The Origin and Evolution of Model Organisms
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Vertebrate Outline 2014
Winter 2014 EVOLUTION OF VERTEBRATES – LECTURE OUTLINE January 6 Introduction January 8 Unit 1 Vertebrate diversity and classification January 13 Unit 2 Chordate/Vertebrate bauplan January 15 Unit 3 Early vertebrates and agnathans January 20 Unit 4 Gnathostome bauplan; Life in water January 22 Unit 5 Early gnathostomes January 27 Unit 6 Chondrichthyans January 29 Unit 7 Major radiation of fishes: Osteichthyans February 3 Unit 8 Tetrapod origins and the invasion of land February 5 Unit 9 Extant amphibians: Lissamphibians February 10 Unit 10 Evolution of amniotes; Anapsids February 12 Midterm test (Units 1-8) February 17/19 Study week February 24 Unit 11 Lepidosaurs February 26 Unit 12 Mesozoic archosaurs March 3 March 5 Unit 13 Evolution of birds March 10 Unit 14 Avian flight March 12 Unit 15 Avian ecology and behaviour March 17 March 19 Unit 16 Rise of mammals March 24 Unit 17 Monotremes and marsupials March 26 Unit 18 Eutherians March 31 End of term test (Units 9-18) April 2 No lecture Winter 2014 EVOLUTION OF VERTEBRATES – LAB OUTLINE January 8 No lab January 15 Lab 1 Integuments and skeletons January 22 No lab January 29 Lab 2 Aquatic locomotion February 5 No lab February 12 Lab 3 Feeding: Form and function February 19 Study week February 26 Lab 4 Terrestrial locomotion March 5 No lab March 12 Lab 5 Flight March 19 No lab March 26 Lab 6 Sensory systems April 2 Lab exam Winter 2014 GENERAL INFORMATION AND MARKING SCHEME Professor: Dr. Janice M. Hughes Office: CB 4052; Telephone: 343-8280 Email: [email protected] Technologist: Don Barnes Office: CB 3015A; Telephone: 343-8490 Email: don [email protected] Suggested textbook: Pough, F.H., C, M, Janis, and J. -
Red Algae (Bangia Atropurpurea) Ecological Risk Screening Summary
Red Algae (Bangia atropurpurea) Ecological Risk Screening Summary U.S. Fish & Wildlife Service, February 2014 Revised, March 2016, September 2017, October 2017 Web Version, 6/25/2018 1 Native Range and Status in the United States Native Range From NOAA and USGS (2016): “Bangia atropurpurea has a widespread amphi-Atlantic range, which includes the Atlantic coast of North America […]” Status in the United States From Mills et al. (1991): “This filamentous red alga native to the Atlantic Coast was observed in Lake Erie in 1964 (Lin and Blum 1977). After this sighting, records for Lake Ontario (Damann 1979), Lake Michigan (Weik 1977), Lake Simcoe (Jackson 1985) and Lake Huron (Sheath 1987) were reported. It has become a major species of the littoral flora of these lakes, generally occupying the littoral zone with Cladophora and Ulothrix (Blum 1982). Earliest records of this algae in the basin, however, go back to the 1940s when Smith and Moyle (1944) found the alga in Lake Superior tributaries. Matthews (1932) found the alga in Quaker Run in the Allegheny drainage basin. Smith and 1 Moyle’s records must have not resulted in spreading populations since the alga was not known in Lake Superior as of 1987. Kishler and Taft (1970) were the most recent workers to refer to the records of Smith and Moyle (1944) and Matthews (1932).” From NOAA and USGS (2016): “Established where recorded except in Lake Superior. The distribution in Lake Simcoe is limited (Jackson 1985).” From Kipp et al. (2017): “Bangia atropurpurea was first recorded from Lake Erie in 1964. During the 1960s–1980s, it was recorded from Lake Huron, Lake Michigan, Lake Ontario, and Lake Simcoe (part of the Lake Ontario drainage). -
Timeline of the Evolutionary History of Life
