Automated Conservation Assessment of the Orchid Family Using Deep Learning
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
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 Complete Chloroplast Genome Sequence of Asparagus (Asparagus Officinalis L.) and Its Phy- Logenetic Positon Within Asparagales
Central International Journal of Plant Biology & Research Bringing Excellence in Open Access Research Note *Corresponding author Wentao Sheng, Department of Biological Technology, Nanchang Normal University, Nanchang 330032, The Complete Chloroplast Jiangxi, China, Tel: 86-0791-87619332; Fax: 86-0791- 87619332; Email: Submitted: 14 September 2017 Genome Sequence of Accepted: 09 October 2017 Published: 10 October 2017 Asparagus (Asparagus ISSN: 2333-6668 Copyright © 2017 Sheng et al. officinalis L.) and its OPEN ACCESS Keywords Phylogenetic Positon within • Asparagus officinalis L • Chloroplast genome • Phylogenomic evolution Asparagales • Asparagales Wentao Sheng*, Xuewen Chai, Yousheng Rao, Xutang, Tu, and Shangguang Du Department of Biological Technology, Nanchang Normal University, China Abstract Asparagus (Asparagus officinalis L.) is a horticultural homology of medicine and food with health care. The entire chloroplast (cp) genome of asparagus was sequenced with Hiseq4000 platform. The complete cp genome maps a circular molecule of 156,699bp built with a quadripartite organization: two inverted repeats (IRs) of 26,531bp, separated by a large single copy (LSC) sequence of 84,999bp and a small single copy (SSC) sequence of 18,638bp. A total of 112 genes comprising of 78 protein-coding genes, 30 tRNAs and 4 rRNAs were successfully annotated, 17 of which included introns. The identity, number and GC content of asparagus cp genes were similar to those of other asparagus species genomes. Analysis revealed 81 simple sequence repeat (SSR) loci, most composed of A or T, contributing to a bias in base composition. A maximum likelihood phylogenomic evolution analysis showed that asparagus was closely related to Polygonatum cyrtonema that belonged to the genus Asparagales. -
E29695d2fc942b3642b5dc68ca
ISSN 1409-3871 VOL. 9, No. 1—2 AUGUST 2009 Orchids and orchidology in Central America: 500 years of history CARLOS OSSENBACH INTERNATIONAL JOURNAL ON ORCHIDOLOGY LANKESTERIANA INTERNATIONAL JOURNAL ON ORCHIDOLOGY Copyright © 2009 Lankester Botanical Garden, University of Costa Rica Effective publication date: August 30, 2009 Layout: Jardín Botánico Lankester. Cover: Chichiltic tepetlauxochitl (Laelia speciosa), from Francisco Hernández, Rerum Medicarum Novae Hispaniae Thesaurus, Rome, Jacobus Mascardus, 1628. Printer: Litografía Ediciones Sanabria S.A. Printed copies: 500 Printed in Costa Rica / Impreso en Costa Rica R Lankesteriana / International Journal on Orchidology No. 1 (2001)-- . -- San José, Costa Rica: Editorial Universidad de Costa Rica, 2001-- v. ISSN-1409-3871 1. Botánica - Publicaciones periódicas, 2. Publicaciones periódicas costarricenses LANKESTERIANA i TABLE OF CONTENTS Introduction 1 Geographical and historical scope of this study 1 Political history of Central America 3 Central America: biodiversity and phytogeography 7 Orchids in the prehispanic period 10 The area of influence of the Chibcha culture 10 The northern region of Central America before the Spanish conquest 11 Orchids in the cultures of Mayas and Aztecs 15 The history of Vanilla 16 From the Codex Badianus to Carl von Linné 26 The Codex Badianus 26 The expedition of Francisco Hernández to New Spain (1570-1577) 26 A new dark age 28 The “English American” — the journey through Mexico and Central America of Thomas Gage (1625-1637) 31 The renaissance of science -
Phylogenetic Relationships of Discyphus
