DOCSLIB.ORG

Comparative Morphology and Molecular Evolution of Marine Interstitial Cercozoans

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Comparative Morphology and Molecular Evolution of Marine Interstitial Cercozoans COMPARATIVE MORPHOLOGY AND MOLECULAR EVOLUTION OF MARINE INTERSTITIAL CERCOZOANS by CHITCHAI CHANTANGSI B.Sc., Chulalongkorn University, 2001 M.Sc., The University of Guelph, 2006 A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY in THE FACULTY OF GRADUATE STUDIES (Zoology) THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver) August 2009 © Chitchai Chantangsi, 2009 ABSTRACT The Cercozoa is an extremely diverse and poorly understood group of amoeboflagellated microeukaryotes that are united mainly by molecular phylogenetic data; a concrete synapomorphy at the morphological level has yet to be identified for the group. In order to better understand the biodiversity and evolutionary history of this lineage, I explored several marine benthic habitats in British Columbia, Canada and characterized novel cercozoans with high-resolution light microscopy and electron microscopy. Comparative ultrastructural studies using scanning and transmission electron microscopy on some of the newly discovered taxa demonstrated several novel features, including putative primary endosymbionts in one lineage (i.e., Auranticordis) and homologous patterns of muciferous bodies beneath the cell surface in another lineage. I coupled these morphological data with molecular phylogenetic analyses of small subunit (SSU) and large subunit (LSU) rDNA sequences and comparative analyses of polyubiquitin genes. This approach provided evidence that a concatenation of SSU and LSU rDNA sequences improves the phylogenetic resolution within the Cercozoa and that an insertion of one or two amino acids at the junctions between monomers in the polyubiquitin gene is a universal molecular signature for cercozoans (and foraminiferans). This study also enabled me to discover and describe eleven new species and five new genera, which underscores how poorly we currently understand the diversity of these marine microeukaryotic predators. The acquired SSU rDNA sequences from these novel lineages enabled me to provide the cellular identities of several environmental DNA sequence clades previously containing only uncharacterized taxa; these data also demonstrated the effectiveness of using a 600-bp fragment of the SSU rRNA gene for delimiting cercozoan species with limited morphological variation. ii TABLE OF CONTENTS ABSTRACT ............................................................................................................................ ii TABLE OF CONTENTS ....................................................................................................... iii LIST OF TABLES................................................................................................................ viii LIST OF FIGURES ................................................................................................................ ix ACKNOWLEDGEMENTS.................................................................................................... xi DEDICATION...................................................................................................................... xiii CO-AUTHORSHIP STATEMENT ..................................................................................... xiv CHAPTER 1: INTRODUCTION.............................................................................................1 1.1 Cercozoa and the six eukaryote supergroups ...............................................................1 1.2 General biology of the Cercozoa ..................................................................................1 1.3 Morphological characteristics of the Cercozoa ............................................................2 1.3.1 Microscopic features of the Cercozoa ................................................................2 1.3.2 Ultrastructural features of the Cercozoa.............................................................3 1.4 Biodiversity of the Cercozoa ........................................................................................5 1.5 Classification of the Cercozoa......................................................................................6 1.6 Identification of the Cercozoa ......................................................................................8 1.7 Phylogeny of the Cercozoa...........................................................................................9 1.7.1 The phylogeny of the Cercozoa as inferred from small subunit ribosomal DNA sequences ..................................................................................................9 1.7.2 The phylogeny of the Cercozoa and its novel polyubiquitin insertions .............9 1.8 Thesis goals and scope................................................................................................10 1.8.1 Specific aim 1 ...................................................................................................11 1.8.2 Specific aim 2 ...................................................................................................12 1.8.3 Specific aim 3 ...................................................................................................13 1.8.4 Specific aim 4 ...................................................................................................13 1.8.5 Specific aim 5 ...................................................................................................14 1.9 References ..................................................................................................................17 iii CHAPTER 2: AN SSU rDNA BARCODING APPROACH TO THE DIVERSITY OF MARINE INTERSTITIAL CERCOZOANS, INCLUDING DESCRIPTIONS OF FOUR NOVEL GENERA AND NINE NOVEL SPECIES ..................................................24 2.1 Introduction ................................................................................................................24 2.2 Materials and methods................................................................................................26 2.2.1 Sampling and light microscopy (LM) ..............................................................26 2.2.2 DNA extraction and PCR amplification...........................................................27 2.2.3 Sequence alignment..........................................................................................28 2.2.4 Phylogenetic analyses.......................................................................................29 2.2.5 Genetic distance analyses .................................................................................30 2.2.6 Sequence availability........................................................................................30 2.3 Results ........................................................................................................................33 2.3.1 Identification of the examined flagellates.........................................................33 2.3.2 The Cryomonadida clade..................................................................................33 2.3.3 The Botuliformidae lineage ..............................................................................36 2.3.4 The Ventrifissuridae clade................................................................................37 2.3.5 The Verrucomonadidae clade...........................................................................40 2.3.6 The Discomonadidae clade...............................................................................42 2.3.7 DNA barcoding marine benthic cercozoans.....................................................43 2.3.8 Molecular phylogenetic analyses of marine benthic cercozoans......................44 2.4 Discussion...................................................................................................................44 2.4.1 Hidden diversity of marine benthic cercozoans................................................44 2.4.2 The current composition of Protaspis ..............................................................45 2.4.3 Cryothecomonas longipes is more closely related to Protaspis sensu stricto ..46 2.4.4 The benthic Botuliforma benthica gen. et sp. nov. is closely related to the planktonic Ebria tripartita................................................................................48 2.4.5 The cellular identities of previously undescribed cercozoans ..........................49 2.4.6 Barcoding marine benthic cercozoans..............................................................51 2.5 References ..................................................................................................................66 CHAPTER 3: ULTRASTRUCTURE, LIFE CYCLE AND MOLECULAR PHYLOGENETIC POSITION OF A NOVEL MARINE SAND-DWELLING iv CERCOZOAN: CLAUTRIAVIA BIFLAGELLATA N. SP......................................................70 3.1 Introduction ................................................................................................................70 3.2 Materials and methods................................................................................................71 3.2.1 Sample collection .............................................................................................71 3.2.2 Light microscopy (LM) ....................................................................................71 3.2.3 Culture establishment .......................................................................................72 3.2.4 Scanning electron microscopy (SEM)..............................................................72 3.2.5 Transmission
Load more

Recommended publications
  • WA488 3831 P1825-T43-Nr4 AP.Pdf
    Acta Protozool. (2004) 43: 291 - 301 Syndrome of the Failure to Turn off Mitotic Activity in Tetrahymena thermophila: in cdaA1 Phenotypes Ewa JOACHIMIAK, Janina KACZANOWSKA, Mauryla KIERSNOWSKA and Andrzej KACZANOWSKI Department of Cytophysiology, Institute of Zoology, Warsaw University, Warsaw, Poland Summary. During early micronuclear mitosis of a wild type Tetrahymena thermophila, basal body proliferation and cortical growth are localized in the equatorial region of the pre-dividing cell. These processes are arrested prior to cytokinesis when the fission line gaps appear in ciliary rows. Then a putative marker of cellular polarity, the fenestrin antigen, appears in the apical zone of the dividing cell and around the old oral apparatus (OA1) and in the cortex localized posterior to the fission line gaps and around the new oral apparatus (OA2) i.e. in the apical cortex of the prospective posterior daughter cell. Prior to cytokinesis, the membranelles within OA1 and OA2 oral apparatuses are strongly labeled with the MPM2 antibody against mitotic phosphoproteins. The transition to cytokinesis is correlated with disappearance of both the polar fenestrin staining and of the phosphoprotein antigens in OA1 and OA2. cdaA1 (cell division arrest) mutant cells grown at the restrictive temperature do not produce a fission line and they do not undergo cytokinesis thereby generating irregular chains. The cdaA1 phenotypes continue elongation of their ciliary rows in equatorial regions, mostly without formation of the fission line gaps, accompanied with repetitive micronuclear mitoses and repetitive formation of the defective oral structures. In cdaA1 cells at restrictive temperature, the fenestrin antigen was recruited and then permanently found in the apical regions and around all oral apparatuses, and was always absent in equatorial regions, in spite of variability of immunostaining patterns, sizes and advancement of organization of OAs in different specimens of the same sample.