Timeline of the evolutionary history of life This timeline of the evolutionary history of life represents the current scientific theory Life timeline Ice Ages outlining the major events during the 0 — Primates Quater nary Flowers ←Earliest apes development of life on planet Earth. In P Birds h Mammals – Plants Dinosaurs biology, evolution is any change across Karo o a n ← Andean Tetrapoda successive generations in the heritable -50 0 — e Arthropods Molluscs r ←Cambrian explosion characteristics of biological populations. o ← Cryoge nian Ediacara biota – z ← Evolutionary processes give rise to diversity o Earliest animals ←Earliest plants at every level of biological organization, i Multicellular -1000 — c from kingdoms to species, and individual life ←Sexual reproduction organisms and molecules, such as DNA and – P proteins. The similarities between all present r -1500 — o day organisms indicate the presence of a t – e common ancestor from which all known r Eukaryotes o species, living and extinct, have diverged -2000 — z o through the process of evolution. More than i Huron ian – c 99 percent of all species, amounting to over ←Oxygen crisis [1] five billion species, that ever lived on -2500 — ←Atmospheric oxygen Earth are estimated to be extinct.[2][3] Estimates on the number of Earth's current – Photosynthesis Pong ola species range from 10 million to 14 -3000 — A million,[4] of which about 1.2 million have r c been documented and over 86 percent have – h [5] e not yet been described. However, a May a -3500 — n ←Earliest oxygen 2016 -
Seasonal and Interannual Changes in Ciliate and Dinoflagellate
ORIGINAL RESEARCH published: 07 February 2017 doi: 10.3389/fmars.2017.00016 Seasonal and Interannual Changes in Ciliate and Dinoflagellate Species Assemblages in the Arctic Ocean (Amundsen Gulf, Beaufort Sea, Canada) Edited by: Deo F. L. Onda 1, 2, 3, Emmanuelle Medrinal 1, 3, André M. Comeau 1, 3 †, Mary Thaler 1, 2, 3, George S. Bullerjahn, Marcel Babin 1, 2 and Connie Lovejoy 1, 2, 3* Bowling Green State University, USA Reviewed by: 1 Département de Biologie and Québec-Océan, Université Laval, Quebec, QC, Canada, 2 Takuvik, Joint International Rebecca Gast, Laboratory, UMI 3376, Centre National de la Recherche Scientifique (CNRS, France) and Université Laval, Québec, QC, Woods Hole Oceanographic Canada, 3 Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec, QC, Canada Institution, USA Alison Clare Cleary, Independent Researcher, San Recent studies have focused on how climate change could drive changes in Francisco, United States phytoplankton communities in the Arctic. In contrast, ciliates and dinoflagellates that can *Correspondence: contribute substantially to the mortality of phytoplankton have received less attention. Connie Lovejoy Some dinoflagellate and ciliate species can also contribute to net photosynthesis, [email protected] which suggests that species composition could reflect food web complexity. To identify †Present Address: André M. Comeau, potential seasonal and annual species occurrence patterns and to link species with Centre for Comparative Genomics and environmental conditions, we first examined the seasonal pattern of microzooplankton Evolutionary Bioinformatics-Integrated Microbiome Resource, Department of and then performed an in-depth analysis of interannual species variability. We used Pharmacology, Dalhousie University, high-throughput amplicon sequencing to identify ciliates and dinoflagellates to the lowest Canada taxonomic level using a curated Arctic 18S rRNA gene database. -
A Wide Diversity of Previously Undetected Freeliving
Environmental Microbiology (2010) 12(10), 2700–2710 doi:10.1111/j.1462-2920.2010.02239.x A wide diversity of previously undetected free-living relatives of diplomonads isolated from marine/saline habitatsemi_2239 2700..2710 Martin Kolisko,1 Jeffrey D. Silberman,2 Kipferlia n. gen. The remaining isolates include rep- Ivan Cepicka,3 Naoji Yubuki,4† Kiyotaka Takishita,5 resentatives of three other lineages that likely repre- Akinori Yabuki,4 Brian S. Leander,6 Isao Inouye,4 sent additional undescribed genera (at least). Small- Yuji Inagaki,7 Andrew J. Roger8 and subunit ribosomal RNA gene phylogenies show that Alastair G. B. Simpson1* CLOs form a cloud of six major clades basal to the Departments of 1Biology and 8Biochemistry and diplomonad-retortamonad grouping (i.e. each of the Molecular Biology, Dalhousie University, Halifax, Nova six CLO clades is potentially