Phytotaxa 173 (2): 127–139 ISSN 1179-3155 (print edition) www.mapress.com/phytotaxa/ PHYTOTAXA Copyright © 2014 Magnolia Press Article ISSN 1179-3163 (online edition) http://dx.doi.org/10.11646/phytotaxa.173.2.3 Phylogenetic relationships of Discyphus scopulariae (Orchidaceae, Cranichideae) inferred from plastid and nuclear DNA sequences: evidence supporting recognition of a new subtribe, Discyphinae GERARDO A. SALAZAR1, CÁSSIO VAN DEN BERG2 & ALEX POPOVKIN3 1Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Apartado Postal 70-367, 04510 México, Distrito Federal, México; E-mail: [email protected] 2Universidade Estadual de Feira de Santana, Departamento de Ciências Biológicas, Av. Transnordestina s.n., 44036-900, Feira de Santana, Bahia, Brazil 3Fazenda Rio do Negro, Entre Rios, Bahia, Brazil Abstract The monospecific genus Discyphus, previously considered a member of Spiranthinae (Orchidoideae: Cranichideae), displays both vegetative and floral morphological peculiarities that are out of place in that subtribe. These include a single, sessile, cordate leaf that clasps the base of the inflorescence and lies flat on the substrate, petals that are long-decurrent on the column, labellum margins free from sides of the column and a column provided with two separate, cup-shaped stigmatic areas. Because of its morphological uniqueness, the phylogenetic relationships of Discyphus have been considered obscure. In this study, we analyse nucleotide sequences of plastid and nuclear DNA under maximum parsimony -
Vaspuez Appendix
Org. Divers. Evol. 3, Electr. Suppl. 4: 1–14 (2003) © Gesellschaft für Biologische Systematik http://senckenberg.de/odes/03-04.htm Preliminary list of Bolivian Orchid species Electr. Suppl. 4. – to: Vásquez, R., Ibisch, P.L. & Gerkmann, B. (2003): Diversity of Bolivian Orchidaceae – a challenge for taxonomic, floristic and conservation research. Org. Divers. Evol. 3(2): 93–102. E = endemic to Bolivia Lit = records based on literature RV... = records based on herbarium vouchers in Herbarium Vasquezianum, Santa Cruz, Bolivia (made by Roberto Vásquez) T = terrestrial (species without T are considered to be predominantly epiphytic) Ecoregions: (1 = Southwest Amazon:) 1.1 = Subandean Amazon Humid Forests, 1.2 = Preandean Amazon Humid Forests, 1.3 = Northern Amazon Humid Forests, 1.4 = Southern Amazon Humid Forests; 2 = Varzea and Igapo; (3 = Amazon Campos:) 3.1 = La Paz Amazon Campos, 3.2 = Beni Amazon Campos; (4 = Flooded Savannas:) 4.1= Moxos Plain Flooded Savannas, 4.2= Pantanal Flooded Savannas; 5 = Dry Chiquitano Forest; 6 = Cerrado; 7 = Gran Chaco Dry Forest; 8 = Yungas; 9 = Tucuman-Bolivian For- est; 10 = Montane Chaco; 11 = Dry Interandean Forests; 12 = Prepuna; 13 = Yungas Paramo; 14 = High-Andean Vegetation; (15 = Puna:) 15.1 = Humid Puna, 15.2 = Semihumid Puna, 15.3 = Dry Puna, 15.4 = Desert Puna. If no ecoregion number is given, the collection locality cannot be assigned to any ecoregion or is completely unknown. Unidentified specimens are included when it is highly probable that they will turn out to represent new species or new records for Bolivia. In some cases, however, species could later be assigned to recorded but hardly known taxa (especially Notylia, Oncidium). -
Die Orchidaceengattungen Altensteinia H. B. Et Kth., Aa Rchb
Die Orchidaceen-Gattungen Altensteinia H. B. et Kth., Aa. Rchb. 147 XXXII. Die Orchidaceen-Gattungen Altensteinia H. B. et Kth., Aa Rchb. f. u. Myrosmodes Rchb. f. Von R. Schlechter. (Originalarbeit.) Die Gattung AZtensteinia H. B. et Kth. wurde von den Autoren im Jahre 1815 in ihren ,Nova Genera et Species" im Band I auf Seite 332 beschrieben und mit zwei Arten, A. fimbriata H. B. et Kth. auf Tafel 72 und A. pilifera H. €3. et Kth. auf Tafel 73, abgebildet. Schon bei ober- flachlicher Betrachtung Tallt bei diesen beiden Arten der grosse Unter- schied auf, welchsr zwischen ihnen zu finden ist. Die einzelnen Teile des Perigoniums sowohl wie die Kolumna sind so ganzlich verschieden, dass man bald auf den Gedanken kommen muss, es hier mit zwei ver- schiedenen Gattungen zu tun zu haben. Im Jahre 1822 wurde dann von Kunth in seiner ,Synopsis" vol. I, p. 325 