenada]” From Acevedo-Rodríguez and Strong (2012): “Native to […] Lesser Antilles (St. Vincent) […]” According to USDA, NRCS (2021), this species is native to the following U.S. -
Wetland Plants of the Townsville − Burdekin
WETLAND PLANTS OF THE TOWNSVILLE − BURDEKIN Dr Greg Calvert & Laurence Liessmann (RPS Group, Townsville) For Lower Burdekin Landcare Association Incorporated (LBLCA) Working in the local community to achieve sustainable land use THIS PUBLICATION WAS MADE POSSIBLE THROUGH THE SUPPORT OF: Burdekin Shire Council Calvert, Greg Liessmann, Laurence Wetland Plants of the Townsville–Burdekin Flood Plain ISBN 978-0-9925807-0-4 First published 2014 by Lower Burdekin Landcare Association Incorporated (LBLCA) PO Box 1280, Ayr, Qld, 4807 Graphic Design by Megan MacKinnon (Clever Tangent) Printed by Lotsa Printing, Townsville © Lower Burdekin Landcare Association Inc. Copyright protects this publication. Except for purposes permitted under the Copyright Act, reproduction by whatever means is prohibited without prior permission of LBLCA All photographs copyright Greg Calvert Please reference as: Calvert G., Liessmann L. (2014) Wetland Plants of the Townsville–Burdekin Flood Plain. Lower Burdekin Landcare Association Inc., Ayr. The Queensland Wetlands Program supports projects and activities that result in long-term benefits to the sustainable management, wise use and protection of wetlands in Queensland. The tools developed by the Program help wetlands landholders, managers and decision makers in government and industry. The Queensland Wetlands Program is currently funded by the Queensland Government. Disclaimer: This document has been prepared with all due diligence and care, based on the best available information at the time of publication. The authors and funding bodies hold no responsibility for any errors or omissions within this document. Any decisions made by other parties based on this document are solely the responsibility of those parties. Information contained in this document is from a number of sources and, as such, does not necessarily represent government or departmental policy. -
Native Vascular Flora of the City of Alexandria, Virginia
Native Vascular Flora City of Alexandria, Virginia Photo by Gary P. Fleming December 2015 Native Vascular Flora of the City of Alexandria, Virginia December 2015 By Roderick H. Simmons City of Alexandria Department of Recreation, Parks, and Cultural Activities, Natural Resources Division 2900-A Business Center Drive Alexandria, Virginia 22314 [email protected] Suggested citation: Simmons, R.H. 2015. Native vascular flora of the City of Alexandria, Virginia. City of Alexandria Department of Recreation, Parks, and Cultural Activities, Alexandria, Virginia. 104 pp. Table of Contents Abstract ............................................................................................................................................ 2 Introduction ...................................................................................................................................... 2 Climate ..................................................................................................................................... 2 Geology and Soils .................................................................................................................... 3 History of Botanical Studies in Alexandria .............................................................................. 5 Methods ............................................................................................................................................ 7 Results and Discussion .................................................................................................................... -
Vegetation Community Monitoring at Congaree National Park: 2014 Data Summary
National Park Service U.S. Department of the Interior Natural Resource Stewardship and Science Vegetation Community Monitoring at Congaree National Park 2014 Data Summary Natural Resource Data Series NPS/SECN/NRDS—2016/1016 ON THIS PAGE Tiny, bright yellow blossoms of Hypoxis hirsuta grace the forest floor at Congaree National Park. Photograph courtesy of Sarah C. Heath, Southeast Coast Network. ON THE COVER Spiraling compound leaf of green dragon (Arisaema dracontium) at Congaree National Park. Photograph courtesy of Sarah C. Heath, Southeast Coast Network Vegetation Community Monitoring at Congaree National Park 2014 Data Summary Natural Resource Data Series NPS/SECN/NRDS—2016/1016 Sarah Corbett Heath1 and Michael W. Byrne2 1National Park Service Southeast Coast Inventory and Monitoring Network Cumberland Island National Seashore 101 Wheeler Street Saint Marys, GA 31558 2National Park Service Southeast Coast Inventory and Monitoring Network 135 Phoenix Drive Athens, GA 30605 May 2016 U.S. Department of the Interior National Park Service Natural Resource Stewardship and Science Fort Collins, Colorado The National Park Service, Natural Resource Stewardship and Science office in Fort Collins, Colorado, publishes a range of reports that address natural resource topics. These reports are of interest and applicability to a broad audience in the National Park Service and others in natural resource management, including scientists, conservation and environmental constituencies, and the public. The Natural Resource Data Series is intended for the timely release of basic data sets and data summaries. Care has been taken to assure accuracy of raw data values, but a thorough analysis and interpretation of the data has not been completed.