The Kingdoms Monera, Protoctista and Fungi MODULE - 1 Diversity and Evolution of Life
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S41467-021-25308-W.Pdf
ARTICLE https://doi.org/10.1038/s41467-021-25308-w OPEN Phylogenomics of a new fungal phylum reveals multiple waves of reductive evolution across Holomycota ✉ ✉ Luis Javier Galindo 1 , Purificación López-García 1, Guifré Torruella1, Sergey Karpov2,3 & David Moreira 1 Compared to multicellular fungi and unicellular yeasts, unicellular fungi with free-living fla- gellated stages (zoospores) remain poorly known and their phylogenetic position is often 1234567890():,; unresolved. Recently, rRNA gene phylogenetic analyses of two atypical parasitic fungi with amoeboid zoospores and long kinetosomes, the sanchytrids Amoeboradix gromovi and San- chytrium tribonematis, showed that they formed a monophyletic group without close affinity with known fungal clades. Here, we sequence single-cell genomes for both species to assess their phylogenetic position and evolution. Phylogenomic analyses using different protein datasets and a comprehensive taxon sampling result in an almost fully-resolved fungal tree, with Chytridiomycota as sister to all other fungi, and sanchytrids forming a well-supported, fast-evolving clade sister to Blastocladiomycota. Comparative genomic analyses across fungi and their allies (Holomycota) reveal an atypically reduced metabolic repertoire for sanchy- trids. We infer three main independent flagellum losses from the distribution of over 60 flagellum-specific proteins across Holomycota. Based on sanchytrids’ phylogenetic position and unique traits, we propose the designation of a novel phylum, Sanchytriomycota. In addition, our results indicate that most of the hyphal morphogenesis gene repertoire of multicellular fungi had already evolved in early holomycotan lineages. 1 Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France. 2 Zoological Institute, Russian Academy of Sciences, St. ✉ Petersburg, Russia. 3 St. -
Biological Classification Chapter 2
16 BIOLOGY CHAPTER 2 BIOLOGICAL CLASSIFICATION 2.1 Kingdom Monera Since the dawn of civilisation, there have been many attempts to classify living organisms. It was done instinctively not using criteria that were 2.2 Kingdom Protista scientific but borne out of a need to use organisms for our own use – for 2.3 Kingdom Fungi food, shelter and clothing. Aristotle was the earliest to attempt a more 2.4 Kingdom Plantae scientific basis for classification. He used simple morphological characters to classify plants into trees, shrubs and herbs. He also divided animals 2.5 Kingdom into two groups, those which had red blood and those that did not. Animalia In Linnaeus' time a Two Kingdom system of classification with 2.6 Viruses, Viroids Plantae and Animalia kingdoms was developed that included all plants and Lichens and animals respectively. This system was used till very recently. This system did not distinguish between the eukaryotes and prokaryotes, unicellular and multicellular organisms and photosynthetic (green algae) and non-photosynthetic (fungi) organisms. Classification of organisms into plants and animals was easily done and was easy to understand, inspite, a large number of organisms did not fall into either category. Hence the two kingdom classification used for a long time was found inadequate. A need was also felt for including, besides gross morphology, other characteristics like cell structure, nature of wall, mode of nutrition, habitat, methods of reproduction, evolutionary relationships, etc. Classification systems for the living organisms have hence, undergone several changes over time. Though plant and animal kingdoms have been a constant under all different systems, the understanding of what groups/organisms be included under these kingdoms have been changing; the number and nature of other kingdoms have also been understood differently by different scientists over time. -
1. in Whittaker's System of Classification, Prokaryotes Are Placed in the Kingdom (A) Protista (B) Monera (C) Plantae (D) Animal
