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Molecular Data and the Evolutionary History of Dinoflagellates by Juan Fernando Saldarriaga Echavarria Diplom, Ruprecht-Karls-Un
Molecular data and the evolutionary history of dinoflagellates by Juan Fernando Saldarriaga Echavarria Diplom, Ruprecht-Karls-Universitat Heidelberg, 1993 A THESIS SUBMITTED IN PARTIAL FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY in THE FACULTY OF GRADUATE STUDIES Department of Botany We accept this thesis as conforming to the required standard THE UNIVERSITY OF BRITISH COLUMBIA November 2003 © Juan Fernando Saldarriaga Echavarria, 2003 ABSTRACT New sequences of ribosomal and protein genes were combined with available morphological and paleontological data to produce a phylogenetic framework for dinoflagellates. The evolutionary history of some of the major morphological features of the group was then investigated in the light of that framework. Phylogenetic trees of dinoflagellates based on the small subunit ribosomal RNA gene (SSU) are generally poorly resolved but include many well- supported clades, and while combined analyses of SSU and LSU (large subunit ribosomal RNA) improve the support for several nodes, they are still generally unsatisfactory. Protein-gene based trees lack the degree of species representation necessary for meaningful in-group phylogenetic analyses, but do provide important insights to the phylogenetic position of dinoflagellates as a whole and on the identity of their close relatives. Molecular data agree with paleontology in suggesting an early evolutionary radiation of the group, but whereas paleontological data include only taxa with fossilizable cysts, the new data examined here establish that this radiation event included all dinokaryotic lineages, including athecate forms. Plastids were lost and replaced many times in dinoflagellates, a situation entirely unique for this group. Histones could well have been lost earlier in the lineage than previously assumed. -
The Planktonic Protist Interactome: Where Do We Stand After a Century of Research?
bioRxiv preprint doi: https://doi.org/10.1101/587352; this version posted May 2, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Bjorbækmo et al., 23.03.2019 – preprint copy - BioRxiv The planktonic protist interactome: where do we stand after a century of research? Marit F. Markussen Bjorbækmo1*, Andreas Evenstad1* and Line Lieblein Røsæg1*, Anders K. Krabberød1**, and Ramiro Logares2,1** 1 University of Oslo, Department of Biosciences, Section for Genetics and Evolutionary Biology (Evogene), Blindernv. 31, N- 0316 Oslo, Norway 2 Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta, 37-49, ES-08003, Barcelona, Catalonia, Spain * The three authors contributed equally ** Corresponding authors: Ramiro Logares: Institute of Marine Sciences (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Catalonia, Spain. Phone: 34-93-2309500; Fax: 34-93-2309555. [email protected] Anders K. Krabberød: University of Oslo, Department of Biosciences, Section for Genetics and Evolutionary Biology (Evogene), Blindernv. 31, N-0316 Oslo, Norway. Phone +47 22845986, Fax: +47 22854726. [email protected] Abstract Microbial interactions are crucial for Earth ecosystem function, yet our knowledge about them is limited and has so far mainly existed as scattered records. Here, we have surveyed the literature involving planktonic protist interactions and gathered the information in a manually curated Protist Interaction DAtabase (PIDA). In total, we have registered ~2,500 ecological interactions from ~500 publications, spanning the last 150 years. -
Pusillus Poseidon's Guide to Protozoa