    [Show full text]
  • Author's Manuscript (764.7Kb)
    1 BROADLY SAMPLED TREE OF EUKARYOTIC LIFE Broadly Sampled Multigene Analyses Yield a Well-resolved Eukaryotic Tree of Life Laura Wegener Parfrey1†, Jessica Grant2†, Yonas I. Tekle2,6, Erica Lasek-Nesselquist3,4, Hilary G. Morrison3, Mitchell L. Sogin3, David J. Patterson5, Laura A. Katz1,2,* 1Program in Organismic and Evolutionary Biology, University of Massachusetts, 611 North Pleasant Street, Amherst, Massachusetts 01003, USA 2Department of Biological Sciences, Smith College, 44 College Lane, Northampton, Massachusetts 01063, USA 3Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, 7 MBL Street, Woods Hole, Massachusetts 02543, USA 4Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman Street, Providence, Rhode Island 02912, USA 5Biodiversity Informatics Group, Marine Biological Laboratory, 7 MBL Street, Woods Hole, Massachusetts 02543, USA 6Current address: Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, Connecticut 06520, USA †These authors contributed equally *Corresponding author: L.A.K - [email protected] Phone: 413-585-3825, Fax: 413-585-3786 Keywords: Microbial eukaryotes, supergroups, taxon sampling, Rhizaria, systematic error, Excavata 2 An accurate reconstruction of the eukaryotic tree of life is essential to identify the innovations underlying the diversity of microbial and macroscopic (e.g. plants and animals) eukaryotes. Previous work has divided eukaryotic diversity into a small number of high-level ‘supergroups’, many of which receive strong support in phylogenomic analyses. However, the abundance of data in phylogenomic analyses can lead to highly supported but incorrect relationships due to systematic phylogenetic error. Further, the paucity of major eukaryotic lineages (19 or fewer) included in these genomic studies may exaggerate systematic error and reduces power to evaluate hypotheses.
    [Show full text]
  • Ebriid Phylogeny and the Expansion of the Cercozoa
    ARTICLE IN PRESS Protist, Vol. 157, 279—290, May 2006 http://www.elsevier.de/protis Published online date 26 May 2006 ORIGINAL PAPER Ebriid Phylogeny and the Expansion of the Cercozoa Mona Hoppenrath1, and Brian S. Leander Canadian Institute for Advanced Research, Program in Evolutionary Biology, Departments of Botany and Zoology, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4 Submitted November 30, 2005; Accepted March 4, 2006 Monitoring Editor: Herve´ Philippe Ebria tripartita is a phagotrophic flagellate present in marine coastal plankton communities worldwide. This is one of two (possibly four) described extant species in the Ebridea, an enigmatic group of eukaryotes with an unclear phylogenetic position. Ebriids have never been cultured, are usually encountered in low abundance and have a peculiar combination of ultrastructural characters including a large nucleus with permanently condensed chromosomes and an internal skeleton composed of siliceous rods. Consequently, the taxonomic history of the group has been tumultuous and has included a variety of affiliations, such as silicoflagellates, dinoflagellates, ‘radiolarians’ and ‘neomonads’. Today, the Ebridea is treated as a eukaryotic taxon incertae sedis because no morphological or molecular features have been recognized that definitively relate ebriids with any other eukaryotic lineage. We conducted phylogenetic analyses of small subunit rDNA sequences from two multi-specimen isolations of Ebria tripartita. The closest relatives to the sequences from Ebria tripartita are environmental sequences from a submarine caldera floor. This newly recognized Ebria clade was most closely related to sequences from described species of Cryothecomonas and Protaspis. These molecular phylogenetic relationships were consistent with current ultrastructural data from all three genera, leading to a robust placement of ebriids within the Cercozoa.
