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Resolution of Deep Angiosperm Phylogeny Using Conserved Nuclear Genes and Estimates of Early Divergence Times
ARTICLE Received 24 Mar 2014 | Accepted 11 Aug 2014 | Published 24 Sep 2014 DOI: 10.1038/ncomms5956 OPEN Resolution of deep angiosperm phylogeny using conserved nuclear genes and estimates of early divergence times Liping Zeng1, Qiang Zhang2, Renran Sun1, Hongzhi Kong3, Ning Zhang1,4 & Hong Ma1,5 Angiosperms are the most successful plants and support human livelihood and ecosystems. Angiosperm phylogeny is the foundation of studies of gene function and phenotypic evolution, divergence time estimation and biogeography. The relationship of the five divergent groups of the Mesangiospermae (B99.95% of extant angiosperms) remains uncertain, with multiple hypotheses reported in the literature. Here transcriptome data sets are obtained from 26 species lacking sequenced genomes, representing each of the five groups: eudicots, monocots, magnoliids, Chloranthaceae and Ceratophyllaceae. Phylogenetic analyses using 59 carefully selected low-copy nuclear genes resulted in highly supported relationships: sisterhood of eudicots and a clade containing Chloranthaceae and Ceratophyllaceae, with magnoliids being the next sister group, followed by monocots. Our topology allows a re-examination of the evolutionary patterns of 110 morphological characters. The molecular clock estimates of Mesangiospermae diversification during the late to middle Jurassic correspond well to the origins of some insects, which may have been a factor facilitating early angiosperm radiation. 1 State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratoryof Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Science, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 220 Handan Road, Yangpu District, Shanghai 200433, China. 2 Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and the Chinese Academy of Sciences, Guilin 541006, China. -
Reconstructing the Basal Angiosperm Phylogeny: Evaluating Information Content of Mitochondrial Genes
55 (4) • November 2006: 837–856 Qiu & al. • Basal angiosperm phylogeny Reconstructing the basal angiosperm phylogeny: evaluating information content of mitochondrial genes Yin-Long Qiu1, Libo Li, Tory A. Hendry, Ruiqi Li, David W. Taylor, Michael J. Issa, Alexander J. Ronen, Mona L. Vekaria & Adam M. White 1Department of Ecology & Evolutionary Biology, The University Herbarium, University of Michigan, Ann Arbor, Michigan 48109-1048, U.S.A. [email protected] (author for correspondence). Three mitochondrial (atp1, matR, nad5), four chloroplast (atpB, matK, rbcL, rpoC2), and one nuclear (18S) genes from 162 seed plants, representing all major lineages of gymnosperms and angiosperms, were analyzed together in a supermatrix or in various partitions using likelihood and parsimony methods. The results show that Amborella + Nymphaeales together constitute the first diverging lineage of angiosperms, and that the topology of Amborella alone being sister to all other angiosperms likely represents a local long branch attrac- tion artifact. The monophyly of magnoliids, as well as sister relationships between Magnoliales and Laurales, and between Canellales and Piperales, are all strongly supported. The sister relationship to eudicots of Ceratophyllum is not strongly supported by this study; instead a placement of the genus with Chloranthaceae receives moderate support in the mitochondrial gene analyses. Relationships among magnoliids, monocots, and eudicots remain unresolved. Direct comparisons of analytic results from several data partitions with or without RNA editing sites show that in multigene analyses, RNA editing has no effect on well supported rela- tionships, but minor effect on weakly supported ones. Finally, comparisons of results from separate analyses of mitochondrial and chloroplast genes demonstrate that mitochondrial genes, with overall slower rates of sub- stitution than chloroplast genes, are informative phylogenetic markers, and are particularly suitable for resolv- ing deep relationships. -
Patrones De Distribución De La Flora Vascular Acuática Estricta En El