1. In Whittaker's system of classification, prokaryotes are placed 12. An organism having cytoplasm i.e. DNA and RNA but no in the kingdom cell wall is (a) Protista (b) Monera (a) Cyanobacterium (b) Mycoplasma (c) Plantae (d) Animalia (c) Bacterium (d) Virus 2. In the five kingdom system of classification, which single 13. Kingdom monera comprises the – kingdom out of the following can include blue-green algae, (a) Plants of economic importance nitrogen fixing bacteria and methanogenic archaebacteria ? (b) All the plants studied in botany (a) Monera (b) Fungi (c) Prokaryotic organisms (c) Plantae (d) Protista (d) Plants of Thallophyta group 3. Which of the following kingdom does not have nuclear 14. The cell wall of green plants is made up of membrane? (a) Pectin (b) Suberin (a) Protista (b) Fungi (c) Cellulose (d) Chitin (c) Monera (d) Plantae 15. Which of the following is not a blue-green algae ? 4. What type of mode of nutrition is found in the kingdom (a) Nostoc (b) Anabaena Animalia? (c) Lichen (d) Aulosiras (a) Autotrophic and heterotrophic 16. During rainy seasons, the ground becomes slippery due to (b) Chemosynthetic and photosynthetic dense growth of (c) Saprophytic and parasitic (a) Lichens (b) Bacteria (d) Holozoic and saprophytic (c) Green algae (d) Cyanobacteria 5. The separation of living beings into five kingdoms is based 17. Paramecium is a on – (a) Protozoan (b) Bacterium (a) Complexity of cell structure (c) Virus (d) Annelid (b) Complexity of organism's body 18. Protists are (c) Mode of obtaining nutrition (a) single-celled eukaryotes (b) multicellular eukaryotes (d) All of the above (c) single-celled prokaryotes (d) single-celled akaryote 6. -
A Higher-Level Phylogenetic Classification of the Fungi
mycological research 111 (2007) 509–547 available at www.sciencedirect.com journal homepage: www.elsevier.com/locate/mycres A higher-level phylogenetic classification of the Fungi David S. HIBBETTa,*, Manfred BINDERa, Joseph F. BISCHOFFb, Meredith BLACKWELLc, Paul F. CANNONd, Ove E. ERIKSSONe, Sabine HUHNDORFf, Timothy JAMESg, Paul M. KIRKd, Robert LU¨ CKINGf, H. THORSTEN LUMBSCHf, Franc¸ois LUTZONIg, P. Brandon MATHENYa, David J. MCLAUGHLINh, Martha J. POWELLi, Scott REDHEAD j, Conrad L. SCHOCHk, Joseph W. SPATAFORAk, Joost A. STALPERSl, Rytas VILGALYSg, M. Catherine AIMEm, Andre´ APTROOTn, Robert BAUERo, Dominik BEGEROWp, Gerald L. BENNYq, Lisa A. CASTLEBURYm, Pedro W. CROUSl, Yu-Cheng DAIr, Walter GAMSl, David M. GEISERs, Gareth W. GRIFFITHt,Ce´cile GUEIDANg, David L. HAWKSWORTHu, Geir HESTMARKv, Kentaro HOSAKAw, Richard A. HUMBERx, Kevin D. HYDEy, Joseph E. IRONSIDEt, Urmas KO˜ LJALGz, Cletus P. KURTZMANaa, Karl-Henrik LARSSONab, Robert LICHTWARDTac, Joyce LONGCOREad, Jolanta MIA˛ DLIKOWSKAg, Andrew MILLERae, Jean-Marc MONCALVOaf, Sharon MOZLEY-STANDRIDGEag, Franz OBERWINKLERo, Erast PARMASTOah, Vale´rie REEBg, Jack D. ROGERSai, Claude ROUXaj, Leif RYVARDENak, Jose´ Paulo SAMPAIOal, Arthur SCHU¨ ßLERam, Junta SUGIYAMAan, R. Greg THORNao, Leif TIBELLap, Wendy A. UNTEREINERaq, Christopher WALKERar, Zheng WANGa, Alex WEIRas, Michael WEISSo, Merlin M. WHITEat, Katarina WINKAe, Yi-Jian YAOau, Ning ZHANGav aBiology Department, Clark University, Worcester, MA 01610, USA bNational Library of Medicine, National Center for Biotechnology Information, -
Haeckel's 1866 Tree of Life and the Origin of Eukaryotes
PUBLISHED: 26 JULY 2016 | ARTICLE NUMBER: 16114 | DOI: 10.1038/NMICROBIOL.2016.114 correspondence Haeckel’s 1866 tree of life and the origin of eukaryotes To the Editor — In their Letter describing were summarized under the domain an expanded version of the tree of life, Eukarya, which includes all eukaryotic Hug et al.1 refer to a key publication of micro- and macroorganisms (from amoebae Carl Woese and co-workers2, wherein a to humans). 16S rRNA-phylogenetic scheme of the In chapter 26 entitled ‘Phylogenetic domains Bacteria, Archaea and Eukarya is theses’, Haeckel3 re-interpreted and shown. However, the first three-kingdom supplemented Darwin’s evolutionary tree of life that included microorganisms deductions of 1859. With reference to the was depicted by Ernst Haeckel (pictured simplest protists (bacteria), which form the at around 26 years old) in his General root of his ‘oak tree’ (see Fig. 6 in ref. 5), Morphology of Organisms, a seminal book Haeckel3 concluded that “all organisms that was published one hundred and are the descendants of such autogenous fifty years ago3. Moneren”. Hence, according to this In his Origin of Species, Charles Darwin Haeckelian interpretation of the phylogeny refers to the Linnean two-kingdom of life, the Monera (that is, Bacteria and system, with ‘Animalia’ and ‘Vegetabilia’ Archaea)2 are the progenitors of all more as the only two branches of the living complex living beings on Earth. world. Haeckel3, who was also known This 150-year-old idea is consistent with as the German Darwin4, introduced a recent discoveries and genomic analyses that three-kingdom scheme in which, as a support an archaeal origin of eukaryotes1,8. -
