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Protocols for Monitoring Harmful Algal Blooms for Sustainable Aquaculture and Coastal Fisheries in Chile (Supplement Data)
Protocols for monitoring Harmful Algal Blooms for sustainable aquaculture and coastal fisheries in Chile (Supplement data) Provided by Kyoko Yarimizu, et al. Table S1. Phytoplankton Naming Dictionary: This dictionary was constructed from the species observed in Chilean coast water in the past combined with the IOC list. Each name was verified with the list provided by IFOP and online dictionaries, AlgaeBase (https://www.algaebase.org/) and WoRMS (http://www.marinespecies.org/). The list is subjected to be updated. Phylum Class Order Family Genus Species Ochrophyta Bacillariophyceae Achnanthales Achnanthaceae Achnanthes Achnanthes longipes Bacillariophyta Coscinodiscophyceae Coscinodiscales Heliopeltaceae Actinoptychus Actinoptychus spp. Dinoflagellata Dinophyceae Gymnodiniales Gymnodiniaceae Akashiwo Akashiwo sanguinea Dinoflagellata Dinophyceae Gymnodiniales Gymnodiniaceae Amphidinium Amphidinium spp. Ochrophyta Bacillariophyceae Naviculales Amphipleuraceae Amphiprora Amphiprora spp. Bacillariophyta Bacillariophyceae Thalassiophysales Catenulaceae Amphora Amphora spp. Cyanobacteria Cyanophyceae Nostocales Aphanizomenonaceae Anabaenopsis Anabaenopsis milleri Cyanobacteria Cyanophyceae Oscillatoriales Coleofasciculaceae Anagnostidinema Anagnostidinema amphibium Anagnostidinema Cyanobacteria Cyanophyceae Oscillatoriales Coleofasciculaceae Anagnostidinema lemmermannii Cyanobacteria Cyanophyceae Oscillatoriales Microcoleaceae Annamia Annamia toxica Cyanobacteria Cyanophyceae Nostocales Aphanizomenonaceae Aphanizomenon Aphanizomenon flos-aquae -
Biology and Systematics of Heterokont and Haptophyte Algae1
American Journal of Botany 91(10): 1508±1522. 2004. BIOLOGY AND SYSTEMATICS OF HETEROKONT AND HAPTOPHYTE ALGAE1 ROBERT A. ANDERSEN Bigelow Laboratory for Ocean Sciences, P.O. Box 475, West Boothbay Harbor, Maine 04575 USA In this paper, I review what is currently known of phylogenetic relationships of heterokont and haptophyte algae. Heterokont algae are a monophyletic group that is classi®ed into 17 classes and represents a diverse group of marine, freshwater, and terrestrial algae. Classes are distinguished by morphology, chloroplast pigments, ultrastructural features, and gene sequence data. Electron microscopy and molecular biology have contributed signi®cantly to our understanding of their evolutionary relationships, but even today class relationships are poorly understood. Haptophyte algae are a second monophyletic group that consists of two classes of predominately marine phytoplankton. The closest relatives of the haptophytes are currently unknown, but recent evidence indicates they may be part of a large assemblage (chromalveolates) that includes heterokont algae and other stramenopiles, alveolates, and cryptophytes. Heter- okont and haptophyte algae are important primary producers in aquatic habitats, and they are probably the primary carbon source for petroleum products (crude oil, natural gas). Key words: chromalveolate; chromist; chromophyte; ¯agella; phylogeny; stramenopile; tree of life. Heterokont algae are a monophyletic group that includes all (Phaeophyceae) by Linnaeus (1753), and shortly thereafter, photosynthetic organisms with tripartite tubular hairs on the microscopic chrysophytes (currently 5 Oikomonas, Anthophy- mature ¯agellum (discussed later; also see Wetherbee et al., sa) were described by MuÈller (1773, 1786). The history of 1988, for de®nitions of mature and immature ¯agella), as well heterokont algae was recently discussed in detail (Andersen, as some nonphotosynthetic relatives and some that have sec- 2004), and four distinct periods were identi®ed. -
Centers of Endemism of Freshwater Protists Deviate from Pattern of Taxon Richness on a Continental Scale Jana L
