AUSTRALIAN PLANTS SOCIETY (SGAP) Warrnambool & District
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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. -
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. -
Flora of Australia, Volume 46, Iridaceae to Dioscoreaceae
FLORA OF AUSTRALIA Volume 46 Iridaceae to Dioscoreaceae This volume was published before the Commonwealth Government moved to Creative Commons Licensing. © Commonwealth of Australia 1986. This work is copyright. You may download, display, print and reproduce this material in unaltered form only (retaining this notice) for your personal, non-commercial use or use within your organisation. Apart from any use as permitted under the Copyright Act 1968, no part may be reproduced or distributed by any process or stored in any retrieval system or data base without prior written permission from the copyright holder. Requests and inquiries concerning reproduction and rights should be addressed to: [email protected] FLORA OF AUSTRALIA The nine families in this volume of the Flora of Australia are Iridaceae, Aloeaceae, Agavaceae, Xanthorrhoeaceae, Hanguan- aceae, Taccaceae, Stemonaceae, Smilacaceae and Dioscoreaceae. The Xanthorrhoeaceae has the largest representation with 10 genera and 99 species. Most are endemic with a few species of Lomandra and Romnalda extending to neighbouring islands. The family includes the spectacular blackboys and grass-trees. The Iridaceae is largely represented by naturalised species with 52 of the 78 species being introduced. Many of the introductions are ornamentals and several have become serious weeds. Patersonia is the largest genus with all 17 species endemic. Some of these are cultivated as ornamentals. The Dioscoreaccae is a family of economic significance, particularly in the old world tropics where some species are cultivated or collected for their tubers and bulbils. In Australia there are 5 species, one of which is a recent introduction. The endemic and native species, commonly known as yams, are traditionally eaten by the Aborigines. -
Population Diversity of Doryanthes Excelsa (Doryanthaceae) in Eastern Australia
Population diversity of Doryanthes excelsa (Doryanthaceae) in eastern Australia A. M. Dimech1, 2, *, P.K. Ades3, P.W.J. Taylor2, R. Cross1 and R. Ford2 1 Royal Botanic Gardens Melbourne, South Yarra, Victoria, 3141 AUSTRALIA. (* Current address: Biosciences Research Division, Dept of Primary Industries, Bundoora, Victoria, 3083 AUSTRALIA). Email [email protected] 2 Dept of Agriculture and Food Systems, University of Melbourne, Victoria, 3010 AUSTRALIA. 3 Dept of Forest and Ecosystem Science, University of Melbourne, Victoria, 3010 AUSTRALIA. Abstract: The population diversity of Doranthes excelsa Corrêa (Doryanthaceae) was measured from nine distinct geographic populations across eastern Australia, using random amplified polymorphic DNA (RAPD) markers. An UPGMA dendrogram of individuals was derived from squared Euclidian distances based on the Dice (1945) algorithm. Three clusters corresponding to populations at Somersby, Newfoundland and Kremnos Creek populations were found to be distinct from the remainder of the sampled individuals. A ΦST value of 0.443 indicated that a significant diversity between geographic populations existed; this appeared to be a product of geographical distance and isolation between some of the populations. (PCR = Polymerase Chain Reaction; RAPD = Random Amplified Polymorphic DNA) The results suggest that there is lesser gene flow between the‘northern’ populations (Kremnos Creek and Newfoundland) when compared to the ‘southern’ populations and that they have a significant level of genetic isolation. The two ‘northern’ populations should therefore be regarded as being of considerable value for conservation authorities and the commercial breeding sector and should be given priority for conservation. The plants there appear to exhibit a smaller phenotype but confirming this requires further quantification. -
WRA Species Report
