Tree of Life
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Handout Lec. 25
Introduction to Biosystematics - Zool 575 Introduction to Biosystematics Confidence - Assessment of the Strength of Lecture 25 - Confidence - Assessment 2 the Phylogenetic Signal - part 2 1. Consistency Index 2. g1 statistic, PTP - test “Quantifying the uncertainty of a phylogenetic 3. Consensus trees estimate is at least as important a goal as obtaining the phylogenetic estimate itself.” 4. Decay index (Bremer Support) - Huelsenbeck & Rannala (2004) 5. Bootstrapping / Jackknifing 6. Statistical hypothesis testing (frequentist) 7. Posterior probability (see lecture on Bayesian) Derek S. Sikes University of Calgary Zool 575 Multiple optimal trees Multiple optimal trees • Many methods can yield multiple equally • If multiple optimal trees are found we know optimal trees that all of them are wrong except, possibly, (hopefully) one • We can further select among these trees with additional criteria, but • Some have argued against consensus tree methods for this reason • Typically, relationships common to all the optimal trees are summarized with • Debate over quest for true tree (point consensus trees estimate) versus quantification of uncertainty Consensus methods Strict consensus methods • A consensus tree is a summary of the agreement • Strict consensus methods require agreement among a set of fundamental trees across all the fundamental trees • There are many consensus methods that differ in: • They show only those relationships that are 1. the kind of agreement unambiguously supported by the data 2. the level of agreement • The commonest -
Two New Species of Eimeria and Three New Species of Isospora (Apicomplexa, Eimeriidae) from Brazilian Mammals and Birds
Bull. Mus. nain. Hist. nat., Paris, 4' sér., 11, 1989, section A, n° 2 : 349-365. Two new species of Eimeria and three new species of Isospora (Apicomplexa, Eimeriidae) from Brazilian mammals and birds by R. LAINSON and J. J. SHAW Abstract. — Thirteen " four-eyed opossums ", Philander o. opossum, from Para State, north Brazil, were examined for coccidial oocysts in faecal samples. Five were infected with an eimerian, considered a new species, 2 with an isosporan which is possibly /. boughtoni Volk, and 2 with both thèse parasites. Oocysts of Eimeria philanderi n. sp., are spherical to subspherical and average 23.50 x 22.38 (21.25- 27.50 x 18.75-25.00) (xm : single polar body : no oocyst residuum. Oocyst wall 1.88 [ira, with mamillated surface and composed of two striated layers, the inner brown-yellow and the outer colourless : no micropyle. Sporocysts average 11.35 x 8.13 (10.00-12.00 x 7.50-8.75) (xm, oval to ellipsoidal, with prominent nipple-like Stieda body : residuum bulky, compact or scattered between two recurved sporozoites. Oocysts of the Isospora sp., close to /. boughtoni initially sub-spherical, 17.92 x 16.53 (16.25- 20.00 x 13.75-18.75) (xm : latterly deformed by collapse of the délicate, colourless wall : no micropyle, oocyst residuum or polar body. Sporocysts 13.35 x 9.88 (12.50-13.75 x 8.75-11.25) (xm, ellipsoidal, with no Stieda body. Two of 5 " woolly opossums ", Caluromys p. philander, were infected with an eimerian considered as a new species, Eimeria caluromydis n. -
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. -
Some Parasites of the Common Crow, Corvus Brachyrhynchos Brehm, from Ohio1' 2
SOME PARASITES OF THE COMMON CROW, CORVUS BRACHYRHYNCHOS BREHM, FROM OHIO1' 2 JOSEPH JONES, JR. Biology Department, Saint Augustine's College, Raleigh, North Carolina ABSTRACT Thirty-one species of parasites were taken from 339 common crows over a twenty- month period in Ohio. Of these, nine are new host records: the cestodes Orthoskrjabinia rostellata and Hymenolepis serpentulus; the nematodes Physocephalus sexalatus, Splendido- filaria quiscali, and Splendidofilaria flexivaginalis; and the arachnids Laminosioptes hymenop- terus, Syringophilus bipectinatus, Analges corvinus, and Gabucinia delibata. Twelve parasites not previously reported from the crow in Ohio were also recognized. Two tables, one showing the incidence and intensity of parasitism in the common crow in Ohio, the other listing previous published and unpublished records of common crow parasites, are included. INTRODUCTION Although the crow is of common and widespread occurrence east of the Rockies, no comprehensive, year-round study of parasitism in this bird has been reported. Surveys of parasites of