eine dritte Art der Gattuhg als Altensteinia paleacea Klh. beigefiigt, welche friiher als Ophrys paleacea H. B. et Kth. von den drei Autoren der Gattung Altensteink in dem oben zitierten Werke auf p. 334, also einige Seiten dahinter, veroffentlicht war. Dadurch wurde nun der Gattungscharakter noch ganz erheblich erweitert, denn diese Art ist in ihrer Bliitenstruktur ebenso verschieden von den beiden ersten Arten, wie diese untereinander. Als Lindley im Jahre 1840 in seinen ,Genera and Species of Orchidaceous Plants" die Gattung AZtensteinia H. B. et Kth. behandelte, war ihm nur die zuletzt publizierte A. paleacea Kth. bekannt, und daher ist es wohl erklarlich, dass er die drei Arten nicht generisch trennte, sondern nur bei A. -
Phylogeny, Genome Size, and Chromosome Evolution of Asparagales J
Aliso: A Journal of Systematic and Evolutionary Botany Volume 22 | Issue 1 Article 24 2006 Phylogeny, Genome Size, and Chromosome Evolution of Asparagales J. Chris Pires University of Wisconsin-Madison; University of Missouri Ivan J. Maureira University of Wisconsin-Madison Thomas J. Givnish University of Wisconsin-Madison Kenneth J. Systma University of Wisconsin-Madison Ole Seberg University of Copenhagen; Natural History Musem of Denmark See next page for additional authors Follow this and additional works at: http://scholarship.claremont.edu/aliso Part of the Botany Commons Recommended Citation Pires, J. Chris; Maureira, Ivan J.; Givnish, Thomas J.; Systma, Kenneth J.; Seberg, Ole; Peterson, Gitte; Davis, Jerrold I.; Stevenson, Dennis W.; Rudall, Paula J.; Fay, Michael F.; and Chase, Mark W. (2006) "Phylogeny, Genome Size, and Chromosome Evolution of Asparagales," Aliso: A Journal of Systematic and Evolutionary Botany: Vol. 22: Iss. 1, Article 24. Available at: http://scholarship.claremont.edu/aliso/vol22/iss1/24 Phylogeny, Genome Size, and Chromosome Evolution of Asparagales Authors J. Chris Pires, Ivan J. Maureira, Thomas J. Givnish, Kenneth J. Systma, Ole Seberg, Gitte Peterson, Jerrold I. Davis, Dennis W. Stevenson, Paula J. Rudall, Michael F. Fay, and Mark W. Chase This article is available in Aliso: A Journal of Systematic and Evolutionary Botany: http://scholarship.claremont.edu/aliso/vol22/iss1/ 24 Asparagales ~£~2COTSgy and Evolution Excluding Poales Aliso 22, pp. 287-304 © 2006, Rancho Santa Ana Botanic Garden PHYLOGENY, GENOME SIZE, AND CHROMOSOME EVOLUTION OF ASPARAGALES 1 7 8 1 3 9 J. CHRIS PIRES, • • IVAN J. MAUREIRA, THOMAS J. GIVNISH, 2 KENNETH J. SYTSMA, 2 OLE SEBERG, · 9 4 6 GITTE PETERSEN, 3· JERROLD I DAVIS, DENNIS W. -
Phylogenetic Relationships of Discyphus Scopulariae
Phytotaxa 173 (2): 127–139 ISSN 1179-3155 (print edition) www.mapress.com/phytotaxa/ PHYTOTAXA Copyright © 2014 Magnolia Press Article ISSN 1179-3163 (online edition) http://dx.doi.org/10.11646/phytotaxa.173.2.3 Phylogenetic relationships of Discyphus scopulariae (Orchidaceae, Cranichideae) inferred from plastid and nuclear DNA sequences: evidence supporting recognition of a new subtribe, Discyphinae GERARDO A. SALAZAR1, CÁSSIO VAN DEN BERG2 & ALEX POPOVKIN3 1Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Apartado Postal 70-367, 04510 México, Distrito Federal, México; E-mail: [email protected] 2Universidade Estadual de Feira de Santana, Departamento de Ciências Biológicas, Av. Transnordestina s.n., 44036-900, Feira de Santana, Bahia, Brazil 3Fazenda Rio do Negro, Entre Rios, Bahia, Brazil Abstract The monospecific genus Discyphus, previously considered a member of Spiranthinae (Orchidoideae: Cranichideae), displays both vegetative and floral morphological peculiarities that are out of place in that subtribe. These include a single, sessile, cordate leaf that clasps the base of the inflorescence and lies flat on the substrate, petals that are long-decurrent on the column, labellum margins free from sides of the column and a column provided with two separate, cup-shaped stigmatic areas. Because of its morphological uniqueness, the phylogenetic relationships of Discyphus have been considered obscure. In this study, we analyse nucleotide sequences of plastid and nuclear DNA under maximum parsimony -
