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GENOME EVOLUTION in MONOCOTS a Dissertation
GENOME EVOLUTION IN MONOCOTS A Dissertation Presented to The Faculty of the Graduate School At the University of Missouri In Partial Fulfillment Of the Requirements for the Degree Doctor of Philosophy By Kate L. Hertweck Dr. J. Chris Pires, Dissertation Advisor JULY 2011 The undersigned, appointed by the dean of the Graduate School, have examined the dissertation entitled GENOME EVOLUTION IN MONOCOTS Presented by Kate L. Hertweck A candidate for the degree of Doctor of Philosophy And hereby certify that, in their opinion, it is worthy of acceptance. Dr. J. Chris Pires Dr. Lori Eggert Dr. Candace Galen Dr. Rose‐Marie Muzika ACKNOWLEDGEMENTS I am indebted to many people for their assistance during the course of my graduate education. I would not have derived such a keen understanding of the learning process without the tutelage of Dr. Sandi Abell. Members of the Pires lab provided prolific support in improving lab techniques, computational analysis, greenhouse maintenance, and writing support. Team Monocot, including Dr. Mike Kinney, Dr. Roxi Steele, and Erica Wheeler were particularly helpful, but other lab members working on Brassicaceae (Dr. Zhiyong Xiong, Dr. Maqsood Rehman, Pat Edger, Tatiana Arias, Dustin Mayfield) all provided vital support as well. I am also grateful for the support of a high school student, Cady Anderson, and an undergraduate, Tori Docktor, for their assistance in laboratory procedures. Many people, scientist and otherwise, helped with field collections: Dr. Travis Columbus, Hester Bell, Doug and Judy McGoon, Julie Ketner, Katy Klymus, and William Alexander. Many thanks to Barb Sonderman for taking care of my greenhouse collection of many odd plants brought back from the field. -
The Chloroplast Genome of Arthropodium Bifurcatum
Copyright is owned by the Author of the thesis. Permission is given for a copy to be downloaded by an individual for the purpose of research and private study only. The thesis may not be reproduced elsewhere without the permission of the Author. The Chloroplast Genome of Arthropodium bifurcatum. A thesis presented in partial fulfillment of the requirements for the degree of Master of Science in Biological Sciences Massey University Palmerston North, New Zealand Simon James Lethbridge Cox 2010 Abstract This thesis describes the application of high throughput (Illumina) short read sequencing and analyses to obtain the chloroplast genome sequence of Arthropodium bifurcatum and chloroplast genome markers for future testing of hypotheses that explain geographic distributions of Rengarenga – the name Maori give to species of Arthropodium in New Zealand. It has been proposed that A.cirratum was translocated from regions in the north of New Zealand to zones further south due to its value as a food crop. In order to develop markers to test this hypothesis, the chloroplast genome of the closely related A.bifurcatum was sequenced and annotated. A range of tools were used to handle the large quantities of data produced by the Illumina GAIIx. Programs included the de novo assembler Velvet, alignment tools BWA and Bowtie, the viewer Tablet and the quality control program SolexaQA. The A.bifurcatum genome was then used as a reference to align long range PCR products amplified from multiple accessions of A.cirratum and A.bifurcatum sampled from a range of geographic locations. From this alignment variable SNP markers were identified. -
TELOPEA Publication Date: 13 October 1983 Til
Volume 2(4): 425–452 TELOPEA Publication Date: 13 October 1983 Til. Ro)'al BOTANIC GARDENS dx.doi.org/10.7751/telopea19834408 Journal of Plant Systematics 6 DOPII(liPi Tmst plantnet.rbgsyd.nsw.gov.au/Telopea • escholarship.usyd.edu.au/journals/index.php/TEL· ISSN 0312-9764 (Print) • ISSN 2200-4025 (Online) Telopea 2(4): 425-452, Fig. 1 (1983) 425 CURRENT ANATOMICAL RESEARCH IN LILIACEAE, AMARYLLIDACEAE AND IRIDACEAE* D.F. CUTLER AND MARY GREGORY (Accepted for publication 20.9.1982) ABSTRACT Cutler, D.F. and Gregory, Mary (Jodrell(Jodrel/ Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, England) 1983. Current anatomical research in Liliaceae, Amaryllidaceae and Iridaceae. Telopea 2(4): 425-452, Fig.1-An annotated bibliography is presented covering literature over the period 1968 to date. Recent research is described and areas of future