www.nature.com/scientificreports OPEN Centers of endemism of freshwater protists deviate from pattern of taxon richness on a continental scale Jana L. Olefeld1, Christina Bock1, Manfred Jensen1, Janina C. Vogt2, Guido Sieber1, Dirk Albach2 & Jens Boenigk1* Here, we analyzed patterns of taxon richness and endemism of freshwater protists in Europe. Even though the signifcance of physicochemical parameters but also of geographic constraints for protist distribution is documented, it remains unclear where regional areas of high protist diversity are located and whether areas of high taxon richness harbor a high proportion of endemics. Further, patterns may be universal for protists or deviate between taxonomic groups. Based on amplicon sequencing campaigns targeting the SSU and ITS region of the rDNA we address these patterns at two diferent levels of phylogenetic resolution. Our analyses demonstrate that protists have restricted geographical distribution areas. For many taxonomic groups the regions of high taxon richness deviate from those having a high proportion of putative endemics. In particular, the diversity of high mountain lakes as azonal habitats deviated from surrounding lowlands, i.e. many taxa were found exclusively in high mountain lakes and several putatively endemic taxa occurred in mountain regions like the Alps, the Pyrenees or the Massif Central. Beyond that, taxonomic groups showed a pronounced accumulation of putative endemics in distinct regions, e.g. Dinophyceae along the Baltic Sea coastline, and Chrysophyceae in Scandinavia. Many other groups did not have pronounced areas of increased endemism but geographically restricted taxa were found across Europe. Restricted distribution and endemism has been demonstrated for numerous protist taxa by now 1–4. -
Phylogeny and Morphology of a Chattonella (Raphidophyceae) Species from the Mediterranean Sea: What Is C
This article was downloaded by: [Stiftung Alfred Wegener Institute für Polar- und Meeresforschung ] On: 17 April 2013, At: 02:13 Publisher: Taylor & Francis Informa Ltd Registered in England and Wales Registered Number: 1072954 Registered office: Mortimer House, 37-41 Mortimer Street, London W1T 3JH, UK European Journal of Phycology Publication details, including instructions for authors and subscription information: http://www.tandfonline.com/loi/tejp20 Phylogeny and morphology of a Chattonella (Raphidophyceae) species from the Mediterranean Sea: what is C. subsalsa? Sascha Klöpper a , Uwe John a , Adriana Zingone b , Olga Mangoni c , Wiebe H.C.F. Kooistra b & Allan D. Cembella a a Alfred Wegener Institute for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany b Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy c Department of Biological Sciences, University Federico II, Via Mezzocannone 8, 80138, Naples, Italy Version of record first published: 13 Mar 2013. To cite this article: Sascha Klöpper , Uwe John , Adriana Zingone , Olga Mangoni , Wiebe H.C.F. Kooistra & Allan D. Cembella (2013): Phylogeny and morphology of a Chattonella (Raphidophyceae) species from the Mediterranean Sea: what is C. subsalsa?, European Journal of Phycology, 48:1, 79-92 To link to this article: http://dx.doi.org/10.1080/09670262.2013.771412 PLEASE SCROLL DOWN FOR ARTICLE Full terms and conditions of use: http://www.tandfonline.com/page/terms-and-conditions This article may be used for research, teaching, and private study purposes. Any substantial or systematic reproduction, redistribution, reselling, loan, sub-licensing, systematic supply, or distribution in any form to anyone is expressly forbidden. -
Proposal for Practical Multi-Kingdom Classification of Eukaryotes Based on Monophyly 2 and Comparable Divergence Time Criteria
bioRxiv preprint doi: https://doi.org/10.1101/240929; this version posted December 29, 2017. 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 4.0 International license. 1 Proposal for practical multi-kingdom classification of eukaryotes based on monophyly 2 and comparable divergence time criteria 3 Leho Tedersoo 4 Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia 5 Contact: email: [email protected], tel: +372 56654986, twitter: @tedersoo 6 7 Key words: Taxonomy, Eukaryotes, subdomain, phylum, phylogenetic classification, 8 monophyletic groups, divergence time 9 Summary 10 Much of the ecological, taxonomic and biodiversity research relies on understanding of 11 phylogenetic relationships among organisms. There are multiple available classification 12 systems that all suffer from differences in naming, incompleteness, presence of multiple non- 13 monophyletic entities and poor correspondence of divergence times. These issues render 14 taxonomic comparisons across the main groups of eukaryotes and all life in general difficult 15 at best. By using the monophyly criterion, roughly comparable time of divergence and 16 information from multiple phylogenetic reconstructions, I propose an alternative 17 classification system for the domain Eukarya to improve hierarchical taxonomical 18 comparability for animals, plants, fungi and multiple protist groups. Following this rationale, 19 I propose 32 kingdoms of eukaryotes that are treated in 10 subdomains. These kingdoms are 20 further separated into 43, 115, 140 and 353 taxa at the level of subkingdom, phylum, 21 subphylum and class, respectively (http://dx.doi.org/10.15156/BIO/587483). -