Family: Doryanthaceae Taxon: Doryanthes excelsa Synonym: NA Common Name: giant lily flame lily spear lily Illawarra lily Gymea Lily Questionaire : current 20090513 Assessor: Chuck Chimera Designation: L Status: Assessor Approved Data Entry Person: Chuck Chimera WRA Score 0 101 Is the species highly domesticated? y=-3, n=0 n 102 Has the species become naturalized where grown? y=1, n=-1 103 Does the species have weedy races? y=1, n=-1 201 Species suited to tropical or subtropical climate(s) - If island is primarily wet habitat, then (0-low; 1-intermediate; 2- Intermediate substitute "wet tropical" for "tropical or subtropical" high) (See Appendix 2) 202 Quality of climate match data (0-low; 1-intermediate; 2- High high) (See Appendix 2) 203 Broad climate suitability (environmental versatility) y=1, n=0 y 204 Native or naturalized in regions with tropical or subtropical climates y=1, n=0 n 205 Does the species have a history of repeated introductions outside its natural range? y=-2, ?=-1, n=0 y 301 Naturalized beyond native range y = 1*multiplier (see n Appendix 2), n= question 205 302 Garden/amenity/disturbance weed n=0, y = 1*multiplier (see n Appendix 2) 303 Agricultural/forestry/horticultural weed n=0, y = 2*multiplier (see n Appendix 2) 304 Environmental weed n=0, y = 2*multiplier (see n Appendix 2) 305 Congeneric weed n=0, y = 1*multiplier (see n Appendix 2) 401 Produces spines, thorns or burrs y=1, n=0 n 402 Allelopathic y=1, n=0 n 403 Parasitic y=1, n=0 n 404 Unpalatable to grazing animals y=1, n=-1 405 Toxic to animals y=1, n=0 n -
5, and J. Chris Pires
American Journal of Botany 99(2): 330–348. 2012. Q UALITY AND QUANTITY OF DATA RECOVERED FROM MASSIVELY PARALLEL SEQUENCING: EXAMPLES IN 1 ASPARAGALES AND POACEAE P . R OXANNE S TEELE 2 , K ATE L. HERTWECK 3 , D USTIN M AYFIELD 4 , M ICHAEL R. MCKAIN 5 , J AMES L EEBENS-MACK 5 , AND J. CHRIS P IRES 3,6 2 Department of Biology, 6001 W. Dodge Street, University of Nebraska at Omaha, Omaha, Nebraska 68182-0040 USA; 3 National Evolutionary Synthesis Center, 2024 W. Main Street, Suite A200, Durham, North Carolina 27705-4667 USA; 4 Biological Sciences, 1201 Rollins St., Bond LSC 311, University of Missouri, Columbia, Missouri 65211 USA; and 5 Plant Biology, 4504 Miller Plant Sciences, University of Georgia, Athens, Georgia 30602 USA • Premise of the study: Genome survey sequences (GSS) from massively parallel sequencing have potential to provide large, cost-effective data sets for phylogenetic inference, replace single gene or spacer regions as DNA barcodes, and provide a plethora of data for other comparative molecular evolution studies. Here we report on the application of this method to estimat- ing the molecular phylogeny of core Asparagales, investigating plastid gene losses, assembling complete plastid genomes, and determining the type and quality of assembled genomic data attainable from Illumina 80 – 120-bp reads. • Methods: We sequenced total genomic DNA from samples in two lineages of monocotyledonous plants, Poaceae and Aspara- gales, on the Illumina platform in a multiplex arrangement. We compared reference-based assemblies to de novo contigs, evaluated consistency of assemblies resulting from use of various references sequences, and assessed our methods to obtain sequence assemblies in nonmodel taxa. -
Flowering Plants
Australian Plants Society NORTH SHORE GROUP Ku-ring-gai Wildflower Garden Monocotyledons John Ray, at the end of the 17th century realised that there were two radically different kinds of flowering plants, which he called Monocotyledons (one seed leaf) and Dicotyledons (two seed leaves). Modern botany has proved, maintained and amplified the discovery. It has added differences in leaf, flower and internal structure, though none by itself is as distinctive as the number of seed leaves. It’s important to note that a specific plant we regard as a Monocot or a Dicot may not exhibit all the characteristics to be mentioned. A good example of variation includes leaf venation. Summary of Main Differences between Monocots and Dicots: Characteristic Monocots Dicots Cotyledons (seed leaves) one two Roots fibrous tap with laterals Flower parts in 3s usually in 4s or 5s Leaf venation parallel usually netlike usually Stems: primary vascular bundles scattered in a ring Stems: true secondary growth absent present usually with vascular cambium ___ A contrast in the number of flower parts: Monocots: 3 or 6 (Patersonia sericea) Dicots: 4 or 5 (Crowea saligna) 1 Leaf Structure and Venation Sometimes included as a difference is that monocot leaves generally do not have a central vein or petiole (leaf stem) and often have a stem clasping leaf. The leaves of monocots are often basal, giving a tufted appearance to the plants. Most have parallel veins. They grow from the base and being eaten off or cut at the tops does not affect their further growth, hence it is possible to graze or mow them without permanent damage. -