work are discussed. INTRODUCTION In this article, the literature for the past twelve or so years is recorded on the anatomy of Liliaceae, AmarylIidaceae and Iridaceae and the smaller, related families, Alliaceae, Haemodoraceae, Hypoxidaceae, Ruscaceae, Smilacaceae and Trilliaceae. Subjects covered range from embryology, vegetative and floral anatomy to seed anatomy. A format is used in which references are arranged alphabetically, numbered and annotated, so that the reader can rapidly obtain an idea of the range and contents of papers on subjects of particular interest to him. The main research trends have been identified, classified, and check lists compiled for the major headings. Current systematic anatomy on the 'Anatomy of the Monocotyledons' series is reported. Comment is made on areas of research which might prove to be of future significance. -
Supporting Information Appendix Pliocene Reversal of Late Neogene
1 Supporting Information Appendix 2 Pliocene reversal of late Neogene aridification 3 4 J.M.K. Sniderman, J. Woodhead, J. Hellstrom, G.J. Jordan, R.N. Drysdale, J.J. Tyler, N. 5 Porch 6 7 8 SUPPLEMENTARY MATERIALS AND METHODS 9 10 Pollen analysis. We attempted to extract fossil pollen from 81 speleothems collected from 11 16 caves from the Western Australian portion of the Nullarbor Plain. Nullarbor speleothems 12 and caves are essentially “fossil” features that appear to have been preserved by very slow 13 rates of landscape change in a semi-arid landscape. Sample collection targeted fallen, well 14 preserved speleothems in multiple caves. U-Pb dates of these speleothems (Table S3) 15 ranged from late Miocene (8.19 Ma) to Middle Pleistocene (0.41 Ma), with an average age 16 of 4.11 Ma. 17 Fossil pollen typically is present in speleothems in very low concentrations, so pollen 18 processing techniques were developed to minimize contamination by modern pollen (1), but 19 also to maximize recovery, to accommodate the highly variable organic matter content of the 20 speleothems, and to remove a clay- to fine silt-sized mineral fraction present in many 21 samples, which was resistant to cold HF and which can become electrostatically attracted to 22 pollen grains, inhibiting their identification. Stalagmite and flowstone samples of 30-200 g 23 mass were first cut on a diamond rock saw in order to remove any obviously porous material. 24 All subsequent physical and chemical processes were carried out within a HEPA-filtered 25 exhausting clean air cabinet in an ISO Class 7 clean room. -
Networks in a Large-Scale Phylogenetic Analysis: Reconstructing Evolutionary History of Asparagales (Lilianae) Based on Four Plastid Genes
Networks in a Large-Scale Phylogenetic Analysis: Reconstructing Evolutionary History of Asparagales (Lilianae) Based on Four Plastid Genes Shichao Chen1., Dong-Kap Kim2., Mark W. Chase3, Joo-Hwan Kim4* 1 College of Life Science and Technology, Tongji University, Shanghai, China, 2 Division of Forest Resource Conservation, Korea National Arboretum, Pocheon, Gyeonggi- do, Korea, 3 Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, United Kingdom, 4 Department of Life Science, Gachon University, Seongnam, Gyeonggi-do, Korea Abstract Phylogenetic analysis aims to produce a bifurcating tree, which disregards conflicting signals and displays only those that are present in a large proportion of the data. However, any character (or tree) conflict in a dataset allows the exploration of support for various evolutionary hypotheses. Although data-display network approaches exist, biologists cannot easily and routinely use them to compute rooted phylogenetic networks on real datasets containing hundreds of taxa. Here, we constructed an original neighbour-net for a large dataset of Asparagales to highlight the aspects of the resulting network that will be important for interpreting phylogeny. The analyses were largely conducted with new data collected for the same loci as in previous studies, but from different species accessions and greater sampling in many cases than in published analyses. The network tree summarised the majority data pattern in the characters of plastid sequences before tree building, which largely confirmed the currently recognised phylogenetic relationships. Most conflicting signals are at the base of each group along the Asparagales backbone, which helps us to establish the expectancy and advance our understanding of some difficult taxa relationships and their phylogeny. -