Clade (Kingdom Fungi, Phylum Chytridiomycota)
TAXONOMIC STATUS OF GENERA IN THE “NOWAKOWSKIELLA” CLADE (KINGDOM FUNGI, PHYLUM CHYTRIDIOMYCOTA): PHYLOGENETIC ANALYSIS OF MOLECULAR CHARACTERS WITH A REVIEW OF DESCRIBED SPECIES by SHARON ELIZABETH MOZLEY (Under the Direction of David Porter) ABSTRACT Chytrid fungi represent the earliest group of fungi to have emerged within the Kingdom Fungi. Unfortunately despite the importance of chytrids to understanding fungal evolution, the systematics of the group is in disarray and in desperate need of revision. Funding by the NSF PEET program has provided an opportunity to revise the systematics of chytrid fungi with an initial focus on four specific clades in the order Chytridiales. The “Nowakowskiella” clade was chosen as a test group for comparing molecular methods of phylogenetic reconstruction with the more traditional morphological and developmental character system used for classification in determining generic limits for chytrid genera. Portions of the 18S and 28S nrDNA genes were sequenced for isolates identified to genus level based on morphology to seven genera in the “Nowakowskiella” clade: Allochytridium, Catenochytridium, Cladochytrium, Endochytrium, Nephrochytrium, Nowakowskiella, and Septochytrium. Bayesian, parsimony, and maximum likelihood methods of phylogenetic inference were used to produce trees based on one (18S or 28S alone) and two-gene datasets in order to see if there would be a difference depending on which optimality criterion was used and the number of genes included. In addition to the molecular analysis, taxonomic summaries of all seven genera covering all validly published species with a listing of synonyms and questionable species is provided to give a better idea of what has been described and the morphological and developmental characters used to circumscribe each genus. -
Archaea, Eukarya
Chapter 3 To study the diversity of life, biologists use a classification system to name organisms and group them in a logical manner. Common names can be confusing . An organism may have the same name in different languages. It can be misleading! Also common names often refer to more than one organism. What we call corn is wheat in Britain Scientist use scientific names to exchange info and be certain that they are referring to the same organism When taxonomists classify organisms, they organize them into groups that have biological significance. In the discipline of taxonomy, scientists classify organisms and assign each organism a universally accepted name. In a good system of classification, organisms placed into a particular group are more similar to each other than they are to organisms in other groups. Copyright Pearson Prentice Hall Common names of organisms vary from country to country (or even within countries), so scientists assign one specific scientific name for each species. Because 18th century scientists around the world understood Latin and Greek, they used those languages for scientific names. This practice is still followed in naming new species. Copyright Pearson Prentice Hall Early Efforts at Naming Organisms The first attempts at standard scientific names described the physical characteristics of a species in great detail. The name of a wild violet might be: “small purple flower with four petals and heart shaped leaves that grows by the brook in the spring.” These names were not standardized because different scientists described different characteristics. Copyright Pearson Prentice Hall Binomial Nomenclature What is binomial nomenclature? Carolus Linneaus developed a naming system called binomial nomenclature. -
Simmonsa,*, Timothy Y
