DOCSLIB.ORG

The Evolutionary Dynamics of Genes and Genomes: Copy Number Variation of the Chalcone Synthase Gene in the Context of Brassicaceae Evolution

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
The Evolutionary Dynamics of Genes and Genomes: Copy Number Variation of the Chalcone Synthase Gene in the Context of Brassicaceae Evolution The Evolutionary Dynamics of Genes and Genomes: Copy Number Variation of the Chalcone Synthase Gene in the Context of Brassicaceae Evolution Dissertation submitted to the Combined Faculties for Natural Sciences and for Mathematics of the Ruperto-Carola University of Heidelberg, Germany for the degree of Doctor of Natural Sciences presented by Liza Paola Ding born in Mosbach, Baden-Württemberg, Germany Oral examination: 22.12.2014 Referees: Prof. Dr. Marcus A. Koch Prof. Dr. Claudia Erbar Table of contents INTRODUCTION ............................................................................................................. 18 1 THE MUSTARD FAMILY ....................................................................................... 19 2 THE TRIBAL SYSTEM OF THE BRASSICACEAE ........................................... 22 3 CHALCONE SYNTHASE ........................................................................................ 23 PART 1: TROUBLE WITH THE OUTGROUP............................................................ 27 4 MATERIAL AND METHODS ................................................................................. 28 4.1 Experimental set-up ......................................................................................................................... 28 4.1.1 Plant material and data composition .............................................................................................. 28 4.1.2 DNA extraction and PCR amplification ......................................................................................... 29 4.1.3 DNA cloning and sequencing .......................................................................................................... 31 4.1.4 Internal validation with ITS ............................................................................................................ 32 4.2 Bioinformatical data analysis .......................................................................................................... 32 4.2.1 Sequence editing and alignment ..................................................................................................... 32 4.3 Comparative phylogenetic reconstructions and analyses ............................................................. 33 4.3.1 Tests applied on data set prior to phylogenetic analyses .............................................................. 33 4.3.2 Phylogenetic analysis ....................................................................................................................... 34 4.3.2.1 Divergence time estimates ............................................................................................................... 35 4.4 Sequence analysis ............................................................................................................................. 37 4.4.1 Alignment analysis of the complete data ........................................................................................ 37 4.4.2 Identifying gene regions ................................................................................................................... 37 4.4.2.1 Trinucleotide frequency (k-mers) ................................................................................................... 38 5 RESULTS .................................................................................................................... 38 5.1 Comparative phylogenetic reconstructions and analyses ............................................................. 38 5.1.1 Tests applied on data set prior to phylogenetic analysis ............................................................... 38 5.1.2 Comparative phylogenetic reconstructions.................................................................................... 39 5.1.3 Divergence time estimates ............................................................................................................... 43 5.2 Sequence analysis ............................................................................................................................. 45 5.2.1 Alignment analysis of complete data .............................................................................................. 45 5.2.2 Alignment analysis of complete data set with focus on tribes ...................................................... 47 5.2.3 Alignment analysis of complete data set with focus on sequences ............................................... 49 5.2.4 Identifying gene regions ................................................................................................................... 52 5.2.4.1 Promoter ........................................................................................................................................... 52 5.2.4.2 Intron ................................................................................................................................................ 54 5.2.4.3 Exon 1 ................................................................................................................................................ 55 5.2.4.4 Exon 2 ................................................................................................................................................ 55 5.2.5 Conserved residues of the complete gene ....................................................................................... 