Pusillus Poseidon’s guide to PROTOZOA GENERAL NOTES ABOUT PROTOZOANS Protozoa are also called protists. The word “protist” is the more general term and includes all types of single-celled eukaryotes, whereas “protozoa” is more often used to describe the protists that are animal-like (as opposed to plant-like or fungi-like). Protists are measured using units called microns. There are 1000 microns in one millimeter. A millimeter is the smallest unit on a metric ruler and can be estimated with your fingers: The traditional way of classifying protists is by the way they look (morphology), by the way they move (mo- tility), and how and what they eat. This gives us terms such as ciliates, flagellates, ameboids, and all those colors of algae. Recently, the classification system has been overhauled and has become immensely complicated. (Infor- mation about DNA is now the primary consideration for classification, rather than how a creature looks or acts.) If you research these creatures on Wikipedia, you will see this new system being used. Bear in mind, however, that the categories are constantly shifting as we learn more and more about protist DNA. Here is a visual overview that might help you understand the wide range of similarities and differences. Some organisms fit into more than one category and some don’t fit well into any category. Always remember that classification is an artificial construct made by humans. The organisms don’t know anything about it and they don’t care what we think! CILIATES Eats anything smaller than Blepharisma looks slightly pink because it Blepharisma itself, even smaller Bleph- makes a red pigment that senses light (simi- arismas. -
Protistology an International Journal Vol
Protistology An International Journal Vol. 10, Number 2, 2016 ___________________________________________________________________________________ CONTENTS INTERNATIONAL SCIENTIFIC FORUM «PROTIST–2016» Yuri Mazei (Vice-Chairman) Welcome Address 2 Organizing Committee 3 Organizers and Sponsors 4 Abstracts 5 Author Index 94 Forum “PROTIST-2016” June 6–10, 2016 Moscow, Russia Website: http://onlinereg.ru/protist-2016 WELCOME ADDRESS Dear colleagues! Republic) entitled “Diplonemids – new kids on the block”. The third lecture will be given by Alexey The Forum “PROTIST–2016” aims at gathering Smirnov (Saint Petersburg State University, Russia): the researchers in all protistological fields, from “Phylogeny, diversity, and evolution of Amoebozoa: molecular biology to ecology, to stimulate cross- new findings and new problems”. Then Sandra disciplinary interactions and establish long-term Baldauf (Uppsala University, Sweden) will make a international scientific cooperation. The conference plenary presentation “The search for the eukaryote will cover a wide range of fundamental and applied root, now you see it now you don’t”, and the fifth topics in Protistology, with the major focus on plenary lecture “Protist-based methods for assessing evolution and phylogeny, taxonomy, systematics and marine water quality” will be made by Alan Warren DNA barcoding, genomics and molecular biology, (Natural History Museum, United Kingdom). cell biology, organismal biology, parasitology, diversity and biogeography, ecology of soil and There will be two symposia sponsored by ISoP: aquatic protists, bioindicators and palaeoecology. “Integrative co-evolution between mitochondria and their hosts” organized by Sergio A. Muñoz- The Forum is organized jointly by the International Gómez, Claudio H. Slamovits, and Andrew J. Society of Protistologists (ISoP), International Roger, and “Protists of Marine Sediments” orga- Society for Evolutionary Protistology (ISEP), nized by Jun Gong and Virginia Edgcomb. -
Some Observations Upon Spirostomum Ambiguum (Ehrenberg). Ann Bishop, 31.Sc
Some Observations upon Spirostomum ambiguum (Ehrenberg). By Ann Bishop, 31.Sc, Victoria University, Manchester. With Plates 22 and 23 and 9 Text-figures. CONTENTS. PAGE 1. HISTORICAL 392 2. MATERIAL AND METHODS ....... 393 Fixation 393 Staining 394 Observations on Living Specimens ..... 394 Feeding Methods ........ 395 3. OBSERVATIONS ON THE MORPHOLOGY OF SPIROSTOMUM AMBIGUUM 395 Contractile Vacuole ........ 395 Endoplasm and Nuclei ....... 397 The Micronuclei . • - . • • .399 Abnormalities in the form of the Meganucleus . .401 >i. METHODS OF CULTIVATION 402 5. FOOD CYCLE 406 6. VARIETIES OF SPIROSTOMUM AMBIGUUM 409 7. REPRODUCTION . .41.1 A. Observations on the Growth and Reproduction of Spiro- stomum ambiguum during cultivation . .411 B. Fission 416 C. Conjugation 422 8. LITERATURE .... 431 9. EXPLANATION OF PLATES 22 AND 23 ..... 