mycological research 113 (2009) 450–460 journal homepage: www.elsevier.com/locate/mycres Lobulomycetales, a new order in the Chytridiomycota D. Rabern SIMMONSa,*, Timothy Y. JAMESb, Allen F. MEYERc, Joyce E. LONGCOREa aSchool of Biology and Ecology, University of Maine, Orono, ME 04469, USA bDepartment of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA cDepartment of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA article info abstract Article history: The Chytridiales, one of the four orders in the Chytridiomycetes (Chytridiomycota), is polyphy- Received 13 February 2008 letic, but contains several well-supported clades. One of these clades is referred to as the Received in revised form Chytriomyces angularis clade, and the phylogenetic placement of this group within the Chy- 23 October 2008 tridiomycetes is uncertain. The morphology and zoospore ultrastructure of C. angularis have Accepted 13 November 2008 been studied using LM and were shown to differ from those of the type species of Chytrio- Published online 25 December 2008 myces, which is in the Chytridiaceae and is phylogenetically distinct from the C. angularis Corresponding Editor: clade. In this study, chytrids with morphologies or rDNA sequences similar to C. angularis, Gordon W. Beakes including two isolates of the morphologically similar C. poculatus, were isolated and their phylogenetic relationships determined using molecular sequence data. Results of Bayesian Keywords: and MP analyses of nuSSU and partial nuLSU rDNA sequences grouped the new isolates Chytridium polysiphoniae and the type isolate of C. angularis in a monophyletic clade within the Chytridiomycota Clydaea but distinct from the Chytridiaceae. -
6.7 Classification, Natural Selection and Adaptations
CLASSIFICATION, NATURAL SELECTION AND ADAPTIONS Grade 6 Activity Plan Reviews and Updates 6.7 Classification, Natural Selection and Adaptions Objectives: 1. To understand how living things can be subdivided into small groups of related organisms. 2. To learn how to classify organisms based on similar characteristics. 3. To understand how new organisms arise from previously existing ones through evolution. 4. To see how living things adapt to their surroundings/environment through evolution and natural selection. Keywords/concepts: Classification, Hierarchy, Organism, Diversity, Survival, Adaptation, Evolution, Natural selection, Heterotroph, Autotroph, Eukaryote, Prokaryote, Replication, DNA, Mutation. Curriculum Outcomes: Grade 6: Outcome 6 concepts: Bullets 1, 2, 3, 4. Outcome 6 indicators: Bullets 1, 2, 3, 4. Focus: Bullet 1. Take-home product: Model of an imaginary ideal species. Written by: Dario Brooks, June, July 2016. Edited by: Bai Bintou Kaira, July 2016. Segment Details African Every cackling hen was an egg at first. Proverb Rwanda (5 min.) Ask some questions to get the students to start thinking about how we classify living things, and how organisms adapt to their environment. • What are some things that set living things apart from each other? Give some examples, such as shape, colours, or sounds. • Give some examples of plants or animals and explain Pre-test how you think their characteristics help them survive in (10 min.) their environment, such as fur, claws for defence, or camouflage. • Brainstorm on how you think animals develop the traits they have to help them thrive. Mentors: Help the students think about organisms that live in harsh environments, such as camels and cold- blooded lizards. -
Evolution and Phylogeny of Fungi
Dr. Archana Dutta Study material for M.Sc Botany- First Semester Assistant Professor(Guest Faculty) Dept. of Botany, MLT College, Saharsa [email protected] Mob No. - 9065558829 Evolution And Phylogeny Of Fungi Fungi have ancient origins, with evidence indicating they likely first appeared about one billion years ago, though the fossil record of fungi is scanty. Fungal hyphae evident within the tissues of the oldest plant fossils confirm that fungi are an extremely ancient group. Indeed, some of the oldest terrestrial plantlike fossils known, called Prototaxites, which were common in all parts of the world throughout the Devonian Period (419.2 million to 358.9 million years ago), are interpreted as large saprotrophic fungi (possibly even Basidiomycota). Fossils of Tortotubus protuberans, a filamentous fungus, date to the early Silurian Period (440 million years ago) and are thought to be the oldest known fossils of a terrestrial organism. However, in the absence of an extensive fossil record, biochemical characters have served as useful markers in mapping the