56 5.2.6 Trinucleotide frequency (k-mers) ................................................................................................... 58 6 DISCUSSION ............................................................................................................. 60 PART 2: TROUBLE WITH THE TRIBAL ARRANGEMENT .................................. 64 7 MATERIAL AND METHODS ................................................................................. 65 7.1 Comparative phylogenetic reconstructions and analyses ............................................................. 65 7.1.1 Test for recombination .................................................................................................................... 66 7.1.2 Divergence time estimates ............................................................................................................... 66 7.1.3 Lineage through time plots (LTT) .................................................................................................. 66 7.2 Sequence analysis ............................................................................................................................. 67 7.2.1 Alignment analysis of the complete data ........................................................................................ 67 7.2.2 Identifying gene regions ................................................................................................................... 67 7.2.3 DNA motif search among gene ........................................................................................................ 67 7.2.4 Transition/transversion rate bias .................................................................................................... 68 7.3 Compositional heterogeneity among DNA ..................................................................................... 68 7.3.1 GC content ........................................................................................................................................ 68 7.3.2 Base composition .............................................................................................................................. 69 7.3.3 Trinucleotide frequency .................................................................................................................. 69 7.4 Adaptive evolution ........................................................................................................................... 69 7.4.1 Origin of purifying selection ........................................................................................................... 70 7.4.2 Synonymous substitution rate ......................................................................................................... 71 7.4.3 Ancestral sequence reconstruction ................................................................................................. 71 8 RESULTS .................................................................................................................... 71 8.1 Comparative phylogenetic reconstructions and analyses ............................................................. 71 8.1.1 Test for recombination .................................................................................................................... 74 8.1.2 Divergence time estimates ............................................................................................................... 75 8.1.3 Lineage through time plots .............................................................................................................. 76 8.2 Identifying gene regions ................................................................................................................... 77 8.2.1 Promoter ........................................................................................................................................... 77 8.2.2 Intron ................................................................................................................................................ 78 8.2.3 Exon 1 ...............................................................................................................................................
Load more

Recommended publications
  • The Vascular Plants of Massachusetts
    The Vascular Plants of Massachusetts: The Vascular Plants of Massachusetts: A County Checklist • First Revision Melissa Dow Cullina, Bryan Connolly, Bruce Sorrie and Paul Somers Somers Bruce Sorrie and Paul Connolly, Bryan Cullina, Melissa Dow Revision • First A County Checklist Plants of Massachusetts: Vascular The A County Checklist First Revision Melissa Dow Cullina, Bryan Connolly, Bruce Sorrie and Paul Somers Massachusetts Natural Heritage & Endangered Species Program Massachusetts Division of Fisheries and Wildlife Natural Heritage & Endangered Species Program The Natural Heritage & Endangered Species Program (NHESP), part of the Massachusetts Division of Fisheries and Wildlife, is one of the programs forming the Natural Heritage network. NHESP is responsible for the conservation and protection of hundreds of species that are not hunted, fished, trapped, or commercially harvested in the state. The Program's highest priority is protecting the 176 species of vertebrate and invertebrate animals and 259 species of native plants that are officially listed as Endangered, Threatened or of Special Concern in Massachusetts. Endangered species conservation in Massachusetts depends on you! A major source of funding for the protection of rare and endangered species comes from voluntary donations on state income tax forms. Contributions go to the Natural Heritage & Endangered Species Fund, which provides a portion of the operating budget for the Natural Heritage & Endangered Species Program. NHESP protects rare species through biological inventory,