Cunninghamia Date of Publication: 18/11/2013 a Journal of Plant Ecology for Eastern Australia
Cunninghamia Date of Publication: 18/11/2013 A journal of plant ecology for eastern Australia ISSN 0727- 9620 (print) • ISSN 2200 - 405X (Online) Impact of broom, Cytisus scoparius (Fabaceae), in naturally treeless sub-alpine frost-hollow vegetation communities at the Barrington Tops, south-eastern Australia John R. Hosking1,3, Mellesa Schroder2 and Bruce McCorkell1 1Tamworth Agricultural Institute, NSW Department of Primary Industries, 4 Marsden Park Road, Calala, NSW 2340 AUSTRALIA. email [email protected] 2NSW Office of Environment and Heritage, National Parks and Wildlife Service, corner of Kosciusko Way and Thredbo Terrace, Jindabyne, NSW 2627 AUSTRALIA. email [email protected] 3current address: NCW Beadle Herbarium, University of New England, Armidale, NSW 2351 AUSTRALIA. email [email protected] Abstract: The exotic shrub Cytisus scoparius (L.) Link (family Fabaceae), known as broom, is having a major impact on native vegetation in naturally treeless sub-alpine frost-hollow areas (c. 32o 01’ 37” S, 151o 26’ 12” E’, 1440 m elevation) at the Barrington Tops, New South Wales, in south-eastern Australia. This vegetation is of limited extent and has significant biogeographical and ecological importance. Nine paired 10 m line transects were compared, with one of the pair in areas of almost 100% Cytisus scoparius and the other in adjacent areas without Cytisus scoparius. Results were compared with species recorded from this area in the 1930s. There are obvious differences in native vegetation in areas with and without Cytisus scoparius. On average there were 5.1 (range 2–10) species per 10 m in areas of almost 100% Cytisus scoparius cover and 17.0 (12–25) species per 10 m in areas adjacent to infested areas but without Cytisus scoparius. -
On the Flora of Australia
L'IBRARY'OF THE GRAY HERBARIUM HARVARD UNIVERSITY. BOUGHT. THE FLORA OF AUSTRALIA, ITS ORIGIN, AFFINITIES, AND DISTRIBUTION; BEING AN TO THE FLORA OF TASMANIA. BY JOSEPH DALTON HOOKER, M.D., F.R.S., L.S., & G.S.; LATE BOTANIST TO THE ANTARCTIC EXPEDITION. LONDON : LOVELL REEVE, HENRIETTA STREET, COVENT GARDEN. r^/f'ORElGN&ENGLISH' <^ . 1859. i^\BOOKSELLERS^.- PR 2G 1.912 Gray Herbarium Harvard University ON THE FLORA OF AUSTRALIA ITS ORIGIN, AFFINITIES, AND DISTRIBUTION. I I / ON THE FLORA OF AUSTRALIA, ITS ORIGIN, AFFINITIES, AND DISTRIBUTION; BEIKG AN TO THE FLORA OF TASMANIA. BY JOSEPH DALTON HOOKER, M.D., F.R.S., L.S., & G.S.; LATE BOTANIST TO THE ANTARCTIC EXPEDITION. Reprinted from the JJotany of the Antarctic Expedition, Part III., Flora of Tasmania, Vol. I. LONDON : LOVELL REEVE, HENRIETTA STREET, COVENT GARDEN. 1859. PRINTED BY JOHN EDWARD TAYLOR, LITTLE QUEEN STREET, LINCOLN'S INN FIELDS. CONTENTS OF THE INTRODUCTORY ESSAY. § i. Preliminary Remarks. PAGE Sources of Information, published and unpublished, materials, collections, etc i Object of arranging them to discuss the Origin, Peculiarities, and Distribution of the Vegetation of Australia, and to regard them in relation to the views of Darwin and others, on the Creation of Species .... iii^ § 2. On the General Phenomena of Variation in the Vegetable Kingdom. All plants more or less variable ; rate, extent, and nature of variability ; differences of amount and degree in different natural groups of plants v Parallelism of features of variability in different groups of individuals (varieties, species, genera, etc.), and in wild and cultivated plants vii Variation a centrifugal force ; the tendency in the progeny of varieties being to depart further from their original types, not to revert to them viii Effects of cross-impregnation and hybridization ultimately favourable to permanence of specific character x Darwin's Theory of Natural Selection ; — its effects on variable organisms under varying conditions is to give a temporary stability to races, species, genera, etc xi § 3. -
CURRICULUM VITAE John Godfrey Conran