    [Show full text]
  • Evolutionary Relationships Among Marine Cercozoans As Inferred from Combined SSU and LSU Rdna Sequences and Polyubiquitin Insertions
    Molecular Phylogenetics and Evolution 57 (2010) 518–527 Contents lists available at ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev Evolutionary relationships among marine cercozoans as inferred from combined SSU and LSU rDNA sequences and polyubiquitin insertions Chitchai Chantangsi a,b,*, Mona Hoppenrath a,1, Brian S. Leander a a Canadian Institute for Advanced Research, Program in Integrated Microbial Biodiversity, Departments of Zoology and Botany, University of British Columbia, Vancouver, BC, Canada V6T 1Z4 b Department of Biology, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok 10330, Thailand article info abstract Article history: An insertion of one or two amino acids at the monomer–monomer junctions of polyubiquitin is a distinct Received 23 October 2009 and highly conserved molecular character that is shared by two very diverse clades of microeukaryotes, Revised 15 July 2010 the Cercozoa and the Foraminifera. It has been suggested that an insertion consisting of one amino acid, Accepted 15 July 2010 like that found in foraminiferans and some cercozoans, represents an ancestral state, and an insertion Available online 21 July 2010 consisting of two amino acids represents a derived state. However, the limited number of cercozoan taxa examined so far limits inferences about the number and frequency of state changes associated with this Keywords: character over deep evolutionary time. Cercozoa include a very diverse assemblage of mainly unculti- Cercozoa vated amoeboflagellates, and their tenuous phylogenetic interrelationships have been based largely on Ebria LSU rDNA small subunit (SSU) rDNA sequences. Because concatenated datasets consisting of both SSU and large Molecular phylogeny subunit (LSU) rDNA sequences have been shown to more robustly recover the phylogenetic relationships Polyubiquitin of other major groups of eukaryotes, we employed a similar approach for the Cercozoa.
    [Show full text]
  • Influence of Sea Ice on Protist Community Structure in the Central Arctic Ocean
    Table of Contents Influence of sea ice on protist community structure in the Central Arctic Ocean by Kristin Hardge A thesis submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biology Approved Dissertation Committee: Dr. Katja Metfies1, 2 Prof. Dr. Matthias Ullrich1 Dr. Mona Hoppenrath3 Dr. Eva-Maria Nöthig2 1 Jacobs University Bremen 2 Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven 3 Senckenberg Research Institute, German Centre for Marine Biodiversity Research, Wilhelmshaven Date of Defense: 10 August 2016 1 Table of Contents 2 Table of Contents “In the case of all things which have several parts and in which the totality is not, as it were, a mere heap, but the whole is something besides the parts, there is a cause.” Aristotle, Metaphysics 3 Table of Contents 4 Table of Contents Table of Contents 1 Summary ....................................................................................................................................... 7 2 General Introduction ..................................................................................................................... 9 2.1 Global warming ....................................................................................................................... 9 2.2 Changes in Arctic sea ice ........................................................................................................ 9 2.3 Protist biodiversity in the Arctic Ocean ...............................................................................
    [Show full text]
  • The Revised Classification of Eukaryotes
    Published in Journal of Eukaryotic Microbiology 59, issue 5, 429-514, 2012 which should be used for any reference to this work 1 The Revised Classification of Eukaryotes SINA M. ADL,a,b ALASTAIR G. B. SIMPSON,b CHRISTOPHER E. LANE,c JULIUS LUKESˇ,d DAVID BASS,e SAMUEL S. BOWSER,f MATTHEW W. BROWN,g FABIEN BURKI,h MICAH DUNTHORN,i VLADIMIR HAMPL,j AARON HEISS,b MONA HOPPENRATH,k ENRIQUE LARA,l LINE LE GALL,m DENIS H. LYNN,n,1 HILARY MCMANUS,o EDWARD A. D. MITCHELL,l SHARON E. MOZLEY-STANRIDGE,p LAURA W. PARFREY,q JAN PAWLOWSKI,r SONJA RUECKERT,s LAURA SHADWICK,t CONRAD L. SCHOCH,u ALEXEY SMIRNOVv and FREDERICK W. SPIEGELt aDepartment of Soil Science, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada, and bDepartment of Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada, and