as phylogenetically Scotia, Canada. distinct as diplomonads and retortamonads). CLOs 2Department of Biological Sciences, University of will be valuable for tracing the evolution of Arkansas, Fayetteville, AR, USA. diplomonad cellular features, for example, their 3Department of Zoology, Faculty of Science, Charles extremely reduced mitochondrial organelles. It is University in Prague, Prague, Czech Republic. striking that the majority of CLO diversity was unde- 4Institute of Biological Sciences, Graduate School of Life tected by previous light microscopy surveys and and Environmental Sciences and 7Center for environmental PCR studies, even though they inhabit Computational Sciences and Institute of Biological a commonly sampled environment. There is no Sciences, University of Tsukuba, Tsukuba, Ibaraki, reason to assume this is a unique situation – it is Japan. likely that undersampling at the level of major lin- 5Japan Agency for Marine-Earth Science and eages is still widespread for protists. -
Placing Birds on a Dynamic Evolutionary Map: Using Digital Tools to Update the Evolutionary Metaphor of the "Tree of Life"
University of Central Florida STARS Electronic Theses and Dissertations, 2004-2019 2012 Placing Birds On A Dynamic Evolutionary Map: Using Digital Tools To Update The Evolutionary Metaphor Of The "Tree Of Life" Sonia Stephens University of Central Florida Part of the Ecology and Evolutionary Biology Commons, Graphic Communications Commons, and the Rhetoric Commons Find similar works at: https://stars.library.ucf.edu/etd University of Central Florida Libraries http://library.ucf.edu This Doctoral Dissertation (Open Access) is brought to you for free and open access by STARS. It has been accepted for inclusion in Electronic Theses and Dissertations, 2004-2019 by an authorized administrator of STARS. For more information, please contact [email protected]. STARS Citation Stephens, Sonia, "Placing Birds On A Dynamic Evolutionary Map: Using Digital Tools To Update The Evolutionary Metaphor Of The "Tree Of Life"" (2012). Electronic Theses and Dissertations, 2004-2019. 2264. https://stars.library.ucf.edu/etd/2264 PLACING BIRDS ON A DYNAMIC EVOLUTIONARY MAP: USING DIGITAL TOOLS TO UPDATE THE EVOLUTIONARY METAPHOR OF THE “TREE OF LIFE” by SONIA H. STEPHENS B.S. University of Hawaii, 1999 M.S. University of Hawaii, 2003 A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of English in the College of Arts and Humanities at the University of Central Florida Orlando, Florida Spring Term 2012 Major Professor: Paul Dombrowski ©2012 Sonia H. Stephens ii ABSTRACT This dissertation describes and presents a new type of interactive visualization for communicating about evolutionary biology, the dynamic evolutionary map. This web-based tool utilizes a novel map-based metaphor to visualize evolution, rather than the traditional “tree of life.” The dissertation begins with an analysis of the conceptual affordances of the traditional tree of life as the dominant metaphor for evolution. -
Identification of a Giardia Krr1 Homolog Gene and the Secondarily Anucleolate Condition of Giaridia Lamblia
Identification of a Giardia krr1 Homolog Gene and the Secondarily Anucleolate Condition of Giaridia lamblia De-Dong Xin,* Jian-Fan Wen,* De He,* and Si-Qi Luà *Key Laboratory of Cellular and Molecular Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Graduate School of the Chinese Academy of Sciences, Beijing, China; and àCapital University of Medical Sciences, Beijing, China Giaridia lamblia was long considered to be one of the most primitive eukaryotes and to lie close to the transition between prokaryotes and eukaryotes, but several supporting features, such as lack of mitochondrion and Golgi, have been challenged recently. It was also reported previously that G. lamblia lacked nucleolus, which is the site of pre-rRNA processing and ribosomal assembling in the other eukaryotic cells. Here, we report the identification of the yeast homolog gene, krr1, in the anucleolate eukaryote, G. lamblia. The krr1 gene, encoding