common crows, collected for the most part during the winter season, have been made by Ward (1934), Morgan and Waller (1941), and Daly (1959). In addition, records of parasitism in the common crow, reported as a part of general surveys of bird parasites, are included in publications by Ransom (1909), Mayhew (1925), Cram (1927), Canavan (1929), Rankin (1946), Denton and Byrd (1951), Mawson (1956; 1957), Robinson (1954; 1955). This paper contains the results of a two-year study made in Ohio, during which 339 crows were examined for internal and external parasites. MATERIALS AND METHODS Juvenile and adult crows were shot in the field and wrapped individually in paper bags prior to transportation to the laboratory. -
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. -
Role of Metopus Es in the Anaerobic Degradation of Organic Matter and Biomethanation Process
Role of Metopus es in the anaerobic degradation of organic matter and biomethanation process Thesis submitted to the University of Kerala for award of the degree of Doctor of Philosophy in Microbiology By Nimi Narayanan Under the Supervision of Dr. V. B. Manilal Process Engineering and Environmental Technology Division, National Institute for Interdisciplinary Science and Technology (NIIST), CSIR, Thiruvananthapuram, Kerala, INDIA - 695019 2011 To my Family DECLARATION I hereby declare that the work presented in this thesis is based on the original work done by me under the guidance of Dr. V. B. Manilal, Principal Scientist, Process Engineering and Environmental Technology Division, National Institute for Interdisciplinary Science and Technology, and that no part of this has been included in any other thesis submitted previously for the award of any degree. Nimi Narayanan Acknowledgement It is a great pleasure to express my sincere gratitude and sense of appreciation to my research guide, Dr. V.B. Manilal, Principal Scientist, Environmental Technology, NIIST, Trivandrum, for his constant encouragement, enthusiastic support and valuable guidance throughout the period of study. I am indebted to him for giving me the ample freedom to do the work and express my ideas during this period. I am grateful to Dr. Ajit Haridas, Scientist-in-charge, Environmental Technology, NIIST for his valuable suggestions and constructive criticism during my tenure. It is an honor for me to thank the present Director, Dr. Suresh Das and the former directors of NIIST, Trivandrum for providing the necessary infrastructural facilities for the successful completion of work. I would like to thank Council of Scientific and Industrial Research, New Delhi, for the research fellowship. -
University of Oklahoma
UNIVERSITY OF OKLAHOMA GRADUATE COLLEGE MACRONUTRIENTS SHAPE MICROBIAL COMMUNITIES, GENE EXPRESSION AND PROTEIN EVOLUTION A DISSERTATION SUBMITTED TO THE GRADUATE FACULTY in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY By JOSHUA THOMAS COOPER Norman, Oklahoma 2017 MACRONUTRIENTS SHAPE MICROBIAL COMMUNITIES, GENE EXPRESSION AND PROTEIN EVOLUTION A DISSERTATION APPROVED FOR THE DEPARTMENT OF MICROBIOLOGY AND PLANT BIOLOGY BY ______________________________ Dr. Boris Wawrik, Chair ______________________________ Dr. J. Phil Gibson ______________________________ Dr. Anne K. Dunn ______________________________ Dr. John Paul Masly ______________________________ Dr. K. David Hambright ii © Copyright by JOSHUA THOMAS COOPER 2017 All Rights Reserved. iii Acknowledgments I would like to thank my two advisors Dr. Boris Wawrik and Dr. J. Phil Gibson for helping me become a better scientist and better educator. I would also like to thank my committee members Dr. Anne K. Dunn, Dr. K. David Hambright, and Dr. J.P. Masly for providing valuable inputs that lead me to carefully consider my research questions. I would also like to thank Dr. J.P. Masly for the opportunity to coauthor a book chapter on the speciation of diatoms. It is still such a privilege that you believed in me and my crazy diatom ideas to form a concise chapter in addition to learn your style of writing has been a benefit to my professional development. I’m also thankful for my first undergraduate research mentor, Dr. Miriam Steinitz-Kannan, now retired from Northern Kentucky University, who was the first to show the amazing wonders of pond scum. Who knew that studying diatoms and algae as an undergraduate would lead me all the way to a Ph.D. -
Morphology and Phylogeny of the Soil Ciliate Metopus Yantaiensis N. Sp