cDepartment of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, 02881, USA, and dBiology Center and Faculty of Sciences, Institute of Parasitology, University of South Bohemia, Cˇeske´ Budeˇjovice, Czech Republic, and eZoology Department, Natural History Museum, London, SW7 5BD, United Kingdom, and fWadsworth Center, New York State Department of Health, Albany, New York, 12201, USA, and gDepartment of Biochemistry, Dalhousie University, Halifax, NS, B3H 4R2, Canada, and hDepartment of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada, and iDepartment of Ecology, University of Kaiserslautern, 67663, Kaiserslautern, Germany, and jDepartment of Parasitology, Charles University, Prague, 128 43, Praha 2, Czech
    [Show full text]
  • Gymnophrys Cometa and Lecythium Sp. Are Core Cercozoa: Evolutionary Implications
    Acta Protozool. (2003) 42: 183 - 190 Gymnophrys cometa and Lecythium sp. are Core Cercozoa: Evolutionary Implications Sergey I. NIKOLAEV1, Cédric BERNEY2, José FAHRNI2, Alexander P. MYLNIKOV3, Vladimir V. ALESHIN1, Nikolai B. PETROV1 and Jan PAWLOWSKI2 1A. N. Belozersky Institute of Physico-Chemical Biology, Department of Evolutionary Biochemistry, Moscow State University, Moscow, Russian Federation; 2Department of Zoology and Animal Biology, University of Geneva, Switzerland; 3Institute for Biology of Inland Waters, RAS, Yaroslavskaya obl., Borok, Russian Federation Summary. Recent phylogenetic analyses based on different molecular markers have revealed the existence of the Cercozoa, a group of protists including such morphologically diverse taxa as the cercomonad flagellates, the euglyphid testate filose amoebae, the chloroplast- bearing chlorarachniophytes, and the plasmodiophorid plant pathogens. Molecular data also indicate a close relationship between Cercozoa and Foraminifera (Granuloreticulosea). Little is known, however, about the origin of both groups and their phylogenetic relationships. Here we present the complete small-subunit ribosomal RNA (SSU rRNA) sequence of Gymnophrys cometa, formerly included in the athalamid Granuloreticulosea, as well as that of the test-bearing filose amoeba Lecythium sp. Our study shows that the two organisms clearly belong to the Cercozoa, and indicates that Gymnophrys is not closely related to Foraminifera, supporting the view that Granuloreticulosea sensu lato do not form a natural assemblage. Phylogenetic analyses including most available SSU rRNA sequences from Cercozoa suggest that a rigid, external cell envelope appeared several times independently during the evolution of the group. Furthermore, our results bring additional evidence for the wide morphological variety among Cercozoa, which now also include protists bearing granular pseudopodia and exhibiting mitochondria with flattened cristae.
    [Show full text]
  • Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes
    PROF. SINA ADL (Orcid ID : 0000-0001-6324-6065) PROF. DAVID BASS (Orcid ID : 0000-0002-9883-7823) DR. CÉDRIC BERNEY (Orcid ID : 0000-0001-8689-9907) DR. PACO CÁRDENAS (Orcid ID : 0000-0003-4045-6718) DR. IVAN CEPICKA (Orcid ID : 0000-0002-4322-0754) DR. MICAH DUNTHORN (Orcid ID : 0000-0003-1376-4109) PROF. BENTE EDVARDSEN (Orcid ID : 0000-0002-6806-4807) DR. DENIS H. LYNN (Orcid ID : 0000-0002-1554-7792) DR. EDWARD A.D MITCHELL (Orcid ID : 0000-0003-0358-506X) PROF. JONG SOO PARK (Orcid ID : 0000-0001-6253-5199) DR. GUIFRÉ TORRUELLA (Orcid ID : 0000-0002-6534-4758) Article DR. VASILY V. ZLATOGURSKY (Orcid ID : 0000-0002-2688-3900) Article type : Original Article Corresponding author mail id: [email protected] Adl et al.---Classification of Eukaryotes Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes Sina M. Adla, David Bassb,c, Christopher E. Laned, Julius Lukeše,f, Conrad L. Schochg, Alexey Smirnovh, Sabine Agathai, Cedric Berneyj, Matthew W. Brownk,l, Fabien Burkim, Paco Cárdenasn, Ivan Čepičkao, Ludmila Chistyakovap, Javier del Campoq, Micah Dunthornr,s, Bente Edvardsent, Yana Eglitu, Laure Guillouv, Vladimír Hamplw, Aaron A. Heissx, Mona Hoppenrathy, Timothy Y. Jamesz, Sergey Karpovh, Eunsoo Kimx, Martin Koliskoe, Alexander Kudryavtsevh,aa, Daniel J. G. Lahrab, Enrique Laraac,ad, Line Le Gallae, Denis H. Lynnaf,ag, David G. Mannah, Ramon Massana i Moleraq, Edward A. D. Mitchellac,ai , Christine Morrowaj, Jong Soo Parkak, Jan W. Pawlowskial, Martha J. Powellam, Daniel J. Richteran, Sonja Rueckertao, Lora Shadwickap, Satoshi Shimanoaq, Frederick W. Spiegelap, Guifré Torruella i Cortesar, Noha Youssefas, Vasily Zlatogurskyh,at, Qianqian Zhangau,av.