    [Show full text]
  • Seed Ecology Iii
    SEED ECOLOGY III The Third International Society for Seed Science Meeting on Seeds and the Environment “Seeds and Change” Conference Proceedings June 20 to June 24, 2010 Salt Lake City, Utah, USA Editors: R. Pendleton, S. Meyer, B. Schultz Proceedings of the Seed Ecology III Conference Preface Extended abstracts included in this proceedings will be made available online. Enquiries and requests for hardcopies of this volume should be sent to: Dr. Rosemary Pendleton USFS Rocky Mountain Research Station Albuquerque Forestry Sciences Laboratory 333 Broadway SE Suite 115 Albuquerque, New Mexico, USA 87102-3497 The extended abstracts in this proceedings were edited for clarity. Seed Ecology III logo designed by Bitsy Schultz. i June 2010, Salt Lake City, Utah Proceedings of the Seed Ecology III Conference Table of Contents Germination Ecology of Dry Sandy Grassland Species along a pH-Gradient Simulated by Different Aluminium Concentrations.....................................................................................................................1 M Abedi, M Bartelheimer, Ralph Krall and Peter Poschlod Induction and Release of Secondary Dormancy under Field Conditions in Bromus tectorum.......................2 PS Allen, SE Meyer, and K Foote Seedling Production for Purposes of Biodiversity Restoration in the Brazilian Cerrado Region Can Be Greatly Enhanced by Seed Pretreatments Derived from Seed Technology......................................................4 S Anese, GCM Soares, ACB Matos, DAB Pinto, EAA da Silva, and HWM Hilhorst
    [Show full text]
  • Nomenclatural Notes on Cruciferae Номенклатурные
    Turczaninowia 22 (4): 210–219 (2019) ISSN 1560–7259 (print edition) DOI: 10.14258/turczaninowia.22.4.18 TURCZANINOWIA http://turczaninowia.asu.ru ISSN 1560–7267 (online edition) УДК 582.683.2:581.961 Nomenclatural notes on Cruciferae D. A. German1, 2 1 South-Siberian Botanical Garden, Altai State University, Lenina Ave., 61, Barnaul, 656049, Russian Federation 2 Department of Biodiversity and Plant Systematics, Centre for Organismal Studies, Heidelberg University, Im Neuenheimer Feld 345; Heidelberg, D-69120, Germany E-mail: [email protected] Keywords: Arabidopsis, Brassicaceae, Dvorakia, Erophila, Eunomia, new combination, Noccaea, Peltariopsis, Pseu- docamelina, taxonomy, typification, validation. Summary. A generic name Dvorakia and combinations Arabidopsis amurensis, A. media, A. multijuga, A. sep- tentrionalis, Dvorakia alaica, D. alyssifolia, Erophila acutidentata, E. aquisgranensis, E. kohlscheidensis, and E. strigosula are validated. Places of valid publication and (except for the first combination) authorship forErysimum krynitzkii, Eunomia bourgaei, E. rubescens, Pseudocamelina aphragmodes, P. campylopoda, and Thlaspi hastulatum are corrected. For Pseudocamelina and Peltariopsis, information on the types is clarified. Some further minor nomen- clatural items are commented. Номенклатурные заметки о крестоцветных (Cruciferae) Д. А. Герман1, 2 1 Южно-Сибирский ботанический сад, Алтайский государственный университет, просп. Ленина, 61, г. Барнаул, 656049, Россия 2 Кафедра биоразнообразия и систематики растений, Центр исследований организмов, Гейдельбергский университет, Им Нойенхаймер Фельд, 345, Гейдельберг, D-69120, Германия Ключевые слова: действительное обнародование, новая комбинация, систематика, типификация, Arabidopsis, Brassicaceae, Dvorakia, Erophila, Eunomia, Noccaea, Peltariopsis, Pseudocamelina. Аннотация. Обнародовано родовое название Dvorakia, а также комбинации Arabidopsis amurensis, A. media, A. multijuga, A. septentrionalis, Dvorakia alaica, D. alyssifolia, Erophila acutidentata, E. aquisgranensis, E. kohlscheidensis и E.
    [Show full text]
  • Crab Spiders Impact Floral-Signal Evolution Indirectly Through Removal
    ARTICLE DOI: 10.1038/s41467-018-03792-x OPEN Crab spiders impact floral-signal evolution indirectly through removal of florivores Anina C. Knauer1, Moe Bakhtiari1,2 & Florian P. Schiestl1 The puzzling diversity of flowers is primarily shaped by selection and evolutionary change caused by the plant’s interaction with animals. The contribution of individual animal species to net selection, however, may vary depending on the network of interacting organisms. Here 1234567890():,; we document that in the buckler mustard, Biscutella laevigata, the crab spider Thomisus onustus reduces bee visits to flowers but also benefits plants by feeding on florivores. Uninfested plants experience a trade-off between pollinator and spider attraction as both bees and crab spiders are attracted by the floral volatile β-ocimene. This trade-off is reduced by the induced emission of β-ocimene after florivore infestation, which is stronger in plant populations where crab spiders are present than where they are absent, suggesting that plants are locally adapted to the presence of crab spiders. Our study demonstrates the context-dependence of selection and shows how crab spiders impact on floral evolution. 1 Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland. 2Present address: Institute of Biology, University of Neuchatel, Rue Emile-Argand 11, 2000 Neuchatel, Switzerland. Correspondence and requests for materials should be addressedto F.P.S. (email: fl[email protected]) NATURE COMMUNICATIONS | (2018) 9:1367 | DOI: 10.1038/s41467-018-03792-x | www.nature.com/naturecommunications 1 ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-03792-x lant–animal interactions are a major driver of plant Crab spiders camouflage themselves on flowers to hunt flower- evolution, including both local adaptation and species visiting insects such as pollinators (Fig.