Journal of Eukaryotic Microbiology ISSN 1066-5234 ORIGINAL ARTICLE Morphology and Phylogeny of the Soil Ciliate Metopus yantaiensis n. sp. (Ciliophora, Metopida), with Identification of the Intracellular Bacteria Atef Omara,b, Qianqian Zhanga, Songbao Zoua,c & Jun Gonga,c a Laboratory of Microbial Ecology and Matter Cycles, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China b Department of Zoology, Al-Azhar University, Assiut 71524, Egypt c University of Chinese Academy of Sciences, Beijing 100049, China Keywords ABSTRACT Anaerobic ciliates; Armophorea; digestion- resistant bacteria; Metopus contortus; The morphology and infraciliature of a new ciliate, Metopus yantaiensis n. sp., Metopus hasei. discovered in coastal soil of northern China, were investigated. It is distin- guished from its congeners by a combination of the following features: nuclear Correspondence apparatus situated in the preoral dome; 18–21 somatic ciliary rows, of which J. Gong, Yantai Institute of Coastal Zone three extend onto the preoral dome (dome kineties); three to five distinctly Research, Chinese Academy of Sciences, elongated caudal cilia, and 21–29 adoral polykinetids. The 18S rRNA genes of Yantai 264003, China this new species and two congeners, Metopus contortus and Metopus hasei, Telephone number: +86-535-2109123; were sequenced and phylogenetically analyzed. The new species is more clo- FAX number: +86-535-2109000; sely related to M. hasei and the clevelandellids than to other congeners; both e-mail: [email protected] the genus Metopus and the order Metopida are not monophyletic. In addition, the digestion-resistant bacteria in the cytoplasm of M. yantaiensis were identi- Received: 13 January 2017; revised 2 March fied, using a 16S rRNA gene clone library, sequencing, and fluorescence 2017; accepted March 8, 2017. -
Development of Molecular Probes for Dinophysis (Dinophyceae) Plastid: a Tool to Predict Blooming and Explore Plastid Origin
Development of Molecular Probes for Dinophysis (Dinophyceae) Plastid: A Tool to Predict Blooming and Explore Plastid Origin Yoshiaki Takahashi,1 Kiyotaka Takishita,2 Kazuhiko Koike,1 Tadashi Maruyama,2 Takeshi Nakayama,3 Atsushi Kobiyama,1 Takehiko Ogata1 1School of Fisheries Sciences, Kitasato University, Sanriku, Ofunato, Iwate, 022-01011, Japan 2Marine Biotechnology Institute, Heita Kamaishi, Iwate, 026-0001, Japan 3Institute of Biological Sciences, University of Tsukuba, Tennoh-dai, Tsukuba, Ibaraki, 305-8577, Japan Received: 9 July 2004 / Accepted: 19 August 2004 / Online publication: 24 March 2005 Abstract Introduction Dinophysis are species of dinoflagellates that cause Some phytoplankton species are known to produce diarrhetic shellfish poisoning. We have previously toxins that accumulate in plankton feeders. In par- reported that they probably acquire plastids from ticular, toxin accumulation in bivalves causes food cryptophytes in the environment, after which they poisoning in humans, and often leads to severe eco- bloom. Thus monitoring the intracellular plastid nomic damage to the shellfish industry. density in Dinophysis and the source cryptophytes Diarrhetic shellfish poisoning (DSP) is a gastro- occurring in the field should allow prediction of intestinal syndrome caused by phytoplankton tox- Dinophysis blooming. In this study the nucleotide ins, including okadaic acid, and several analogues of sequences of the plastid-encoded small subunit dinophysistoxin (Yasumoto et al., 1985). These tox- ribosomal RNA gene and rbcL (encoding the large ins are derived from several species of dinoflagellates subunit of RuBisCO) from Dinophysis spp. were belonging to the genus Dinophysis (Yasumoto et al, compared with those of cryptophytes, and genetic 1980; Lee et al., 1989). Despite extensive studies in probes specific for the Dinophysis plastid were de- the last 2 decades, little is known about the eco- signed. -
Consolidated Version of the Sanpin 2.3.2.1078-01 on Food, Raw Material, and Foodstuff