Flower Flies (Diptera: Syrphidae) of Philippines, Solomon Islands, Wallacea and New Guinea
THOMPSON, F.C., MENGUAL, X., YOUNG, A.D. & SKEVINGSTON, J.H.: Flower flies of Philippines, Solomon Islands, Wallacea ... (Plates 167-172) Flower flies (Diptera: Syrphidae) of Philippines, Solomon Islands, Wallacea and New Guinea F. CHRISTIAN THOMPSON 1, XIMO MENGUAL 2, ANDREW D. YOUNG 3, JEFFREY H. SKEVINGTON 3 1 – Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., U.S.A.; e-mail: [email protected] 2 – Zoologisches Forschungsmuseum Alexander Koenig, Leibniz-Institut für Biodiversität der Tiere, Adenauerallee 160, D–53113, Bonn, Germany; e-mail: [email protected] 3 – Canadian National Collection of Insects, Arachnids and Nematodes, Agriculture and Agri- Food Canada, K.W. Neatby Building, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada and Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada; e-mails: [email protected] (corresponding author), [email protected] Abstract: The flower flies of the Philippines, Solomon Islands, Wallacea and New Guinea are reviewed. An overview of the family is given followed by a key to the genera with a synopsis of each genus. Two new combinations are made: Matsumyia cyaniventris (Sack, 1926) comb. nov. (formerly Criorhina cyaniventris) and Citrogramma calceata (Sack, 1926) comb. nov. (formerly Xanthogramma calceata). Key words: Diptera, Brachycera, Syrphidae, Philippines, Wallacea, New Guinea, Solomon Islands, identification key, Indomalayan (Oriental) Region. Introduction Fully winged; usually with holoptic males (Fig. 5, plate 169 fig. 3, plate 169 fig. 7); females (Fig. 5, Flower flies are an abundant and critical com- plate 170 fig. 7, plate 171 fig. 1) and some males ponent of terrestrial ecosystems. -
Morfoanatomía En Cranichideae (Orchidaceae) De La Estación Loma Redonda Del Parque Nacional “Sierra Nevada”, Mérida, Venezuela
LANKESTERIANA 12(1): 61—75. 2012. MorfoanatomÍA EN CRANICHIDEAE (ORCHIDACEAE) DE LA EstaciÓN LOMA REDONDA DEL PARQUE NACIONAL “SIERRA NevaDA”, MéRIDA, VENEZUELA BLANCA A. DUGARTE CORREDOR1,2 & REBECA LUQUE ARIAS1 1 Centro Jardín Botánico de Mérida, Facultad de Ciencias. Universidad de los Andes, Mérida, estado Mérida, 5101, Venezuela 2 Autor para correspondencia: [email protected] RESUMEN. Se realizó un estudio morfoanatómico de los órganos vegetativos y del pedúnculo de tres representantes de la subtribu Cranichidinae s.l. (Orchidaceae): Aa paleacea, Myrosmodes paludosa y Pterichis multiflora, de la estación Loma Redonda del Teleférico de Mérida, del Parque Nacional Sierra Nevada. Estas tres especies se estudiaron con el fin de determinar la posible existencia de caracteres diagnósticos así como la presencia de caracteres adaptativos al páramo. Se recolectaron plantas adultas. Se determinaron caracteres comunes: raíces rollizas, velamen y exodermis uniestratificado, exodermis con engrosamientos escalareiformes en las paredes radiales, espirantosomas en la corteza y hojas glabras arrosetadas. Se reporta por primera vez mesófilo diferenciado en Cranichideae. Se determinaron los siguientes caracteres diagnósticos: grosor de la corteza radicular; número de corridas de células de la empalizada y esponjoso; diferentes tipos de estelas en el pedúnculo. Algunos de estos caracteres se consideran adaptativos al ambiente: raíces rollizas, corteza compacta; hojas pequeñas y brillantes de cutícula gruesa, desarrollo de empalizada; pedúnculo con epidermis y cutícula gruesa Se considera Myrosmodes paludosa como la más xeromórfica. Se presenta una clave de caracteres morfológicos y otra de caracteres anatómicos. ABSTRACT. A morpho-anatomic study of vegetative organs and peduncle was conducted in three representatives of the subtribe Cranichidinae s.l. -