    [Show full text]
  • Original Article Canarium Album Extract Restrains Lipid Excessive Accumulation in Hepatocarcinoma Cells
    Int J Clin Exp Med 2016;9(9):17509-17518 www.ijcem.com /ISSN:1940-5901/IJCEM0022450 Original Article Canarium album extract restrains lipid excessive accumulation in hepatocarcinoma cells Qingpei Liu1,2, Meiling Zhou1,2, Mingjing Zheng1, Ni Chen1, Xiuli Zheng2, Shaoxiao Zeng1, Baodong Zheng1 1College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, People’s Republic of China; 2Fuzhou Great Olive Co., Ltd, Fuzhou 350101, Fujian, People’s Republic of China Received December 22, 2015; Accepted May 17, 2016; Epub September 15, 2016; Published September 30, 2016 Abstract: Lipid metabolism is an important section of human body metabolism, and lipid metabolism disorder can lead to multiple diseases. Canarium album is a nature food, whose extract has been reported hepatoprotective, anti-inflammatory and antioxidant. In this study, we extracted polyphenol and flavonoid substances from Canarium album fruits, and demonstrated that they restrain lipid excessive accumulation induced by oleic acid in hepatocarci- noma cells. Moreover, polyphenol and flavonoid extracted fromCanarium album fruits facilitated phosphorylation of adenosine monophosphate activated protein kinase (AMPK) and regulated several lipid metabolism related genes expression, including fatty acid synthase (FAS), sterol regulatory element binding protein (SREBP)-1 and peroxisame proliferator activated receptor (PPAR)-α. Therefore, for the first time, we demonstrated thatCanarium album extract restrained lipid excessive accumulation by activating AMPK signaling pathway, downregulating SREBP-1 and FAS, upregulating PPAR-α in hepatocarcinoma cells, which may be of great significance for prevention and clinical treat- ment of lipid metabolism disorders. Keywords: Canarium album, polyphenol, flavonoid, hepatocarcinoma cells, lipid, AMPK Introduction plants including Juniperus lucayana [5], induc- es lipolysis in adipocytes of mice [6, 7].
    [Show full text]
  • Cytotype Associations, Ecological Divergence and Genetic Variation in the Apomictic Complex Paspalum Intermedium Munro Ex Morong (Poaceae)
    Cytotype Associations, Ecological Divergence and Genetic Variation in the Apomictic Complex Paspalum intermedium Munro Ex Morong (Poaceae) Dissertation for the award of the degree “Doctor of Philosophy” Ph.D. Division of Mathematics and Natural Sciences of the Georg-August-Universität Göttingen within the doctoral program Biology of the Georg-August University School of Science (GAUSS) Submitted by Piyal Karunarathne Göttingen, 2018 THESIS COMMITTEE Prof. Dr. Elvira Hörandl Department of Systematics, Biodiversity and Evolution of Plants (with herbarium) Albrecht-von-Haller Institute for Plant Sciences University of Göttingen, Germany Prof. Dr. Holger Kreft Department of Biodiversity, Macroecology & Biogeography Faculty of Forest Sciences and Forest Ecology University of Göttingen, Germany Dr. Diego Hojsgaard Department of Systematics, Biodiversity and Evolution of Plants (with herbarium) Albrecht-von-Haller Institute for Plant Sciences University of Göttingen, Germany MEMBERS OF THE EXAMINATION BOARD Reviewer Prof. Dr. Elvira Hörandl Department of Systematics, Biodiversity and Evolution of Plants (with herbarium), Albrecht-von-Haller Institute for Plant Sciences University of Göttingen, Germany Second Prof. Dr. Holger Kreft reviewer Department of Biodiversity, Macroecology & Biogeography Faculty of Forest Sciences and Forest Ecology University of Göttingen, Germany Further members of the Examination Board Prof. Dr. Stefan Scheu J.F. Blumenbach Institute of Zoology and Anthropology University of Göttingen Prof. Dr. Mark Maraun J.F. Blumenbach Institute of Zoology and Anthropology University of Göttingen Prof. Dr. Thomas Friedl Dept. EPSAG University of Göttingen Dr. Sven Bradler J.F. Blumenbach-Institut für Zoologie und Anthropologie University of Göttingen ii Acknowledgments I would like to place on record my sincere gratitude to Dr. Diego Hojsgaard for choosing me to carry out this research project, his excellent supervision, tremendous help and advice, and for remaining unflappable despite my various crisis.