CURRICULUM VITAE John Godfrey Conran BORN 1960, October 13, Brisbane, Queensland DEPENDENTS Divorced, with two children CURRENT APPOINTMENT Senior Lecturer: School of Earth & Environmental Sciences, The University of Adelaide QUALIFICATIONS 1985: Ph.D. Botany, Univ. of Qld 1981: B.Sc. (Hons 1), Botany, Univ. of Qld 1980: B.Sc. Botany and Entomology, Univ. of Qld The undergraduate degree was broad-based, with subjects from the Agriculture and Science Faculties, with majors in Entomology and Botany. I completed subjects including biometrics, biochemistry, chemistry, computer science and geology, in addition to subjects offered by the Agriculture, Botany, Entomology and Zoology Departments. In Honours, I studied systematics and population variation in Banksia oblongifolia Cav. (Proteaceae). My Ph.D. studied the evolution and ecology of the net-veined petaloid monocots in the rainforests at Springbrook, SE Qld. PRIZES AND SCHOLARSHIPS 2011 The University of Adelaide, Executive Dean of Sciences Excellence in Teaching Award for staff with more than five years of teaching experience 1995 The University of Adelaide, Faculty of Science, Dean's Certificate of Merit for Excellence in Teaching 1982–5 Commonwealth Postgraduate Research Award, University of Qld 1981 F.A. Perkins Prize in Entomology, University of Qld 1980–1 Australian National University Vacation Scholarship LANGUAGES I can, with appropriate dictionaries, translate scientific documents written in Latin, French, German, Spanish, Italian, Portuguese and Afrikaans, and to a much lesser extent Russian. SPECIAL INTERESTS AND EXPERTISE Morphological and molecular systematics, palaeobotany, reproductive/pollination biology and community ecology of the Australasian flora; especially petaloid monocotyledons, southern conifers, carnivorous plants and weeds. PROFESSIONAL EXPERIENCE (APPOINTMENTS) 2006– Affiliate of the State Herbarium of South Australia 2004– Member of the Australian Centre for Ecology & Evolutionary Biology 2000– Lecturer C: The Univ. -
Molecular Systematics of the Lomandra Labill. Complex
Molecular Systematics of the Lomandra Labill. Complex (Asparagales: Laxmanniaceae) by Matthew J. Donnon, B.Sc.Hons A thesis submitted in fulfilment of the requirements for the degree of Doctor of Philosophy Ecology and Evolutionary Biology Faculty of Science The University of Adelaide September 2009 1. General Introduction 1.1 General Introduction Laxmanniaceae (Monocotyledonae: Asparagales) are a tropical to temperate family of 14 genera with approximately 180 species from Australasia, SE Asia, the Mascarenes, New Caledonia, New Guinea, New Zealand, North and South America and the Pacific Islands (Conran 1998). Nevertheless, they are primarily an Australian family with many species spread across the continent, surviving and flourishing in an extraordinary variety of environments ranging from the monsoon tropics and subtropical rainforest to temperate Mediterranean heathlands and coastal sand dunes. Laxmanniaceae have a long historical record, with fossilised leaves of Paracordyline Conran species recognised from Eocene South Australia (Conran and Christophel, 1998), Oligocene Kerguélen Islands (Conran, 1997a) and Cordyline Comm. ex R.Br. pollen identified in Lower Miocene New Zealand sediments (Couper, 1953). Molecular dating work by Janssen and Bremer (2004) based on rbcL sequence data estimated the divergence origin of the Asparagaceae sensu lato (a wider family which includes Laxmanniaceae and thus Lomandra) at approximately 90 million years ago using nonparametric rate smoothing. This age estimation was given additional support by further work incorporating geological area cladogram comparisons and dispersal-vicariance analysis (Bremer and Janssen 2006). This latter study also indicated a South Gondwanan origin for the group. The plants are generally rhizomatous or tufted-caespitose, but the different species and genera are highly variable in size and morphology. -
Details/Summary/ 197892/0]
2017 LanguaL proposals from Australian NUTTAB2010 The Australian NUTTAB2010 data set includes 484 indigenous foods, which presents is a particular challenge for LanguaL indexing, as most of these plants and animals are absent from facet B of the thesaurus. 