Revista Mexicana de Biodiversidad 79: 435- 448, 2008 Patrones de distribución de la fl ora vascular acuática estricta en el estado de Tamaulipas, México Distributional patterns of the strictly aquatic vascular fl ora in the state of Tamaulipas, Mexico Arturo Mora-Olivo1*, José Luis Villaseñor2, Isolda Luna-Vega3 y Juan J. Morrone4 1Instituto de Ecología y Alimentos, Universidad Autónoma de Tamaulipas, 13 Blvd. Adolfo López Mateos 928, Ciudad Victoria 87040, Tamaulipas, México. 2Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México. Apartado postal 70-367, 04510 México, D. F., México. 3Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México , Apartado postal 70-399, 04510 México, D.F., México. 4Museo de Zoología “Alfonso L. Herrera”, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Apartado postal 70-399, 04510 México, D. F., México. *Correspondencia: [email protected] Resumen. Se analizaron los patrones de riqueza y distribución de las plantas vasculares acuáticas estrictas en el estado de Tamaulipas, México. Se registraron 93 especies, 62 de las cuales son típicas de ambientes lénticos. La subcuenca Río Tamesí fue la que registró el mayor número de especies (68, 73.1%). No se registraron especies endémicas del estado, aunque existen 2 especies restringidas al territorio mexicano (Lobelia purpusii y Oserya coulteriana). Se consideran como raras 29 especies (31.2%) por presentarse en una sola subcuenca y sólo 2 especies están distribuidas ampliamente en la mayoría de éstas (Bacopa monnieri y Echinodorus berteroi). Un análisis de parsimonia de endemismos (PAE) de las subcuencas hidrológicas del estado con base en la presencia compartida de especies reveló que las plantas acuáticas estrictas presentan un patrón de distribución anidado. -
UC Davis UC Davis Previously Published Works
UC Davis UC Davis Previously Published Works Title Integrating early Cretaceous fossils into the phylogeny of living angiosperms: Anita lines and relatives of Chloranthaceae Permalink https://escholarship.org/uc/item/3bj1s569 Journal International Journal of Plant Sciences, 175(5) ISSN 1058-5893 Authors Doyle, JA Endress, PK Publication Date 2014 DOI 10.1086/675935 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Int. J. Plant Sci. 175(5):555–600. 2014. ᭧ 2014 by The University of Chicago. All rights reserved. 1058-5893/2014/17505-0006$15.00 DOI: 10.1086/675935 INTEGRATING EARLY CRETACEOUS FOSSILS INTO THE PHYLOGENY OF LIVING ANGIOSPERMS: ANITA LINES AND RELATIVES OF CHLORANTHACEAE James A. Doyle1,* and Peter K. Endress† *Department of Evolution and Ecology, University of California, Davis, California 95616, USA; and †Institute of Systematic Botany, University of Zurich, 8008 Zurich, Switzerland Editor: Patrick S. Herendeen Premise of research. Discoveries of fossil flowers in Cretaceous rocks offer improved evidence for rela- tionships with living clades, but for more secure inferences formal phylogenetic analyses are desirable. We extend previous analyses of magnoliids, monocots, and basal eudicots to Aptian, Albian, and Cenomanian fossils related to the basal “ANITA” lines and Chloranthaceae. Methodology. We performed parsimony analyses of a morphological data set of Recent angiosperms and published fossils, with the arrangement of Recent taxa constrained to backbone trees based primarily on molecular data. Pivotal results. Not only Monetianthus (as previously inferred) but also Carpestella is nested within Nymphaeaceae, while Pluricarpellatia may be a stem relative of Cabombaceae or Nymphaeaceae. Anacostia (with Similipollis pollen) is nested within Austrobaileyales. -
Using Plastid Genome-Scale Data to Resolve Enigmatic Relationships Among Basal Angiosperms
Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms Michael J. Moore†‡, Charles D. Bell§, Pamela S. Soltis¶, and Douglas E. Soltis† †Department of Botany and ¶Florida Museum of Natural History, University of Florida, Gainesville, FL 32611; and §Department of Biological Sciences, University of New Orleans, New Orleans, LA 70149 Communicated by David L. Dilcher, University of Florida, Gainesville, FL, August 28, 2007 (received for review June 15, 2007) Although great progress has been made in clarifying deep-level as sister to magnoliids, Ceratophyllum, or as part of a clade with angiosperm relationships, several early nodes in the angiosperm magnoliids and Chloranthaceae, generally with low support (7, branch of the Tree of Life have proved difficult to resolve. Perhaps 12, 15, 17, 19–24). The unstable relationships exhibited among the last great question remaining in basal angiosperm phylogeny these five