433 D d 2 392 ANN BISHOP 1. HISTORICAL. THE genus Spirostomurn was first mentioned by Ehrenberg, but no definition nor description was given. Its systematic position and the question of the number and identity of the species contained in it was a subject for discussion for many years. Later, Dujardin (7) gave a very satisfactory description of the genus in the following words : ' Corps cylindrique tres-allonge et tres-flexible, souvent tordu sur lui-meme, couvert cle cils disposes suivant les stries obliques ou en helice de la surface; avec une bouches situee lateralement au dela du milieu, a l'extremite d'une rangee de cils plus forts.' He recognized, however, only S p ir o s t o m um a m b i g u u m as a true species. It is to Dr. Stein (28) that w^e are indebted for a comprehen- sive and beautifully illustrated description of the genus, together with a detailed account of the vicissitudes of nomen- clature through which it had passed since its discovery by Ehrenberg. -
Systematic Index
Systematic Index The systematic index contains the scientific names of all taxa mentioned in the book e.g., Anisonema sp., Anopheles and the vernacular names of protists, for example, tintinnids. The index is two-sided, that is, species ap - pear both with the genus-group name first e.g., Acineria incurvata and with the species-group name first ( incurvata , Acineria ). Species and genera, valid and invalid, are in italics print. The scientific name of a subgenus, when used with a binomen or trinomen, must be interpolated in parentheses between the genus-group name and the species- group name according to the International Code of Zoological Nomenclature. In the following index, these paren - theses are omitted to simplify electronic sorting. Thus, the name Apocolpodidium (Apocolpodidium) etoschense is list - ed as Apocolpodidium Apocolpodidium etoschense . Note that this name is also listed under “ Apocolpodidium etoschense , Apocolpodidium ” and “ etoschense , Apocolpodidium Apocolpodidium ”. Suprageneric taxa, communities, and vernacular names are represented in normal type. A boldface page number indicates the beginning of a detailed description, review, or discussion of a taxon. f or ff means include the following one or two page(s), respectively. A Actinobolina vorax 84 Aegyriana paroliva 191 abberans , Euplotes 193 Actinobolina wenrichii 84 aerophila , Centropyxis 87, 191 abberans , Frontonia 193 Actinobolonidae 216 f aerophila sphagnicola , Centropyxis 87 abbrevescens , Deviata 140, 200, 212 Actinophrys sol 84 aerophila sylvatica -
Biologia Celular – Cell Biology
Biologia Celular – Cell Biology BC001 - Structural Basis of the Interaction of a Trypanosoma cruzi Surface Molecule Implicated in Oral Infection with Host Cells and Gastric Mucin CORTEZ, C.*1; YOSHIDA, N.1; BAHIA, D.1; SOBREIRA, T.2 1.UNIFESP, SÃO PAULO, SP, BRASIL; 2.SINCROTRON, CAMPINAS, SP, BRASIL. e-mail:[email protected] Host cell invasion and dissemination within the host are hallmarks of virulence for many pathogenic microorganisms. As concerns Trypanosoma cruzi that causes Chagas disease, the insect vector-derived metacyclic trypomastigotes (MT) initiate infection by invading host cells, and later blood trypomastigotes disseminate to diverse organs and tissues. Studies with MT generated in vitro and tissue culture-derived trypomastigotes (TCT), as counterparts of insect- borne and bloodstream parasites, have implicated members of the gp85/trans-sialidase superfamily, MT gp82 and TCT Tc85-11, in cell invasion and interaction with host factors. Here we analyzed the gp82 structure/function characteristics and compared them with those previously reported for Tc85-11. One of the gp82 sequences identified as a cell binding site consisted of an alpha-helix, which connects the N-terminal beta-propeller domain to the C- terminal beta-sandwich domain where the second binding site is nested. In the gp82 structure model, both sites were exposed at the surface. Unlike gp82, the Tc85-11 cell adhesion sites are located in the N-terminal beta-propeller region. The gp82 sequence corresponding to the epitope for a monoclonal antibody that inhibits MT entry into target cells was exposed on the surface, upstream and contiguous to the alpha-helix. Located downstream and close to the alpha-helix was the gp82 gastric mucin binding site, which plays a central role in oral T. -
Ciliophora, Heterotrichea