1. ANIMAL USED AS FOOD SOURCE Proposals for new animal food sources in facet B are pretty straightforward. ANIMAL USED AS FOOD SOURCE> ANIMAL (MAMMAL) [B1134] BT proposed AI synonyms NUTTAB2010 proposed descriptor ANIMAL POSSUM Phalangeriformes, or possums, any of a number brushtail Trichosurus (MAMMAL) of arboreal marsupial species native to possum, arnhemensis, [B1134] Australia, New Guinea, and Sulawesi: trichosuru northern - Phalangeridae (possums and cuscuses), a s, brushtail family of mammals native to Australia and New pseudoch possum, flesh Guinea containing most of the species referred eirus, cooked; to as "possums" in Australia phalanger Northern - Common brushtail possum (Trichosurus idae Brushtail vulpecula), a common possum in Australian Possum urban areas, invasive in New Zealand [15A20119] - Common ringtail possum (Pseudocheirus Trichosurus peregrinus), also common in Australian urban arnhemensis, areas, absent from New Zealand northern [https://en.wikipedia.org/wiki/Possum] brushtail possum, kidney cooked; Northern Brushtail Possum [15A20120] Trichosurus arnhemensis, northern brushtail possum, liver cooked; Northern Brushtail Possum [15A20121] MARINE SEA COW <SCINAM>Sirenia Illiger, 1811 [ITIS 180676] sirenia, Dugong MAMMAL sirens [B1122] Sirenia, commonly referred to -
Dubbo Region Flora List 2012
Flora List of the Dubbo Area and Central Western Slopes Harlequin Mistletoe Lysiana exocarpi subsp. tenuis Drilliwarrina State Conservation Area Janice Hosking for the Dubbo Field Naturalist and Conservation Society Inc Version: June 2012 www.dubbofieldnats.org.au Flora List of the Dubbo Area and Central Western Slopes Janice Hosking for Dubbo Field Nats This list of approximately 1,300 plant species was prepared by Janice Hosking for the Dubbo Field Naturalist & Conservation Society Inc. Many thanks to Steve Lewer and Chris McRae who spent many hours checking and adding to this list. Cover photo: Anne McAlpine, A map of the area subject to this list is provided below. Data Sources: This list has been compiled from the following information: A Flora of the Dubbo District 25 Miles radius around the city (c. 1950s) compiled by George Althofer, assisted by Andy Graham. Gilgandra Native Flora Reserve Plant List Goonoo State Forest Forestry Commission list, supplemented by Mr. P. Althofer. List No.1 (c 1950s) Goonoo State Forest Dubbo Management Area list of Plants List No.2 The Flora of Mt. Arthur Reserve, Wellington NSW A small list for Goonoo State Forest. Author and date unknown Flora List from Cashells Dam Area, Goonoo State Forest (now CCA) – compiled by Steve Lewer (NSW OEH) Oasis Reserve Plant List (Southwest of Dubbo) – compiled by Robert Gibson (NSW OEH) NSW DECCW Wildlife atlas List 2010,Y.E.T.I. List 2010 PlantNet (NSW Botanic Gardens Records) Various species lists for Dubbo District rural properties – compiled by Steve Lewer (NSW OEH) * Denotes an exotic species ** Now considered to be either locally extinct or possibly a misidentification. -
Impact of Broom, Cytisus Scoparius (Fabaceae), in Naturally Treeless Sub-Alpine Frost-Hollow Vegetation Communities at the Barrington Tops, South-Eastern Australia
Cunninghamia Date of Publication: 18/11/2013 A journal of plant ecology for eastern Australia ISSN 0727- 9620 (print) • ISSN 2200 - 405X (Online) Impact of broom, Cytisus scoparius (Fabaceae), in naturally treeless sub-alpine frost-hollow vegetation communities at the Barrington Tops, south-eastern Australia John R. Hosking1,3, Mellesa Schroder2 and Bruce McCorkell1 1Tamworth Agricultural Institute, NSW Department of Primary Industries, 4 Marsden Park Road, Calala, NSW 2340 AUSTRALIA. email [email protected] 2NSW Office of Environment and Heritage, National Parks and Wildlife Service, corner of Kosciusko Way and Thredbo Terrace, Jindabyne, NSW 2627 AUSTRALIA. email [email protected] 3current address: NCW Beadle Herbarium, University of New England, Armidale, NSW 2351 AUSTRALIA. email [email protected] Abstract: The exotic shrub Cytisus scoparius (L.) Link (family Fabaceae), known as broom, is having a major impact on native vegetation in naturally treeless sub-alpine frost-hollow areas (c. 32o 01’ 37” S, 151o 26’ 12” E’, 1440 m elevation) at the Barrington Tops, New South Wales, in south-eastern Australia. This vegetation is of limited extent and has significant biogeographical and ecological importance. Nine paired 10 m line transects were compared, with one of the pair in areas of almost 100% Cytisus scoparius and the other in adjacent areas without Cytisus scoparius. Results were compared with species recorded from this area in the 1930s. There are obvious differences in native vegetation in areas with and without Cytisus scoparius. On average there were 5.1 (range 2–10) species per 10 m in areas of almost 100% Cytisus scoparius cover and 17.0 (12–25) species per 10 m in areas adjacent to infested areas but without Cytisus scoparius.