    [Show full text]
  • Kingdom Chromista and Its Eight Phyla: a New Synthesis Emphasising Periplastid Protein Targeting, Cytoskeletal and Periplastid Evolution, and Ancient Divergences
    Protoplasma DOI 10.1007/s00709-017-1147-3 ORIGINAL ARTICLE Kingdom Chromista and its eight phyla: a new synthesis emphasising periplastid protein targeting, cytoskeletal and periplastid evolution, and ancient divergences Thomas Cavalier-Smith1 Received: 12 April 2017 /Accepted: 18 July 2017 # The Author(s) 2017. This article is an open access publication Abstract In 1981 I established kingdom Chromista, distin- membranes generates periplastid vesicles that fuse with the guished from Plantae because of its more complex arguably derlin-translocon-containing periplastid reticulum chloroplast-associated membrane topology and rigid tubular (putative red algal trans-Golgi network homologue; present multipartite ciliary hairs. Plantae originated by converting a in all chromophytes except dinoflagellates). I explain chromist cyanobacterium to chloroplasts with Toc/Tic translocons; origin from ancestral corticates and neokaryotes, reappraising most evolved cell walls early, thereby losing phagotrophy. tertiary symbiogenesis; a chromist cytoskeletal synapomor- Chromists originated by enslaving a phagocytosed red alga, phy, a bypassing microtubule band dextral to both centrioles, surrounding plastids by two extra membranes, placing them favoured multiple axopodial origins. I revise chromist higher within the endomembrane system, necessitating novel protein classification by transferring rhizarian subphylum Endomyxa import machineries. Early chromists retained phagotrophy, from Cercozoa to Retaria; establishing retarian subphylum remaining naked and repeatedly reverted to heterotrophy by Ectoreta for Foraminifera plus Radiozoa, apicomonad sub- losing chloroplasts. Therefore, Chromista include secondary classes, new dinozoan classes Myzodinea (grouping phagoheterotrophs (notably ciliates, many dinoflagellates, Colpovora gen. n., Psammosa), Endodinea, Sulcodinea, and Opalozoa, Rhizaria, heliozoans) or walled osmotrophs subclass Karlodinia; and ranking heterokont Gyrista as phy- (Pseudofungi, Labyrinthulea), formerly considered protozoa lum not superphylum.
    [Show full text]
  • Molecular Phylogeny and Taxonomy of Testate Amoebae (Protist) and Host-Symbiont Evolutionary Relationships Within Mixotrophic Taxa
    Molecular Phylogeny and Taxonomy of Testate Amoebae (Protist) and Host-Symbiont Evolutionary Relationships within Mixotrophic Taxa Thesis Submitted to Faculty of Science, University of Neuchâtel in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biological Science By Fatma Gomaa Members of the jury: Prof. Edward Mitchell: University of Neuchâtel, Thesis director, Switzerland Dr. Enrique Lara: University of Neuchâtel, Thesis co-director, Switzerland Dr. Christophe Praz: University of Neuchâtel, Switzerland Prof. Jan Pawlowski: University of Geneva, Switzerland Dr. Alexander Kudryavtsev: University of St-Petersburg, Russia Prof. Milcho Todorov: Bulgarian Academy of Sciences, Bulgaria Accepted in 24/08/2012 University of Neuchâtel 2013 • Faculté des sciences Secrétariat-décanat de Faculté U111e Rue Emile-Argand 11 2000 Neuchatel - Suisse UNIVERSITÉ DE Tél: + 41 (0)32 718 2100 NEUCHÂTEL E-mail: [email protected] IMPRIMATUR POUR TH ESE DE DOCTORAT La Faculté des sciences de l'Université de Neuchâtel autorise l'impression de la présente thèse soutenue par Madame Fatma Fathy Sayed GOMAA Titre : Molecular Phylogeny and Taxonomy of Testate Amoebae (Protist) and Host-Symbiont Evolutionary Relationships Within Mixotrophic Taxa sur le rapport des membres du jury: • Prof. Edward Mitchell, directeur de thèse, UniNe • Dr Enrique Lara, UniNe • Dr Christophe Praz, UniNe • Prof. Jan Pawlowski, Université de Genève • Dr Alexander Kudryavtsev, St. Petersburg State University, Russie • Prof. Milcho Todorov, Académie des Sciences de Bulgarie Neuchâtel, le 30 avril'2013 Le Doyen, Prof. P. Kropf 1 Imprimatur pour thèse de doctorat www.unine.ch/sclences “Travel through the earth and find how I originated creation” (El Ainkabout, 20 Quran 610CE) Contents Abstract 8 Résumé 11 1 Introduction 14 1.