    [Show full text]
  • Nested Whole-Genome Duplications Coincide with Diversification And
    ARTICLE https://doi.org/10.1038/s41467-020-17605-7 OPEN Nested whole-genome duplications coincide with diversification and high morphological disparity in Brassicaceae Nora Walden 1,7, Dmitry A. German 1,5,7, Eva M. Wolf 1,7, Markus Kiefer 1, Philippe Rigault 1,2, Xiao-Chen Huang 1,6, Christiane Kiefer 1, Roswitha Schmickl3, Andreas Franzke 1, Barbara Neuffer4, ✉ Klaus Mummenhoff4 & Marcus A. Koch 1 1234567890():,; Angiosperms have become the dominant terrestrial plant group by diversifying for ~145 million years into a broad range of environments. During the course of evolution, numerous morphological innovations arose, often preceded by whole genome duplications (WGD). The mustard family (Brassicaceae), a successful angiosperm clade with ~4000 species, has been diversifying into many evolutionary lineages for more than 30 million years. Here we develop a species inventory, analyze morphological variation, and present a maternal, plastome-based genus-level phylogeny. We show that increased morphological disparity, despite an apparent absence of clade-specific morphological innovations, is found in tribes with WGDs or diversification rate shifts. Both are important processes in Brassicaceae, resulting in an overall high net diversification rate. Character states show frequent and independent gain and loss, and form varying combinations. Therefore, Brassicaceae pave the way to concepts of phy- logenetic genome-wide association studies to analyze the evolution of morphological form and function. 1 Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany. 2 GYDLE, 1135 Grande Allée Ouest, Québec, QC G1S 1E7, Canada. 3 Department of Botany, Faculty of Science, Charles University, Benátská 2, 128 01, Prague, Czech Republic.
    [Show full text]
  • The First Chloroplast Genome Sequence of Boswellia Sacra, a Resin-Producing Plant in Oman
    RESEARCH ARTICLE The First Chloroplast Genome Sequence of Boswellia sacra, a Resin-Producing Plant in Oman Abdul Latif Khan1, Ahmed Al-Harrasi1*, Sajjad Asaf2, Chang Eon Park2, Gun-Seok Park2, Abdur Rahim Khan2, In-Jung Lee2, Ahmed Al-Rawahi1, Jae-Ho Shin2* 1 UoN Chair of Oman's Medicinal Plants & Marine Natural Products, University of Nizwa, Nizwa, Oman, 2 School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea a1111111111 * [email protected] (AAH); [email protected] (JHS) a1111111111 a1111111111 a1111111111 Abstract a1111111111 Boswellia sacra (Burseraceae), a keystone endemic species, is famous for the production of fragrant oleo-gum resin. However, the genetic make-up especially the genomic informa- tion about chloroplast is still unknown. Here, we described for the first time the chloroplast OPEN ACCESS (cp) genome of B. sacra. The complete cp sequence revealed a circular genome of 160,543 Citation: Khan AL, Al-Harrasi A, Asaf S, Park CE, bp size with 37.61% GC content. The cp genome is a typical quadripartite chloroplast struc- Park G-S, Khan AR, et al. (2017) The First ture with inverted repeats (IRs 26,763 bp) separated by small single copy (SSC; 18,962 bp) Chloroplast Genome Sequence of Boswellia sacra, and large single copy (LSC; 88,055 bp) regions. De novo assembly and annotation showed a Resin-Producing Plant in Oman. PLoS ONE 12 the presence of 114 unique genes with 83 protein-coding regions. The phylogenetic analysis (1): e0169794. doi:10.1371/journal.pone.0169794 revealed that the B. sacra cp genome is closely related to the cp genome of Azadirachta Editor: Xiu-Qing Li, Agriculture and Agri-Food indica and Citrus sinensis, while most of the syntenic differences were found in the non-cod- Canada, CANADA ing regions.