one of the pre-rRNA processing proteins in yeast, is actively transcribed in G. lamblia. The deduced protein sequence of G. lamblia krr1 is highly similar to yeast KRR1p that contains a single-KH domain. Our database searches indicated that krr1 genes actually present in diverse Downloaded from https://academic.oup.com/mbe/article/22/3/391/1075989 by guest on 24 September 2021 eukaryotes and also seem to present in Archaea. However, only the eukaryotic homologs, including that of G. lamblia, have the single-KH domain, which contains the conserved motif KR(K)R. Fibrillarin, another important pre-rRNA processing protein has also been identified previously in G. lamblia. Moreover, our database search shows that nearly half of the other nucleolus-localized protein genes of eukaryotic cells also have their homologs in Giardia. -
Lateral Gene Transfer of Anion-Conducting Channelrhodopsins Between Green Algae and Giant Viruses
bioRxiv preprint doi: https://doi.org/10.1101/2020.04.15.042127; this version posted April 23, 2020. 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. 1 5 Lateral gene transfer of anion-conducting channelrhodopsins between green algae and giant viruses Andrey Rozenberg 1,5, Johannes Oppermann 2,5, Jonas Wietek 2,3, Rodrigo Gaston Fernandez Lahore 2, Ruth-Anne Sandaa 4, Gunnar Bratbak 4, Peter Hegemann 2,6, and Oded 10 Béjà 1,6 1Faculty of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel. 2Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Invalidenstraße 42, Berlin 10115, Germany. 3Present address: Department of Neurobiology, Weizmann 15 Institute of Science, Rehovot 7610001, Israel. 4Department of Biological Sciences, University of Bergen, N-5020 Bergen, Norway. 5These authors contributed equally: Andrey Rozenberg, Johannes Oppermann. 6These authors jointly supervised this work: Peter Hegemann, Oded Béjà. e-mail: [email protected] ; [email protected] 20 ABSTRACT Channelrhodopsins (ChRs) are algal light-gated ion channels widely used as optogenetic tools for manipulating neuronal activity 1,2. Four ChR families are currently known. Green algal 3–5 and cryptophyte 6 cation-conducting ChRs (CCRs), cryptophyte anion-conducting ChRs (ACRs) 7, and the MerMAID ChRs 8. Here we 25 report the discovery of a new family of phylogenetically distinct ChRs encoded by marine giant viruses and acquired from their unicellular green algal prasinophyte hosts. -
Phytoref: a Reference Database of the Plastidial 16S Rrna Gene of Photosynthetic Eukaryotes with Curated Taxonomy
Molecular Ecology Resources (2015) 15, 1435–1445 doi: 10.1111/1755-0998.12401 PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy JOHAN DECELLE,*† SARAH ROMAC,*† ROWENA F. STERN,‡ EL MAHDI BENDIF,§ ADRIANA ZINGONE,¶ STEPHANE AUDIC,*† MICHAEL D. GUIRY,** LAURE GUILLOU,*† DESIRE TESSIER,††‡‡ FLORENCE LE GALL,*† PRISCILLIA GOURVIL,*† ADRIANA L. DOS SANTOS,*† IAN PROBERT,*† DANIEL VAULOT,*† COLOMBAN DE VARGAS*† and RICHARD CHRISTEN††‡‡ *UMR 7144 - Sorbonne Universites, UPMC Univ Paris 06, Station Biologique de Roscoff, Roscoff 29680, France, †CNRS, UMR 7144, Station Biologique de Roscoff, Roscoff 29680, France, ‡Sir Alister Hardy Foundation for Ocean Science, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK, §Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK, ¶Stazione Zoologica Anton Dohrn, Villa Comunale, Naples 80121, Italy, **The AlgaeBase Foundation, c/o Ryan Institute, National University of Ireland, University Road, Galway Ireland, ††CNRS, UMR 7138, Systematique Adaptation Evolution, Parc Valrose, BP71, Nice F06108, France, ‡‡Universite de Nice-Sophia Antipolis, UMR 7138, Systematique Adaptation Evolution, Parc Valrose, BP71, Nice F06108, France Abstract Photosynthetic eukaryotes have a critical role as the main producers in most ecosystems of the biosphere. The ongo- ing environmental metabarcoding revolution opens the perspective for holistic ecosystems biological studies of these organisms, in particular the unicellular microalgae that -
Honey Bee from Wikipedia, the Free Encyclopedia