probable evolutionary relationships of fungi. Fungal groups can be related by cell wall composition (i.e., presence of both chitin and alpha-1,3 and alpha-1,6-glucan), organization of tryptophan enzymes, and synthesis of lysine (i.e., by the aminoadipic acid pathway). Molecular phylogenetic analyses that became possible during the 1990s have greatly contributed to the understanding of fungal origins and evolution. At first, these analyses generated evolutionary trees by comparing a single gene sequence, usually the small subunit ribosomal RNA gene (SSU rRNA). Since then, information from several protein-coding genes has helped correct discrepancies, and phylogenetic trees of fungi are currently built using a wide variety of data largely, but not entirely, molecular in nature. -
Some Chytridiomycota in Soil Recover from Drying and High Temperatures
Mycol. Res. 108 (5): 583–589 (May 2004). f The British Mycological Society 583 DOI: 10.1017/S0953756204009736 Printed in the United Kingdom. Some Chytridiomycota in soil recover from drying and high temperatures 1 2 1 Frank H. GLEASON *, Peter M. LETCHER and Peter A. MCGEE 1 School of Biological Sciences A12, University of Sydney, 2006, Australia. 2 Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA. E-mail : [email protected] Received 21 November 2003; accepted 28 January 2004. Rhizophlyctis rosea was found in 44% of 59 soil samples from national parks, urban reserves and gardens, and agricultural lands of eastern New South Wales, Australia. As some of the soils are periodically dry and hot, we examined possible mechanisms that enable survival in stressful environments such as agricultural lands. Air-dried thalli of R. rosea in soil and pure cultures of R. rosea, two isolates of Allomyces anomalus, one isolate of Catenaria sp., one of Catenophlyctis sp. and one of Spizellomyces sp. recovered following incubation at 90 xC for two days. Powellomyces sp. recovered following incubation at 80 x. Sporangia of all seven fungi shrank during air-drying, and immediately returned to turgidity when rehydrated. Some sporangia of R. rosea released zoospores immediately upon rehydration. These data indicate that some Chytridiomycota have resistant structures that enable survival through periodic drying and high summer temperatures typical of soils used for cropping. Eleven Chytridiomycota isolated from soil did not survive either drying or heat. Neither habitat of the fungus nor morphological type correlated with the capacity to tolerate drying and heat. -
Classifying Monerans and Protists Teacher’S Guide Middle School
Classifying Monerans and Protists Teacher’s Guide Middle School Editors: Brian A. Jerome, Ph.D. Stephanie Zak Jerome Assistant Editors: Louise Marrier Graphics: Dean Ladago Fred Thodal Visual Learning Company 1-800-453-8481 25 Union Street www.visuallearningco.com Brandon, Vermont Classifying Monerans and Protists Use and Copyright The purchase of this video program entitles the user the right to reproduce or duplicate, in whole or in part, this teacher’s guide and the blackline master handouts for the purpose of teaching in conjunction with this video, Classifying Monerans and Protists. The right is restricted only for use with this video program. Any reproduction or duplication, in whole or in part, of this guide and student masters for any purpose other than for use with this video program is prohibited. The video and this teacher’s guide are the exclusive property of the copyright holder. Copying, transmitting or reproducing in any form, or by any means, without prior written permission from the copyright holder is prohibited (Title 17, U.S. Code Sections 501 and 506). Copyright © 2006 ISBN 978-1-59234-138-1 Visual Learning Company 1-800-453-8481 www.visuallearningco.com 2 3 Classifying Monerans and Protists Table of Contents Page A Message From Our Company 5 National Standards Correlations 6 Student Learning Objectives 7 Assessment 8 Introducing the Video 9 Video Viewing Suggestions 9 Video Script 10 Student Assessments and Activities 16 Answers to Student Assessments 17 Answers to Student Activities 18 Assessment and Student Activity Masters 19 www.visuallearningco.com 1-800-453-8481 Visual Learning Company 2 3 Classifying Monerans and Protists Viewing Clearances The video and accompanying teacher’s guide are for instructional use only.