    [Show full text]
  • Inventaire Et Analyse Chimique Des Exsudats Des Plantes D'utilisation Courante Au Congo-Brazzaville
    Inventaire et analyse chimique des exsudats des plantes d’utilisation courante au Congo-Brazzaville Arnold Murphy Elouma Ndinga To cite this version: Arnold Murphy Elouma Ndinga. Inventaire et analyse chimique des exsudats des plantes d’utilisation courante au Congo-Brazzaville. Chimie analytique. Université Paris Sud - Paris XI; Université Marien- Ngouabi (Brazzaville), 2015. Français. NNT : 2015PA112023. tel-01269459 HAL Id: tel-01269459 https://tel.archives-ouvertes.fr/tel-01269459 Submitted on 5 Feb 2016 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. UNIVERSITE MARIEN NGOUABI UNIVERSITÉ PARIS-SUD ÉCOLE DOCTORALE 470: CHIMIE DE PARIS SUD Laboratoire d’Etude des Techniques et d’Instruments d’Analyse Moléculaire (LETIAM) THÈSE DE DOCTORAT CHIMIE par Arnold Murphy ELOUMA NDINGA INVENTAIRE ET ANALYSE CHIMIQUE DES EXSUDATS DES PLANTES D’UTILISATION COURANTE AU CONGO-BRAZZAVILLE Date de soutenance : 27/02/2015 Directeur de thèse : M. Pierre CHAMINADE, Professeur des Universités (France) Co-directeur de thèse : M. Jean-Maurille OUAMBA, Professeur Titulaire CAMES (Congo) Composition du jury : Président : M. Alain TCHAPLA, Professeur Emérite, Université Paris-Sud Rapporteurs : M. Zéphirin MOULOUNGUI, Directeur de Recherche INRA, INP-Toulouse M. Ange Antoine ABENA, Professeur Titulaire CAMES, Université Marien Ngouabi Examinateurs : M.
    [Show full text]
  • May Maritime Alps
    Maritime Alps Spring in Mercantour A Greentours Tour Report 16th to 23rd May 2014 Led by Paul Cardy Daily Accounts and Systematic Lists written by Paul Cardy Our fifth spring tour to the Maritime Alps was superbly productive, especially botanically, and very enjoyable, with almost unbroken perfect weather. Last year had been a late spring in the region, with snow laying much lower than is usual, and some sites inaccessible, but this year the flora was even a little advanced, with several species being recorded for the first time. For the first four nights we were based at a small pleasant family-run hotel in the Valdeblore hamlet of La Bolline, a fine location, well situated for all excursions, and with a small grocery and a bakery just along the street where I could do the daily picnic shopping whilst the group enjoyed breakfast in the hotel. Dinners at the restaurants in the village, in nearby Rimplas, and in St.Dalmas were very good. For the last three nights we moved to the other side of Mercantour National Park, and the hamlet of Casterino, which allowed easy access into the Italian Alpi Marittime, a superbly productive area. On the arrival day, having arrived the previous evening from my home in Italy, a few valleys to the north, at Nice airport I soon met most of the group, and before long we were en route north through ever more impressive scenery. Bob and Marlene were arriving on an afternoon flight, and we met up with them that evening in the hotel.