major lineages of angiosperms are likely due to a involves the branching order among the five major clades of combination of the relatively ancient age of these taxa [at least mesangiosperms (Ceratophyllum, Chloranthaceae, eudicots, mag- four of which have fossil records that extend back Ͼ100 Mya to noliids, and monocots). Previous analyses have found no consistent the Early Cretaceous (25–29)], the short evolutionary branches support for relationships among these clades. In an effort to separating these lineages, and the relatively long branches lead- resolve these relationships, we performed phylogenetic analyses ing to Ceratophyllum and to the basal lineages of monocots (2). of 61 plastid genes (Ϸ42,000 bp) for 45 taxa, including members of The increasing number of complete angiosperm plastid ge- all major basal angiosperm lineages. -
Clear Creek Gambusia Recovery Plan
CLEAR CREEK GAMBUSIA RECOVERY PLAN 1982 REaxERYPLAN Gmbusia heterochir H&bs, 1957 PREPAREDBY THEFUOGRANDEF'ISHESRECOVERYTERM April 16, 1980 TEAMMIaBERs Clark H&bs, Tern Leader, University of Texas Floyd E. Potter, Jr., Texas Parks and Wildlife Departlent AntImy EChelle, CRl.a&na State University Salmdor antreras-Balderas, University of Nuevo Leon Buddy Jensen, U.S. fish and Wildlife Semice Midmel D. Hatch, Nw @z&o Departmnt of Gam and fish TEZM CONSUIiTAJTt’S IMilfmd J?letd?er, National Park Service Willian McPherson, U.S. Soil Conservation Service CONTENTS Preface . ............ i Acknowledgments . ............. ii Part I - Review Background Introduction ........... ............ Description ............ ............. Taxonomic Status ......... ............ Distribution and Description of the Habitat . Habitat Requirements ....... ............ Associated Species ........ ............ Reproduction ........... ............ Threats Hybridization ........... ............ 4 Competition. ........... ............ 4 Development ............ ............ 5 Dam Deterioration ......... ............ 5 Recharge Zone ........... ............ 5 Runoff .............. ............ 6 Stream Perturbations . 6 Conservation Efforts . 7' Literature Cited . 8 Part II - The Action Plan . 9 Step-Down Outline . 9 i, Narrative .......................... Part III - Priorities, Responsibilities, Costs ......... 20 Part IV - Responses and Replies ................ 23 PREFACE The Clear Creek Gambusia Recovery Plan was developed by the Clear Creek Gambusia Recovery Team, -
Dissertação Fernando Alves Ferreira
FERNANDO ALVES FERREIRA COMUNIDADES DE MACRÓFITAS AQUÁTICAS E ASPECTOS FÍSICOS-QUÍMICOS DE TRÊS LAGOAS DO PARQUE ESTADUAL DO RIO DOCE, MG Tese apresentada à Universidade Federal de Viçosa, como parte das exigências do Programa de Pós- Graduação em Botânica, para obtenção do título de Magister Scientiae. VIÇOSA MINAS GERAIS – BRASIIL 2005 À infinita bondade de meu pai, Edson José Ferreira. À minha amada mãe, Terezinha Alves Miranda Ferreira. Aos meus queridos irmãos, Fabrício, Flávio e Vanessa. ii HOMENAGEM ESPECIAL Este trabalho é inteiramente dedicado ao Prof. Dr. Gilberto Pedralli, um verdadeiro expoente do desenvolvimento científico. Guiei-me pela sua sabedoria, seu estímulo, seu compromisso com a ciência e pelo seu caráter de pesquisador, sempre procurando viver a vida em um estado de celebração. Suas risadas serviram de alimento para meu coração e para minha alma, mesmo em momentos complicados sua alegria estava presente. Principalmente nos momentos solitários em que estava escrevendo este trabalho. A cada ida ao campo, sentia sua presença, seus sinais. Demorei muito tempo para aceitar que sua partida era sem volta, não queria ver interrompida uma seqüência de ensinamentos. Sei que está presente de alguma forma como um gigante, continuando a me fortalecer e proteger. Definindo desde sua ida pessoas especiais com as quais devo dedicar-me. Obrigado Pedra’s, pelo suporte que me proporcionou. Por criar a tranqüilidade necessária para que eu chegasse ao final desse trabalho sem sua presença. Você está no meu coração para sempre. iii AGRADECIMENTOS Este trabalho foi possível graças ao apoio de várias pessoas, a quem apresento meus agradecimentos: Ao professor Alexandre Francisco da Silva, pela oportunidade, pela orientação, pela amizade e pelo apoio durante todos os momentos de nosso trabalho. -
Part 7. Cabombaceae, Nymphaeaceae, Nelumbonaceae, and Ceratophyllaceae