"Phycology". In: Encyclopedia of Life Science
Phycology Introductory article Ralph A Lewin, University of California, La Jolla, California, USA Article Contents Michael A Borowitzka, Murdoch University, Perth, Australia . General Features . Uses The study of algae is generally called ‘phycology’, from the Greek word phykos meaning . Noxious Algae ‘seaweed’. Just what algae are is difficult to define, because they belong to many different . Classification and unrelated classes including both prokaryotic and eukaryotic representatives. Broadly . Evolution speaking, the algae comprise all, mainly aquatic, plants that can use light energy to fix carbon from atmospheric CO2 and evolve oxygen, but which are not specialized land doi: 10.1038/npg.els.0004234 plants like mosses, ferns, coniferous trees and flowering plants. This is a negative definition, but it serves its purpose. General Features Algae range in size from microscopic unicells less than 1 mm several species are also of economic importance. Some in diameter to kelps as long as 60 m. They can be found in kinds are consumed as food by humans. These include almost all aqueous or moist habitats; in marine and fresh- the red alga Porphyra (also known as nori or laver), an water environments they are the main photosynthetic or- important ingredient of Japanese foods such as sushi. ganisms. They are also common in soils, salt lakes and hot Other algae commonly eaten in the Orient are the brown springs, and some can grow in snow and on rocks and the algae Laminaria and Undaria and the green algae Caulerpa bark of trees. Most algae normally require light, but some and Monostroma. The new science of molecular biology species can also grow in the dark if a suitable organic carbon has depended largely on the use of algal polysaccharides, source is available for nutrition. -
Seven Gene Phylogeny of Heterokonts
ARTICLE IN PRESS Protist, Vol. 160, 191—204, May 2009 http://www.elsevier.de/protis Published online date 9 February 2009 ORIGINAL PAPER Seven Gene Phylogeny of Heterokonts Ingvild Riisberga,d,1, Russell J.S. Orrb,d,1, Ragnhild Klugeb,c,2, Kamran Shalchian-Tabrizid, Holly A. Bowerse, Vishwanath Patilb,c, Bente Edvardsena,d, and Kjetill S. Jakobsenb,d,3 aMarine Biology, Department of Biology, University of Oslo, P.O. Box 1066, Blindern, NO-0316 Oslo, Norway bCentre for Ecological and Evolutionary Synthesis (CEES),Department of Biology, University of Oslo, P.O. Box 1066, Blindern, NO-0316 Oslo, Norway cDepartment of Plant and Environmental Sciences, P.O. Box 5003, The Norwegian University of Life Sciences, N-1432, A˚ s, Norway dMicrobial Evolution Research Group (MERG), Department of Biology, University of Oslo, P.O. Box 1066, Blindern, NO-0316, Oslo, Norway eCenter of Marine Biotechnology, 701 East Pratt Street, Baltimore, MD 21202, USA Submitted May 23, 2008; Accepted November 15, 2008 Monitoring Editor: Mitchell L. Sogin Nucleotide ssu and lsu rDNA sequences of all major lineages of autotrophic (Ochrophyta) and heterotrophic (Bigyra and Pseudofungi) heterokonts were combined with amino acid sequences from four protein-coding genes (actin, b-tubulin, cox1 and hsp90) in a multigene approach for resolving the relationship between heterokont lineages. Applying these multigene data in Bayesian and maximum likelihood analyses improved the heterokont tree compared to previous rDNA analyses by placing all plastid-lacking heterotrophic heterokonts sister to Ochrophyta with robust support, and divided the heterotrophic heterokonts into the previously recognized phyla, Bigyra and Pseudofungi. Our trees identified the heterotrophic heterokonts Bicosoecida, Blastocystis and Labyrinthulida (Bigyra) as the earliest diverging lineages. -
Cladistic Analyses of Combined Traditional and Moleculardata