A New Family Placement for Australian Blue Squill, Chamaescilla: Xanthorrhoeaceae (Hemerocallidoideae), Not Asparagaceae
Phytotaxa 275 (2): 097–111 ISSN 1179-3155 (print edition) http://www.mapress.com/j/pt/ PHYTOTAXA Copyright © 2016 Magnolia Press Article ISSN 1179-3163 (online edition) http://dx.doi.org/10.11646/phytotaxa.275.2.2 A new family placement for Australian blue squill, Chamaescilla: Xanthorrhoeaceae (Hemerocallidoideae), not Asparagaceae TODD G.B. McLAY* & MICHAEL J. BAYLY School of BioSciences, The University of Melbourne, Vic. 3010, Australia; e-mail: [email protected] *author for correspondence Abstract Chamaescilla is an endemic Australian genus, currently placed in the Asparagaceae, alongside other Australian endemic taxa in the tribe Lomandroideae. A recent molecular phylogeny indicated a relationship with another partly Australian family, the Xanthorrhoeaceae, but was not commented on by the authors. Here we added DNA sequence data for a single Chamaescilla specimen to an alignment representing all families in the Asparagales and performed parsimony and Bayesian phylogenetic analyses. Chamaescilla was strongly resolved as belonging to Xanthorrhoeaceae, subfamily Hemerocallidoideae, along- side two non-Australian members, Simethis and Hemerocallis in the hemerocallid clade. This position is corroborated by morphological characters, including pollen grain shape. We also produced an age-calibrated phylogeny and infer that the geographic distribution of the clade is the result of long distance dispersal between the Eocene and Miocene. Key words: Asphodelaceae, biogeography, phylogeny, taxonomy Introduction Chamaescilla Mueller ex Bentham (1878: 48; commonly known as blue squill, blue stars or mudrut, Fig. 1) is a genus including four species that are endemic to Australia, found in the southwest and southeast of the country (Keighery 2001). All species are small, perennial tuberous herbs with annual leaves and flowers. -
A Theory of the Origin of Monocotyledons, Founded on the Structure of Their Seedlings
A Theory of the Origin of Monocotyledons, founded on the Structure of their Seedlings. BY ETHEL SARGANT. With Plates I-VII and ten Figures in the Text. HEN some years ago I was working out the anatomical W structure of the seedlings of Arum maculatum in collaboration with Mrs. Scott (36), we examined the seedlings of some other Aroids, and compared them with two species of Lilium seedlings. The anatomy of seedling Monocotyle- dons has received but little attention from botanists, and Dr. D. H. Scott suggested that I should pursue the subject by making a comparative study of those already collected by him from the material at Kew, and preserved for future investigation. I have to thank him not only for the start then made, but for his unfailing interest in the work as it developed, and for constant help in obtaining fresh supplies of material. The object proposed from the first was to throw light, if possible, on the relationship between Monocotyledons and Dicotyledons. After some months of work in my own laboratory on the Kew material, I found it desirable to modify and extend the original scheme. The vascular system of the cotyledon, hypocotyl, and primary root appeared in the specimens I examined to be characteristic of the species. One of my [Annals of Botany, Vol. XVII. No. LXV. January, 1903.J B 2 Sargant.—Theory of the Origin of Monocotyledons early observations — the comparison of a seedling Anthurium with seedlings of Arum and Lilium—had suggested that this symmetry might furnish a new systematic character of some importance. -
The Global Flora © 2018 Plant Gateway Ltd