kTION BULLETIN 527 M arch v 1984 U Owl •21 luatic Vascular Plants of New England: Part 7. Cabombaceae, Nymphaeaceae, Nelumbonaceae, and Ceratophyllaceae by C. B. Hellquist and G. E. Crow NEW HAMPSHIRE AGRICULTURAL EXPERIMENT STATION UNIVERSITY OF NEW HAMPSHIRE DURHAM, NEW HAMPSHIRE 03824 ISSN: 0077-8338 University of New Hampshire Library' kTION BULLETIN 527 March, 1984 IU juatic Vascular Plants of New England: Part 7. Cabombaceae, Nymphaeaceae, Nelumbonaceae, and Ceratophyllaceae by C. B. Hellquist and G. E. Crow NEW HAMPSHIRE AGRICULTURAL EXPERIMENT STATION UNIVERSITY OF NEW HAMPSHIRE DURHAM, NEW HAMPSHIRE 03824 5 ACKNOWLEDGEMENTS We wish to thank Edward G. Voss, Carroll E. Wood, and Donald H. Les for their helpful comments on the manuscript. We are also grateful to the curators of the following herbaria for use of their collections: BRU, CONN, CUW, GH, HNH, KIRI, MASS, MAINE, NASC, NCBS, NHA, NEBC, VT, YU. A special thanks is extended to Pamela Bruns Brayton who prepared the illustrations. Permission to redraw some figures from Fassett's Manual of Aquatic Plants used in Figure 7 was kindly provided by the University of Wisconsin Press. This work is a result of research sponsored by the New Hampshire Agricultural Experiment Station. The NHAES reserves the right to reproduce, publish or otherwise use, and to authorize others to use, the work for Government purposes notwithstanding notice of copyright. Copyright £ 1984 by the University of New Hampshire. No part of this work may be reproduced in any manner without permission from the authors and the University of New Hampshire. Programs of the New Hampshire Agricultural Experiment Station are open to all persons without regard to race, color, national origin or sex. -
Phylogenetic Analyses of Cretaceous Fossils Related to Chloranthaceae and Their Evolutionary Implications
UC Davis UC Davis Previously Published Works Title Phylogenetic Analyses of Cretaceous Fossils Related to Chloranthaceae and their Evolutionary Implications Permalink https://escholarship.org/uc/item/0d58r5r0 Journal Botanical Review, 84(2) ISSN 0006-8101 Authors Doyle, JA Endress, PK Publication Date 2018-06-01 DOI 10.1007/s12229-018-9197-6 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Phylogenetic Analyses of Cretaceous Fossils Related to Chloranthaceae and their Evolutionary Implications James A. Doyle & Peter K. Endress The Botanical Review ISSN 0006-8101 Volume 84 Number 2 Bot. Rev. (2018) 84:156-202 DOI 10.1007/s12229-018-9197-6 1 23 Your article is protected by copyright and all rights are held exclusively by The New York Botanical Garden. This e-offprint is for personal use only and shall not be self- archived in electronic repositories. If you wish to self-archive your article, please use the accepted manuscript version for posting on your own website. You may further deposit the accepted manuscript version in any repository, provided it is only made publicly available 12 months after official publication or later and provided acknowledgement is given to the original source of publication and a link is inserted to the published article on Springer's website. The link must be accompanied by the following text: "The final publication is available at link.springer.com”. 1 23 Author's personal copy Bot. Rev. (2018) 84:156–202 https://doi.org/10.1007/s12229-018-9197-6 Phylogenetic Analyses of Cretaceous Fossils Related to Chloranthaceae and their Evolutionary Implications James A. -
Small-Scale Environmental Drivers of Plant Community Structure
diversity Article Small-Scale Environmental Drivers of Plant Community Structure and Diversity in Neotropical Montane Cloud Forests Harboring Threatened Magnolia dealbata in Southern Mexico Reyna Domínguez-Yescas 1, José Antonio Vázquez-García 1,* , Miguel Ángel Muñiz-Castro 1 , Gerardo Hernández-Vera 1, Eduardo Salcedo-Pérez 2, Ciro Rodríguez-Pérez 3 and Sergio Ignacio Gallardo-Yobal 4 1 Centro Universitario de Ciencias Biológicas y Agropecuarias, Departamento de Botánica y Zoología, Universidad de Guadalajara, Jalisco 45200, Mexico; [email protected] (R.D.-Y.); [email protected] (M.Á.M.-C.); [email protected] (G.H.