Phylogeny of two poorly known ciliate genera (Ciliophora, Heterotrichea), with notes on the redenition of Gruberia uninucleata Kahl, 1932 and Linostomella vorticella (Ehrenberg, 1833) based on populations found in China Yong Chi Ocean University of China Yuqing Li Ocean University of China Qianqian Zhang Chinese Academy of Sciences Mingzhen Ma Ocean University of China Alan Warren Natural History Museum Xiangrui Chen ( [email protected] ) Weibo Song Ocean University of China Research article Keywords: Heterotrichous, Morphology, Phylogeny, SSU rDNA Posted Date: February 3rd, 2020 DOI: https://doi.org/10.21203/rs.2.22447/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Version of Record: A version of this preprint was published on October 2nd, 2020. See the published version at https://doi.org/10.1186/s12866-020-01879-4. Page 1/27 Abstract Background Heterotrichous ciliates are common members of microeukaryote communities which play important roles in the transfer of material and energy ow in aquatic food webs. This group has been known over two centuries due to their large body size and cosmopolitan distribution. Nevertheless, species identication and phylogenetic relationships of heterotrichs remain challenging due to the lack of accurate morphological information and insucient molecular data. Results The morphology and phylogeny of two poorly known heterotrichous ciliates, Gruberia uninucleata Kahl, 1932 and Linostomella vorticella (Ehrenberg, 1833) Aescht in Foissner et al. , 1999, were investigated based on their living morphology, infraciliature, and small subunit (SSU) rDNA sequence data. Based on a combination of previous and present studies, detailed morphometric data and the improved diagnoses of both species are supplied here. -
The Cytoplasmic Structures of Spirostomum Ambiguum (Ehrenberg). by Ann Bishop, Ph.D., M.Sc
The Cytoplasmic Structures of Spirostomum ambiguum (Ehrenberg). By Ann Bishop, Ph.D., M.Sc. From the Zoological Department, the University of Manchester. With Plates 17 and 18 and 3 Text-figures. MATERIAL. THE Spirostoma used in this study were obtained from test- tube cultures made with boiled wheat-grains and boiled aqua- rium- or boiled pond-water, or with boiled leaves collected from ponds to which boiled aquarium- or pond-water was added. Details of these culture methods were given in an earlier paper (1, p. 402). Occasionally ' wild ' Spirostoma, collected from a pond on Coe Fen, Cambridge, or from one in Cheshire, were used. The study was made almost entirely upon the large variety of Spirostomum known as Spirostomum am- biguum Major (21), but Spirostomum ambiguum Minor was studied sufficiently to show that the structures are similar in the two varieties. METHODS. A number of different fixatives were tried, including Schau- dinn's solution with varying amounts of glacial acetic acid below 5 per cent. ; the alcoholic modification of Bouin's fluid ; strong Memming's fluid; 1 per cent, osmic acid ; the picro- mercuric fixative used by Yocum (31) having the formula— Mercuric bichloride .... 2 grm. Picric acid ...... 1 grm. 95 per cent, alcohol . .110 c.c. Ether . 20 c.c. Acetic acid . .20 c.c. 40 per cent, formol ..... 50 c.c. L 2 148 ANN BISHOP The fluid used by Neresheimer (17), i.e.— 8 per cent, formol ..... 20 c.c. 2 per cent, calcium bichromate . .20 c.c. Acetic acid ...... 1 c.c. to which a drop of osmic acid is added before using, was also used. -
The Ecology of Marine Microbenthos Ii. the Food of Marine Benthic Ciliates
OPHELIA, 5: 73-121 (May 1968). THE ECOLOGY OF MARINE MICROBENTHOS II. THE FOOD OF MARINE BENTHIC CILIATES TOM FENCHEL Marine Biological Laboratory, 3000 Helsinger, Denmark CONTENTS Abstract 73 Introduction 73 Material and methods. .. .......... .. 74 General part. ............................ .. 75 The mechanical properties of the food. 75 Specificity in choice of food. ............. .. 78 Special part. ............................... 84 Orcer Gymnostomatida .. 84 Order Trichostomatida .................•.. 