Proc. Natl. Acad. Sci. USA Vol. 92, pp. 244-248, January 1995 Evolution Cladistic analyses of combined traditional and molecular data sets reveal an algal lineage (18S rRNA/chromophyte/chrysophyte/diatom/phylogeny) GARY W. SAUNDERSt, DANIEL POTrERt, MICHAEL P. PASKIND§, AND ROBERT A. ANDERSENt$ tBotany School, University of Melbourne, Parkville, Victoria 3052, Australia; tBigelow Laboratory for Ocean Sciences, West Boothbay Harbor, ME 04575; and §BASF Research Corporation, Worcester, MA 01605 Communicated by Hewson Swift, University of Chicago, Chicago, IL, September 12, 1994 ABSTRACT The chromophyte algae are a large and bio- ultrastructural features, especially those of the flagellar appa- logically diverse assemblage of brown seaweeds, diatoms, and ratus. The eukaryotic flagellum (including cilium) probably other golden algae classified in 13 taxonomic classes. One evolved only once, and regardless of life stage, flagella are subgroup (diatoms, pedinellids, pelagophytes, silicoflagel- considered homologous; i.e., a flagellum of a sperm cell is lates, and certain enigmatic genera) is characterized by a considered homologous to that of a flagellate phytoplankter or highly reduced flagellar apparatus. The flagellar apparatus an asexual zoospore (10). Microtubular roots often anchor the lacks microtubular and fibrous roots, and the flagellum basal flagellum or flagella, and they are the major component of the body is attached directly to the nucleus. We hypothesize that cell's cytoskeleton (17), often being active in specific cell the flagellar reduction is the result of a single evolutionary activities [e.g., phagocytosis (18-20) and scale formation (21- series of events. Cladistic analysis of ultrastructural and 23)]. The flagellar apparatus in many chromophyte classes has biochemical data reveals a monophyletic group that unites all four microtubular roots, and in some cases a system II fiber or taxa with a reduced flagellar apparatus, supporting our rhizoplast is also present (Fig. -
Freshwater Algae in Britain and Ireland - Bibliography
Freshwater algae in Britain and Ireland - Bibliography Floras, monographs, articles with records and environmental information, together with papers dealing with taxonomic/nomenclatural changes since 2003 (previous update of ‘Coded List’) as well as those helpful for identification purposes. Theses are listed only where available online and include unpublished information. Useful websites are listed at the end of the bibliography. Further links to relevant information (catalogues, websites, photocatalogues) can be found on the site managed by the British Phycological Society (http://www.brphycsoc.org/links.lasso). Abbas A, Godward MBE (1964) Cytology in relation to taxonomy in Chaetophorales. Journal of the Linnean Society, Botany 58: 499–597. Abbott J, Emsley F, Hick T, Stubbins J, Turner WB, West W (1886) Contributions to a fauna and flora of West Yorkshire: algae (exclusive of Diatomaceae). Transactions of the Leeds Naturalists' Club and Scientific Association 1: 69–78, pl.1. Acton E (1909) Coccomyxa subellipsoidea, a new member of the Palmellaceae. Annals of Botany 23: 537–573. Acton E (1916a) On the structure and origin of Cladophora-balls. New Phytologist 15: 1–10. Acton E (1916b) On a new penetrating alga. New Phytologist 15: 97–102. Acton E (1916c) Studies on the nuclear division in desmids. 1. Hyalotheca dissiliens (Smith) Bréb. Annals of Botany 30: 379–382. Adams J (1908) A synopsis of Irish algae, freshwater and marine. Proceedings of the Royal Irish Academy 27B: 11–60. Ahmadjian V (1967) A guide to the algae occurring as lichen symbionts: isolation, culture, cultural physiology and identification. Phycologia 6: 127–166 Allanson BR (1973) The fine structure of the periphyton of Chara sp. -
C3c5e116de51dfa5b9d704879f6
GBE Gene Arrangement Convergence, Diverse Intron Content, and Genetic Code Modifications in Mitochondrial Genomes of Sphaeropleales (Chlorophyta) Karolina Fucˇı´kova´ 1,*, Paul O. Lewis1, Diego Gonza´lez-Halphen2, and Louise A. Lewis1 1Department of Ecology and Evolutionary Biology, University of Connecticut 2Instituto de Fisiologı´a Celular, Departamento de Gene´tica Molecular Universidad Nacional Auto´ nomadeMe´xico, Ciudad de Me´xico, Mexico *Corresponding author: E-mail: [email protected]. Accepted: August 3, 2014 Data deposition: Nine new complete mitochondrial genome sequences with annotated features have been deposited at GenBank under the accessions KJ806265–KJ806273. Genes from partially sequenced genomes have been deposited at GenBank under the accessions KJ845680– KJ845692, KJ845706–KJ845718, and KJ845693–KJ845705. Gene sequence alignments are available in TreeBase under study number 16246. Abstract The majority of our knowledge about mitochondrial genomes of Viridiplantae comes from land plants, but much less is known about their green algal relatives. In the green algal order Sphaeropleales (Chlorophyta), only one representative mitochondrial genome is currently available—that of Acutodesmus obliquus. Our