THE GLOBAL FLORA © 2018 Plant Gateway Ltd. A practical flora to vascular plant species of the world ISSN 2398-6336 eISSN 2398-6344 www.plantgateway.com/globalflora/ ISBN 978-0-9929993-9-1 i Published online 14 January 2018 PLANT GATEWAy’s THE GLOBAL FLORA A practical flora to vascular plant species of the world INTRODUCTION Introducing The Global Flora The phylogeny of angiosperms poster January 2018 The Global Flora A practical flora to vascular plant species of the world Introduction, Vol. 1: 1-35. Published by Plant Gateway Ltd., 5 Baddeley Gardens, Bradford, BD10 8JL, United Kingdom © Plant Gateway 2018 This work is in copyright. Subject to statutory exception and to the provision of relevant col- lective licensing agreements, no reproduction of any part may take place without the written permission of Plant Gateway Ltd. ISSN 2398-6336 eISSN 2398-6344 ISBN 978-0-9929993-9-1 Plant Gateway has no responsibility for the persistence or accuracy of URLS for external or third-party internet websites referred to in this work, and does not guarantee that any con- tent on such websites is, or will remain, accurate or appropriate. British Library Cataloguing in Publication data A Catalogue record of this book is available from the British Library For information or to purchase other Plant Gateway titles please visit www.plantgateway.com Cover image: Simplified angiosperm phylogeny © James Byng THE GLOBAL FLORA © 2018 Plant Gateway Ltd. A practical flora to vascular plant species of the world ISSN 2398-6336 eISSN 2398-6344 www.plantgateway.com/globalflora/ ISBN 978-0-9929993-9-1 Introducing The Global Flora, a global series of botany James W. -
Giant Spear Lily Doryanthes Palmeri
Plant of the Week GGiiaanntt SSppeeaarr LLiillyy DDoorryyaanntthheess ppaallmmeerrii In recent years, the Giant Spear Lily, Doryanthes palmeri, has become a favourite landscaping plant and the enormous rosettes of tall, sword-shaped leaves have been used to great effect along roadside verges, in parks and in gardens. In Sydney, we are more familiar with Gymea Lilies Photo: Tanja Lenz (Doryanthes excelsa), a close relative which produces flowers in huge, globular heads at the tops of a long, sturdy stems. The flowers of the Giant Spear Lily are equally remarkable but are produced in elongated, compound racemes up to a metre and more in length. The name is quite descriptive, derived from the Greek, δόρυ or dory, a spear and άνθος or ánthos, a flower. They are certainly some of the most unusual and unique plants of eastern Australia. There are only two species in the genus Doryanthes which itself is the only genus in the Australian endemic family Doryanthaceae1. Perhaps it is fortunate that the Giant Spear Lily is now so widely planted as it is listed as vulnerable under the Threatened Species Conservation Act 1995. In its natural environment, the Giant Spear Lily grows on rocky outcrops in wet sclerophyll forest along the ranges that form the Mount Warning caldera1. The flowers of both species of Photo: Tanja Lenz Doryanthes are a rich source of nectar, which, in its fermented state, is known to produce some unpredictable and erratic behaviour amongst our avian friends2. 1 K.L.Wilson, In Harden, G. (Ed.), 1993. Flora of NSW, Vol. 4, pp. -
(Doryanthaceae) in New South Wales 183
Perry, Doryanthes palmeri (Doryanthaceae) in New South Wales 183 The distribution, relative abundance and conservation status of Doryanthes palmeri (Doryanthaceae) in New South Wales Deborah A. Perry Perry, Deborah A. (School of Environmental Science and Management, Southern Cross University, PO Box 157, Lismore, NSW 2480, email: [email protected]) 2001. The distribution, relative abundance and conservation status of Doryanthes palmeri (Doryanthaceae) in New South Wales. Cunninghamia 7(2): 183–193. Doryanthes palmeri is a giant, flowering succulent herb endemic to north-east NSW and south-east Queensland. Prior to this study, only two D. palmeri sites had been reported in NSW. This study revealed a further nine sites, all of which are restricted to the Mt Warning caldera. Doryanthes palmeri occurs on infertile lithosols or grows as a lithophyte on bare rock. It occurs in a narrow band of vegetation along the cliff-tops and on steep cliff-faces or rocky ledges in montane heath next to subtropical rainforest, wet sclerophyll forest or warm temperate forest. There are around 6000 mature D. palmeri plants in north-east NSW. Populations at each site occur as clusters on a relatively small amount of the available habitat. The area of occupancy of D. palmeri is less than 1 km2 with an average distance between sites of 6.3 km. However, the distribution consists of four groups of populations with an average of 15 km between the groups suggesting a poor ability to disperse. There appear to be limits to the extent that plants can expand at some sites which are due mainly to low recruitment of juveniles into the population, illegal seed harvesting and the competition of faster growing native or weed species.