Honey bee From Wikipedia, the free encyclopedia A honey bee (or honeybee) is any member of the genus Apis, primarily distinguished by the production and storage of honey and the Honey bees construction of perennial, colonial nests from wax. Currently, only seven Temporal range: Oligocene–Recent species of honey bee are recognized, with a total of 44 subspecies,[1] PreЄ Є O S D C P T J K Pg N though historically six to eleven species are recognized. The best known honey bee is the Western honey bee which has been domesticated for honey production and crop pollination. Honey bees represent only a small fraction of the roughly 20,000 known species of bees.[2] Some other types of related bees produce and store honey, including the stingless honey bees, but only members of the genus Apis are true honey bees. The study of bees, which includes the study of honey bees, is known as melittology. Western honey bee carrying pollen Contents back to the hive Scientific classification 1 Etymology and name Kingdom: Animalia 2 Origin, systematics and distribution 2.1 Genetics Phylum: Arthropoda 2.2 Micrapis 2.3 Megapis Class: Insecta 2.4 Apis Order: Hymenoptera 2.5 Africanized bee 3 Life cycle Family: Apidae 3.1 Life cycle 3.2 Winter survival Subfamily: Apinae 4 Pollination Tribe: Apini 5 Nutrition Latreille, 1802 6 Beekeeping 6.1 Colony collapse disorder Genus: Apis 7 Bee products Linnaeus, 1758 7.1 Honey 7.2 Nectar Species 7.3 Beeswax 7.4 Pollen 7.5 Bee bread †Apis lithohermaea 7.6 Propolis †Apis nearctica 8 Sexes and castes Subgenus Micrapis: 8.1 Drones 8.2 Workers 8.3 Queens Apis andreniformis 9 Defense Apis florea 10 Competition 11 Communication Subgenus Megapis: 12 Symbolism 13 Gallery Apis dorsata 14 See also 15 References 16 Further reading Subgenus Apis: 17 External links Apis cerana Apis koschevnikovi Etymology and name Apis mellifera Apis nigrocincta The genus name Apis is Latin for "bee".[3] Although modern dictionaries may refer to Apis as either honey bee or honeybee, entomologist Robert Snodgrass asserts that correct usage requires two words, i.e. -
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). -
Extreme Positive Allometry of Animal Adhesive Pads and the Size Limits of Adhesion-Based Climbing
Extreme positive allometry of animal adhesive pads and the size limits of adhesion-based climbing David Labontea,1, Christofer J. Clementeb, Alex Dittrichc, Chi-Yun Kuod, Alfred J. Crosbye, Duncan J. Irschickd, and Walter Federlea aDepartment of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom; bSchool of Science and Engineering, University of the Sunshine Coast, Sippy Downs, QLD 4556, Australia; cDepartment of Life Sciences, Anglia Ruskin University, Cambridge CB1 1PT, United Kingdom; dBiology Department, University of Massachusetts Amherst, Amherst, MA 01003; and eDepartment of Polymer Science and Engineering, University of Massachusetts Amherst, Amherst, MA 01003 Edited by David B. Wake, University of California, Berkeley, CA, and approved December 11, 2015 (received for review October 7, 2015) Organismal functions are size-dependent whenever body surfaces animals to climb smooth vertical or inverted surfaces, thereby supply body volumes. Larger organisms can develop strongly opening up new habitats. Adhesive pads have evolved multiple folded internal surfaces for enhanced diffusion, but in many cases times independently within arthropods, reptiles, amphibians, and areas cannot be folded so that their enlargement is constrained by mammals and show impressive performance: They are rapidly anatomy, presenting a problem for larger animals. Here, we study controllable, can be used repeatedly without any loss of perfor- the allometry of adhesive pad area in 225 climbing animal species, mance, and function on rough, dirty, and flooded surfaces (12). This covering more than seven orders of magnitude in weight. Across performance has inspired a considerable amount of work on tech- all taxa, adhesive pad area showed extreme positive allometry and nical adhesives that mimic these properties (13).