    [Show full text]
  • Floristic Discoveries in Delaware, Maryland, and Virginia
    Knapp, W.M., R.F.C. Naczi, W.D. Longbottom, C.A. Davis, W.A. McAvoy, C.T. Frye, J.W. Harrison, and P. Stango, III. 2011. Floristic discoveries in Delaware, Maryland, and Virginia. Phytoneuron 2011-64: 1–26. Published 15 December 2011. ISSN 2153 733X FLORISTIC DISCOVERIES IN DELAWARE, MARYLAND, AND VIRGINIA WESLEY M. KNAPP 1 Maryland Department of Natural Resources Wildlife and Heritage Service Wye Mills, Maryland 21679 [email protected] ROBERT F. C. NACZI The New York Botanical Garden Bronx, New York 10458-5126 WAYNE D. LONGBOTTOM P.O. Box 634 Preston, Maryland 21655 CHARLES A. DAVIS 1510 Bellona Ave. Lutherville, Maryland 21093 WILLIAM A. MCAVOY Delaware Natural Heritage and Endangered Species Program 4876 Hay Point, Landing Rd. Smyrna, Delaware 19977 CHRISTOPHER T. FRYE Maryland Department of Natural Resources Wildlife and Heritage Service Wye Mills, Maryland 21679 JASON W. HARRISON Maryland Department of Natural Resources Wildlife and Heritage Service Wye Mills, Maryland 21679 PETER STANGO III Maryland Department of Natural Resources, Wildlife and Heritage Service, Annapolis, Maryland 21401 1 Author for correspondence ABSTRACT Over the past decade studies in the field and herbaria have yielded significant advancements in the knowledge of the floras of Delaware, Maryland, and the Eastern Shore of Virginia. We here discuss fifty-two species newly discovered or rediscovered or whose range or nativity is clarified. Eighteen are additions to the flora of Delaware ( Carex lucorum var. lucorum, Carex oklahomensis, Cyperus difformis, Cyperus flavicomus, Elymus macgregorii, Glossostigma cleistanthum, Houstonia pusilla, Juncus validus var. validus, Lotus tenuis, Melothria pendula var. pendula, Parapholis incurva, Phyllanthus caroliniensis subsp.
    [Show full text]
  • Phenotypic Landscape Inference Reveals Multiple Evolutionary Paths to C4 Photosynthesis
    RESEARCH ARTICLE elife.elifesciences.org Phenotypic landscape inference reveals multiple evolutionary paths to C4 photosynthesis Ben P Williams1†, Iain G Johnston2†, Sarah Covshoff1, Julian M Hibberd1* 1Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom; 2Department of Mathematics, Imperial College London, London, United Kingdom Abstract C4 photosynthesis has independently evolved from the ancestral C3 pathway in at least 60 plant lineages, but, as with other complex traits, how it evolved is unclear. Here we show that the polyphyletic appearance of C4 photosynthesis is associated with diverse and flexible evolutionary paths that group into four major trajectories. We conducted a meta-analysis of 18 lineages containing species that use C3, C4, or intermediate C3–C4 forms of photosynthesis to parameterise a 16-dimensional phenotypic landscape. We then developed and experimentally verified a novel Bayesian approach based on a hidden Markov model that predicts how the C4 phenotype evolved. The alternative evolutionary histories underlying the appearance of C4 photosynthesis were determined by ancestral lineage and initial phenotypic alterations unrelated to photosynthesis. We conclude that the order of C4 trait acquisition is flexible and driven by non-photosynthetic drivers. This flexibility will have facilitated the convergent evolution of this complex trait. DOI: 10.7554/eLife.00961.001 Introduction *For correspondence: Julian. The convergent evolution of complex traits is surprisingly common, with examples including camera- [email protected] like eyes of cephalopods, vertebrates, and cnidaria (Kozmik et al., 2008), mimicry in invertebrates and †These authors contributed vertebrates (Santos et al., 2003; Wilson et al., 2012) and the different photosynthetic machineries of equally to this work plants (Sage et al., 2011a).
    [Show full text]