-V.) 2 Centro Universitario de Ciencias Exactas e Ingenierías, Departamento de Madera, Celulosa y Papel, Universidad de Guadalajara, Jalisco 45200, Mexico; [email protected] 3 Instituto Tecnológico del Valle de Oaxaca, Oaxaca 71230, Mexico; [email protected] 4 Instituto Tecnológico Nacional de México/ITS de Huatusco, Veracruz 94100, Mexico; [email protected] * Correspondence: [email protected]; Tel.: +52-33-2714-3490 Received: 30 September 2020; Accepted: 11 November 2020; Published: 24 November 2020 Abstract: Gradient analysis was used to determine factors driving small-scale variation of cloud forest communities harboring Magnolia dealbata, a threatened species and bioculturally relevant tree for the Chinantecan, Mazatecan, Nahuan, and Zapotecan ethnicities in southern Mexico. Particularly, we aimed to: (a) determine factors explaining major community gradients at different heterogeneity scales along a small-scale elevational gradient, (b) test the Decreasing and the Continuum hypotheses along elevation, and (c) classify vegetation to assist in identifying conservation priorities. We used a stratified random sampling scheme for 21 woody stands along a small-scale (352 m) elevational transect. -
Ceratophyllaceae, Page 1 of 5 First Published on the Flora Mesoamericana Website, 2 Sep. 2015
Flora Mesoamericana, Volume 2 (1), Ceratophyllaceae, page 1 of 5 First published on the Flora Mesoamericana Website, 2 Sep. 2015. 52. CERATOPHYLLACEAE By F.R. Barrie. Herbs; perennial; aquatic, submersed; monoecious; aerenchyma present in stems and leaves, glabrous throughout. Roots absent. Stems suspended or anchored to the substrate. Leaves whorled, 3-11 per node, apetiolate, estipulate; blades filiform or two to four or more times dichotomously branched, the ultimate segments linear and finely to coarsely toothed. Flowers solitary, unisexual, actinomorphic, sessile or subsessile, subtended by an involucre of 8 to 15 linear bracts, 1.5 --2 mm; calyx and corolla absent; stamens 3 to numerous, c. 2 mm, 2-locular, longitudinally dehiscent, the connective projecting apically, bearing 2 or more small teeth; ovary 1, superior, 1-locular; ovule 1, pendulous; style 1, terminal, persistent, aciculate or awl-shaped; stigma decurrent within a stylar groove. Fruit an achene, ellipsoid, moderately compressed laterally, the surface smooth to papillose or tuberculate, the margin entire or winged, with or without basal, marginal and apical spines; seed 1, elliptical, without endosperm, the embryo well developed. 1 gen., 6 spp. Cosmopolitan. Bibliography: Les, D.H. Fam. Gen. Vasc. Pl. 2: 246-250 (1993). 1. Ceratophyllum L. Dichotophyllum Moench By F.R. Barrie. Characters as for the family. Ceratophyllum is a genus of submerged aquatic herbs occurring in lakes, ponds, swamps and slow moving streams, found on all continents. It often forms dense vegetative mats. Flowers are submerged at anthesis and pollen is dispersed by water. Flora Mesoamericana, Volume 2 (1), Ceratophyllaceae, page 2 of 5 Duke (1962) suggested that C. -
Professional Resume
PUBLICATIONS EDWARD L. SCHNEIDER Books 1. The Botanical World (with David Northington), 2nd edition. W. C Brown Publishers, Dubuque, Iowa. 1996. 497 pp. An introductory textbook for mixed majors. ISBN 0-697-29211-8 2. CEO’s and Trustees: Building Working Partnerships. E. Schneider, Editor. Allen K. Knoll Publishers, Santa Barbara, California. 1998. 96 pp. ISBN 1-888310-00-6. 3. CEO’s and Trustees: Building Working Partnerships - Part II. E. Schneider and R. Rogers, Editors. Allen K. Knoll Publishers, Santa Barbara, California. 1999. 85 pp. ISBN 1-888310-00-6. 4. Trustee Responsibilities - Enhancing Staff Understanding. R. Rogers & E. Schneider, Editors. Allen K. Knoll Publishers, Santa Barbara, California. 1999. 77 pp. ISBN 1-888310-91-X 5. Trustee Responsibilities - Enhancing Staff Understanding. Part II. R. Rogers & E. Schneider, Editors. Allen K. Knoll Publ., Santa Barbara, California. 2000. 70pp. ISBN 1-888310-91-X. Peer-Reviewed Papers Published (shorter articles, popular articles and theses omitted): 1. Schneider, E.L. 1976. Morphological studies of the Nymphaeaceae. VIII. The floral anatomy of Victoria Schomb. Bot. J. Linnean Soc. 72: 115-148. 2. Schneider, E.L and L.A. Moore. 1977. Morphological studies of Nymphaeaceae. VII. The floral biology of Nuphar luteum subsp. macrophyllum (Sm) E.O. Beal. Brittonia 29: 88-99. 3. Schneider, E.L. 1978. Morphological studies of the Nymphaeaceae. IX. The seed of Barclaya longifolia Wall. Bot. Gaz. 139: 223-230. 4. Schneider, E.L and E.G. Ford. 1978. Morphological studies of the Nymphaeaceae. X. The seed of Ondinea purpurea den Hartog. Bull. Torrey Bot. Club 105(3): 192-200.