study adds nine completely sequenced and three partially sequenced mi- tochondrial genomes spanning the phylogenetic diversity of Sphaeropleales. We show not only a size range of 25–53 kb and variation in intron content (0–11) and gene order but also conservation of 13 core respiratory genes and fragmented ribosomal RNA genes. We also report an unusual case of gene arrangement convergence in Neochloris aquatica, where the two rns fragments were secondarily placed in close proximity. Finally, we report the unprecedented usage of UCG as stop codon in Pseudomuriella schumacherensis.In addition, phylogenetic analyses of the mitochondrial protein-coding genes yield a fully resolved, well-supported phylogeny, showing promise for addressing systematic challenges in green algae. -
Evolution and Unprecedented Variants of the Mitochondrial Genetic Code in a Lineage of Green Algae
Smith ScholarWorks Biological Sciences: Faculty Publications Biological Sciences 10-1-2019 Evolution and Unprecedented Variants of the Mitochondrial Genetic Code in a Lineage of Green Algae David Zihala Ostravská Univerzita v Ostrave Marek Eliáš Ostravská Univerzita v Ostrave Laura A. Katz Smith College, [email protected] Follow this and additional works at: https://scholarworks.smith.edu/bio_facpubs Part of the Biology Commons Recommended Citation Zihala, David; Eliáš, Marek; and Katz, Laura A., "Evolution and Unprecedented Variants of the Mitochondrial Genetic Code in a Lineage of Green Algae" (2019). Biological Sciences: Faculty Publications, Smith College, Northampton, MA. https://scholarworks.smith.edu/bio_facpubs/85 This Article has been accepted for inclusion in Biological Sciences: Faculty Publications by an authorized administrator of Smith ScholarWorks. For more information, please contact [email protected] GBE Evolution and Unprecedented Variants of the Mitochondrial Genetic Code in a Lineage of Green Algae David Zihala 1,2 and Marek Elias1,2,* 1Department of Biology and Ecology, Faculty of Science, University of Ostrava, Czech Republic 2Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Czech Republic *Corresponding author: E-mail: [email protected]. Accepted: July 17, 2019 Downloaded from https://academic.oup.com/gbe/article/11/10/2992/5588413 by guest on 09 April 2021 Abstract Mitochondria of diverse eukaryotes have evolved various departures from the standard genetic code, but the breadth -
Sphaeropleales, Chlorophyceae) No Estado De São Paulo: Levantamento Florístico
ANA MARGARITA LOAIZA RESTANO Família Hydrodictyaceae (Sphaeropleales, Chlorophyceae) no Estado de São Paulo: levantamento florístico Dissertação apresentada ao Instituto de Botânica da Secretaria do Meio Ambiente do Estado de São Paulo como parte dos requisitos exigidos para obtenção do título de Mestre em Biodiversidade Vegetal e Meio Ambiente, Área de Concentração Plantas Avasculares e Fungos em Análises Ambientais. São Paulo 2013 ANA MARGARITA LOAIZA RESTANO Família Hydrodictyaceae (Sphaeropleales, Chlorophyceae) no Estado de São Paulo: levantamento florístico Dissertação apresentada ao Instituto de Botânica da Secretaria do Meio Ambiente do Estado de São Paulo como parte dos requisitos exigidos para obtenção do título de Mestre em Biodiversidade Vegetal e Meio Ambiente, Área de Concentração Plantas Avasculares e Fungos em Análises Ambientais. ORIENTADOR: DR. CARLOS EDUARDO DE MATTOS BICUDO Ficha Catalográfica elaborada pelo NÚCLEO DE BIBLIOTECA E MEMÓRIA Loaiza Restano, Ana Margarita L795f Família Hydrodictyaceae (Sphaeropleales, Chlorophyceae) no Estado de São Paulo: levantamento florístico / Ana Margarita Loaiza Restano -- São Paulo, 2013. 164 p. il. Dissertação (Mestrado) -- Instituto de Botânica da Secretaria de Estado do Meio Ambiente, 2013. Bibliografia. 1. Algas. 2. Taxonomia. 3. Hydrodictyaceae. I. Título CDU: 582.26 iii "E é porque simplicidade e grandiosidade são ambas belas, que procuramos, de preferência, fatos simples e fatos grandiosos; que nos deleitamos tanto em seguir os cursos gigantes das estrelas, assim como com o escrutínio, no microscópio, das prodigiosas minúcias que também são uma grandiosidade; assim como na busca das idades geológicas dos traços do passado que nos atraem devido à sua lonjura". HENRI POINCARÉ (Traduzido de "Science et méthode") (1908) iv AGRADECIMENTOS ostaria de expressar minha gratidão e admiração a todas as pessoas que, de uma ou outra maneira e com seus incalculáveis conhecimentos, me ajudaram a esclarecer dúvidas e me proporcionaram a oportunidade de realizar esta G dissertação.