    [Show full text]
  • Phylogenics and Patterns of Molecular Evolution in Amoebozoa
    University of Massachusetts Amherst ScholarWorks@UMass Amherst Open Access Dissertations 9-1-2011 Phylogenics and Patterns of Molecular Evolution in Amoebozoa Daniel J.G. Lahr University of Massachusetts Amherst, [email protected] Follow this and additional works at: https://scholarworks.umass.edu/open_access_dissertations Part of the Ecology and Evolutionary Biology Commons Recommended Citation Lahr, Daniel J.G., "Phylogenics and Patterns of Molecular Evolution in Amoebozoa" (2011). Open Access Dissertations. 448. https://scholarworks.umass.edu/open_access_dissertations/448 This Open Access Dissertation is brought to you for free and open access by ScholarWorks@UMass Amherst. It has been accepted for inclusion in Open Access Dissertations by an authorized administrator of ScholarWorks@UMass Amherst. For more information, please contact [email protected]. PHYLOGENETICS AND PATTERNS OF MOLECULAR EVOLUTION IN AMOEBOZOA A Dissertation Presented by DANIEL J. G. LAHR Submitted to the Graduate School of the University of Massachusetts Amherst in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY September 2011 Program in Organismic and Evolutionary Biology © Copyright by Daniel J. G. Lahr 2011 All Rights Reserved PHYLOGENETICS AND PATTERNS OF MOLECULAR EVOLUTION IN AMOEBOZOA A Dissertation Presented by DANIEL J. G. LAHR Approved as to style and content by: ____________________________________________________ Laura A. Katz, Chair ____________________________________________________ Benjamin B. Normark, Member ____________________________________________________ Michael E. Hood, Member ____________________________________________________ O. Roger Anderson, Member _____________________________ Elizabeth R. Dumont, Director Organismic and Evolutionary Biology DEDICATION To Paula and my family. “Without trace of nerve elements, and without definite, fixed organs of any kind, internal or external, the Rhizopod,—simplest of all animals, a mere jelly-speck,—moves about with the apparent purposes of more complex creatures.
    [Show full text]
  • Multigene Phylogeny and Cell Evolution of Chromist Infrakingdom Rhizaria: Contrasting Cell Organisation of Sister Phyla Cercozoa and Retaria
    Protoplasma https://doi.org/10.1007/s00709-018-1241-1 ORIGINAL ARTICLE Multigene phylogeny and cell evolution of chromist infrakingdom Rhizaria: contrasting cell organisation of sister phyla Cercozoa and Retaria Thomas Cavalier-Smith1 & Ema E. Chao1 & Rhodri Lewis1 Received: 11 December 2017 /Accepted: 12 March 2018 # The Author(s) 2018 Abstract Infrakingdom Rhizaria is one of four major subgroups with distinct cell body plans that comprise eukaryotic kingdom Chromista. Unlike other chromists, Rhizaria are mostly heterotrophic flagellates, amoebae or amoeboflagellates, commonly with reticulose (net-like) or filose (thread-like) feeding pseudopodia; uniquely for eukaryotes, cilia have proximal ciliary transition-zone hub- lattices. They comprise predominantly flagellate phylum Cercozoa and reticulopodial phylum Retaria, whose exact phylogenetic relationship has been uncertain. Given even less clear relationships amongst cercozoan classes, we sequenced partial transcriptomes of seven Cercozoa representing five classes and endomyxan retarian Filoreta marina to establish 187-gene multiprotein phylogenies. Ectoreta (retarian infraphyla Foraminifera, Radiozoa) branch within classical Cercozoa as sister to reticulose Endomyxa. This supports recent transfer of subphylum Endomyxa from Cercozoa to Retaria alongside subphylum Ectoreta which embraces classical retarians where capsules or tests subdivide cells into organelle-containing endoplasm and anastomosing pseudopodial net-like ectoplasm. Cercozoa are more homogeneously filose, often with filose
    [Show full text]