97 Order Hymenostomatida " 100 Order Heterotrichida 108 Order Odontostomatida 113 Order Oligotrichida I 13 Order Hypotrichida , 114 References. .............................. .. I 19 ABSTRACT The paper brings together knowledge on the food of marine benthic ciliates with the exception of sessile forms. References are given to 260 species of which 90 have been studied by the author. The classification of ciliates according to their natural food and the specificity in choice of food is discussed and the ecological significance of discrimination of food according to size is emphasized. INTRODUCTION In a previous study (Fenchel, 1967) the quantitative importance of protozoa - especially ciliates - in marine microbenthos was investigated and it was concluded Downloaded by [Copenhagen University Library], [Mr Tom Fenchel] at 01:12 22 December 2012 that the ciliates play an important role in certain sediments, viz. fine sands and sulphureta. A further analysis of the structure and function of the microfauna communities requires knowledge of factors which influence the animal popula- tions. Of these food is probably one of the most important. Thus Faure-Fremiet 74 TOM FENCHEL (1950a, b, 1951a), Fenchel & Jansson (1966), Lackey (1961), Noland (1925), Perkins (1958), Picken (1937), Stout (1956) and Webb (1956) all stress the im- portance of the food factor for the structure of protozoan communities. -
Ciliate Biodiversity and Phylogenetic Reconstruction Assessed by Multiple Molecular Markers Micah Dunthorn University of Massachusetts Amherst, [email protected]
University of Massachusetts Amherst ScholarWorks@UMass Amherst Open Access Dissertations 9-2009 Ciliate Biodiversity and Phylogenetic Reconstruction Assessed by Multiple Molecular Markers Micah Dunthorn University of Massachusetts Amherst, [email protected] Follow this and additional works at: https://scholarworks.umass.edu/open_access_dissertations Part of the Life Sciences Commons Recommended Citation Dunthorn, Micah, "Ciliate Biodiversity and Phylogenetic Reconstruction Assessed by Multiple Molecular Markers" (2009). Open Access Dissertations. 95. https://doi.org/10.7275/fyvd-rr19 https://scholarworks.umass.edu/open_access_dissertations/95 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]. CILIATE BIODIVERSITY AND PHYLOGENETIC RECONSTRUCTION ASSESSED BY MULTIPLE MOLECULAR MARKERS A Dissertation Presented by MICAH DUNTHORN 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 2009 Organismic and Evolutionary Biology © Copyright by Micah Dunthorn 2009 All Rights Reserved CILIATE BIODIVERSITY AND PHYLOGENETIC RECONSTRUCTION ASSESSED BY MULTIPLE MOLECULAR MARKERS A Dissertation Presented By MICAH DUNTHORN Approved as to style and content by: _______________________________________ -
Molecular Phylogeny and Surface Morphology of Colpodella Edax (Alveolata): Insights Into the Phagotrophic Ancestry of Apicomplexans
J. Eukaryot. Microbiol., 50(5), 2003 pp. 334±340 q 2003 by the Society of Protozoologists Molecular Phylogeny and Surface Morphology of Colpodella edax (Alveolata): Insights into the Phagotrophic Ancestry of Apicomplexans BRIAN S. LEANDER,a OLGA N. KUVARDINA,b VLADIMIR V. ALESHIN,b ALEXANDER P. MYLNIKOVc and PATRICK J. KEELINGa aCanadian Institute for Advanced Research, Program in Evolutionary Biology, Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada, and bDepartments of Evolutionary Biochemistry and Invertebrate Zoology, Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119 992, Russian Federation, and cInstitute for the Biology of Inland Waters, Russian Academy of Sciences, Borok, Yaroslavskaya oblast, 152742, Russian Federation ABSTRACT. The molecular phylogeny of colpodellids provides a framework for inferences about the earliest stages in apicomplexan evolution and the characteristics of the last common ancestor of apicomplexans and dino¯agellates. We extended this research by presenting phylogenetic analyses of small subunit rRNA gene sequences from Colpodella edax and three unidenti®ed eukaryotes published from molecular phylogenetic surveys of anoxic environments. Phylogenetic analyses consistently showed C. edax and the environmental sequences nested within a colpodellid clade, which formed the sister group to (eu)apicomplexans. We also presented surface details of C. edax using scanning electron microscopy in order to supplement previous ultrastructural investigations of this species using transmission electron microscopy and to provide morphological context for interpreting environmental sequences. The microscopical data con®rmed a sparse distribution of micropores, an amphiesma consisting of small polygonal alveoli, ¯agellar hairs on the anterior ¯agellum, and a rostrum molded by the underlying (open-sided) conoid.