Phylogenetics of Cranichideae with Emphasis on Spiranthinae (Orchidaceae,Orchidoideae): Evidence from Plastid and Nuclear Dna Sequences1
American Journal of Botany 90(5): 777±795. 2003. PHYLOGENETICS OF CRANICHIDEAE WITH EMPHASIS ON SPIRANTHINAE (ORCHIDACEAE,ORCHIDOIDEAE): EVIDENCE FROM PLASTID AND NUCLEAR DNA SEQUENCES1 GERARDO A. SALAZAR,2,5 MARK W. C HASE,2 MIGUEL A. SOTO ARENAS,3 AND MARTIN INGROUILLE4 2Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK 3Herbario AMO, Apartado Postal 53-123, 11320 MeÂxico, D.F., MeÂxico and 4Department of Biology, Birkbeck College, University of London, Malet Street, London WC1E 7HX, UK DNA sequences from plastid rbcL and matK genes and the trnL-F region, as well as the nuclear ribosomal ITS region, were used to evaluate monophyly and subtribal delimitation of Cranichideae and generic relationships in Spiranthinae. Cranichideae are moderately supported as monophyletic, with Chloraeinae and Pterostylis-Megastylis indicated as their collective sisters. Within Cranichideae, Pachyplectroninae and Goodyerinae form a well-supported monophyletic group sister to a ``core spiranthid'' clade that includes, according to their branching order, Galeottiellinae, Manniellinae, and a Prescottiinae-Cranichidinae-Spiranthinae subclade. Inclusion of Galeottiella in Spiranthinae, as in previous classi®cations, renders the latter paraphyletic to all other spiranthid subtribes. Cranichidinae and Spiranthinae (minus Galeottiella) are monophyletic and strongly supported, but Prescottiinae form a grade that includes a strongly supported prescottioid Andean clade and a weakly supported Prescottia-Cranichidinae clade sister to Spiranthinae. Well-supported major clades in Spiranthinae identi®ed in this study do not correspond to previous alliances or the narrowly de®ned subtribes in which they have been divided recently. Morphological characters, especially those that have been used for taxonomic delimitation in Cran- ichideae, are discussed against the framework of the molecular trees, emphasizing putative synapomorphies and problems derived from lack of information or inadequate interpretation of the characters. -
Redalyc.New Species of Aa and New Combinations in Myrosmodes
Lankesteriana International Journal on Orchidology ISSN: 1409-3871 [email protected] Universidad de Costa Rica Costa Rica Trujillo, Delsy; Vargas, Carlos A. New species of Aa and new combinations in Myrosmodes (Orchidaceae: Cranichidinae) from Bolivia and Peru Lankesteriana International Journal on Orchidology, vol. 11, núm. 1, abril, 2011, pp. 1-8 Universidad de Costa Rica Cartago, Costa Rica Disponible en: http://www.redalyc.org/articulo.oa?id=44339820001 Cómo citar el artículo Número completo Sistema de Información Científica Más información del artículo Red de Revistas Científicas de América Latina, el Caribe, España y Portugal Página de la revista en redalyc.org Proyecto académico sin fines de lucro, desarrollado bajo la iniciativa de acceso abierto LANKESTERIANA 11(1): 1—8. 2011. NEW SPECIES OF AA AND NEW COMBInatIONS IN MYROSMODES (ORCHIDACEAE: CRANICHIDINAE) FROM BOLIVIA AND PERU DELSY TRUJILLO1,3 & CARLOS A. VARGAS2 1 Museo de Historia Natural, Universidad Ricardo Palma, Av. Benavides 5440, Lima 33, Perú 2 AECOM, Montréal, Canada 3 Corresponding author: [email protected] ABSTRACT. A new species of Aa from northern Peru is described: Aa aurantiaca, which has highly atypical orange flowers for the genus. Furthermore, two new combinations of Myrosmodes are proposed: M. inaequalis and M. gymnandra, with illustrations and diagnostic features of the new species. RESUMEN. Se describe una nueva especie de Aa del norte del Perú: Aa aurantiaca; la cual tiene las flores de color naranja, siendo éste un color inusual para el género. Se proponen además dos nuevas combinaciones de Myrosmodes: M. inaequalis y M. gymnandra; se presentan ilustraciones y se discuten rasgos diagnósticos de las nuevas especies.