Registered with the Ministry of Justice of the RF, March 22, 2002 No. 3326 MINISTRY OF HEALTH OF THE RUSSIAN FEDERATION CHIEF STATE SANITARY INSPECTOR OF THE RUSSIAN FEDERATION RESOLUTION No. 36 November 14, 2001 ON ENACTMENT OF SANITARY RULES (as amended by Amendments No.1, approved by Resolution No. 27 of Chief State Sanitary Inspector of the RF dated 20.08.2002, Amendments and Additions No. 2, approved by Resolution No. 41 of Chief State Sanitary Inspector of the RF dated15.04.2003, No. 5, approved by Resolution No. 42 of Chief State Sanitary Inspector of the RF dated 25.06.2007, No. 6, approved by Resolution No. 13 of Chief State Sanitary Inspector of the RF dated 18.02.2008, No. 7, approved by Resolution No. 17 of Chief State Sanitary Inspector of the RF dated 05.03.2008, No. 8, approved by Resolution No. 26 of Chief State Sanitary Inspector of the RF dated 21.04.2008, No. 9, approved by Resolution No. 30 of Chief State Sanitary Inspector of the RF dated 23.05.2008, No. 10, approved by Resolution No. 43 of Chief State Sanitary Inspector of the RF dated 16.07.2008, Amendments No.11, approved by Resolution No. 56 of Chief State Sanitary Inspector of the RF dated 01.10.2008, No. 12, approved by Resolution No. 58 of Chief State Sanitary Inspector of the RF dated 10.10.2008, Amendment No. 13, approved by Resolution No. 69 of Chief State Sanitary Inspector of the RF dated 11.12.2008, Amendments No.14, approved by Resolution No. -
The Plankton Lifeform Extraction Tool: a Digital Tool to Increase The
Discussions https://doi.org/10.5194/essd-2021-171 Earth System Preprint. Discussion started: 21 July 2021 Science c Author(s) 2021. CC BY 4.0 License. Open Access Open Data The Plankton Lifeform Extraction Tool: A digital tool to increase the discoverability and usability of plankton time-series data Clare Ostle1*, Kevin Paxman1, Carolyn A. Graves2, Mathew Arnold1, Felipe Artigas3, Angus Atkinson4, Anaïs Aubert5, Malcolm Baptie6, Beth Bear7, Jacob Bedford8, Michael Best9, Eileen 5 Bresnan10, Rachel Brittain1, Derek Broughton1, Alexandre Budria5,11, Kathryn Cook12, Michelle Devlin7, George Graham1, Nick Halliday1, Pierre Hélaouët1, Marie Johansen13, David G. Johns1, Dan Lear1, Margarita Machairopoulou10, April McKinney14, Adam Mellor14, Alex Milligan7, Sophie Pitois7, Isabelle Rombouts5, Cordula Scherer15, Paul Tett16, Claire Widdicombe4, and Abigail McQuatters-Gollop8 1 10 The Marine Biological Association (MBA), The Laboratory, Citadel Hill, Plymouth, PL1 2PB, UK. 2 Centre for Environment Fisheries and Aquacu∑lture Science (Cefas), Weymouth, UK. 3 Université du Littoral Côte d’Opale, Université de Lille, CNRS UMR 8187 LOG, Laboratoire d’Océanologie et de Géosciences, Wimereux, France. 4 Plymouth Marine Laboratory, Prospect Place, Plymouth, PL1 3DH, UK. 5 15 Muséum National d’Histoire Naturelle (MNHN), CRESCO, 38 UMS Patrinat, Dinard, France. 6 Scottish Environment Protection Agency, Angus Smith Building, Maxim 6, Parklands Avenue, Eurocentral, Holytown, North Lanarkshire ML1 4WQ, UK. 7 Centre for Environment Fisheries and Aquaculture Science (Cefas), Lowestoft, UK. 8 Marine Conservation Research Group, University of Plymouth, Drake Circus, Plymouth, PL4 8AA, UK. 9 20 The Environment Agency, Kingfisher House, Goldhay Way, Peterborough, PE4 6HL, UK. 10 Marine Scotland Science, Marine Laboratory, 375 Victoria Road, Aberdeen, AB11 9DB, UK. -
A New Species of Sarcocystis in the Brain of Two Exotic Birds1
© Masson, Paris, 1979 Annales de Parasitologie (Paris) 1979, t. 54, n° 4, pp. 393-400 A new species of Sarcocystis in the brain of two exotic birds by P. C. C. GARNHAM, A. J. DUGGAN and R. E. SINDEN * Imperial College Field Station, Ashurst Lodge, Ascot, Berkshire and Wellcome Museum of Medical Science, 183 Euston Road, London N.W.1., England. Summary. Sarcocystis kirmsei sp. nov. is described from the brain of two tropical birds, from Thailand and Panama. Its distinction from Frenkelia is considered in some detail. Résumé. Une espèce nouvelle de Sarcocystis dans le cerveau de deux Oiseaux exotiques. Sarcocystis kirmsei est décrit du cerveau de deux Oiseaux tropicaux de Thaïlande et de Panama. Les critères de distinction entre cette espèce et le genre Frenkelia sont discutés en détail. In 1968, Kirmse (pers. comm.) found a curious parasite in sections of the brain of an unidentified bird which he had been given in Panama. He sent unstained sections to one of us (PCCG) and on examination the parasite was thought to belong to the Toxoplasmatea, either to a species of Sarcocystis or of Frenkelia. A brief description of the infection was made by Tadros (1970) in her thesis for the Ph. D. (London). The slenderness of the cystozoites resembled those of Frenkelia, but the prominent spines on the cyst wall were more like those of Sarcocystis. The distri bution of the cystozoites within the cyst is characteristic in that the central portion is practically empty while the outer part consists of numerous pockets of organisms, closely packed together.