Genomics and Mapping of Teleostei (Bony fish)
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Article Evolutionary Dynamics of the OR Gene Repertoire in Teleost Fishes
bioRxiv preprint doi: https://doi.org/10.1101/2021.03.09.434524; this version posted March 10, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Article Evolutionary dynamics of the OR gene repertoire in teleost fishes: evidence of an association with changes in olfactory epithelium shape Maxime Policarpo1, Katherine E Bemis2, James C Tyler3, Cushla J Metcalfe4, Patrick Laurenti5, Jean-Christophe Sandoz1, Sylvie Rétaux6 and Didier Casane*,1,7 1 Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198, Gif-sur-Yvette, France. 2 NOAA National Systematics Laboratory, National Museum of Natural History, Smithsonian Institution, Washington, D.C. 20560, U.S.A. 3Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., 20560, U.S.A. 4 Independent Researcher, PO Box 21, Nambour QLD 4560, Australia. 5 Université de Paris, Laboratoire Interdisciplinaire des Energies de Demain, Paris, France 6 Université Paris-Saclay, CNRS, Institut des Neurosciences Paris-Saclay, 91190, Gif-sur- Yvette, France. 7 Université de Paris, UFR Sciences du Vivant, F-75013 Paris, France. * Corresponding author: e-mail: [email protected]. !1 bioRxiv preprint doi: https://doi.org/10.1101/2021.03.09.434524; this version posted March 10, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Teleost fishes perceive their environment through a range of sensory modalities, among which olfaction often plays an important role. -
§4-71-6.5 LIST of CONDITIONALLY APPROVED ANIMALS November
§4-71-6.5 LIST OF CONDITIONALLY APPROVED ANIMALS November 28, 2006 SCIENTIFIC NAME COMMON NAME INVERTEBRATES PHYLUM Annelida CLASS Oligochaeta ORDER Plesiopora FAMILY Tubificidae Tubifex (all species in genus) worm, tubifex PHYLUM Arthropoda CLASS Crustacea ORDER Anostraca FAMILY Artemiidae Artemia (all species in genus) shrimp, brine ORDER Cladocera FAMILY Daphnidae Daphnia (all species in genus) flea, water ORDER Decapoda FAMILY Atelecyclidae Erimacrus isenbeckii crab, horsehair FAMILY Cancridae Cancer antennarius crab, California rock Cancer anthonyi crab, yellowstone Cancer borealis crab, Jonah Cancer magister crab, dungeness Cancer productus crab, rock (red) FAMILY Geryonidae Geryon affinis crab, golden FAMILY Lithodidae Paralithodes camtschatica crab, Alaskan king FAMILY Majidae Chionocetes bairdi crab, snow Chionocetes opilio crab, snow 1 CONDITIONAL ANIMAL LIST §4-71-6.5 SCIENTIFIC NAME COMMON NAME Chionocetes tanneri crab, snow FAMILY Nephropidae Homarus (all species in genus) lobster, true FAMILY Palaemonidae Macrobrachium lar shrimp, freshwater Macrobrachium rosenbergi prawn, giant long-legged FAMILY Palinuridae Jasus (all species in genus) crayfish, saltwater; lobster Panulirus argus lobster, Atlantic spiny Panulirus longipes femoristriga crayfish, saltwater Panulirus pencillatus lobster, spiny FAMILY Portunidae Callinectes sapidus crab, blue Scylla serrata crab, Samoan; serrate, swimming FAMILY Raninidae Ranina ranina crab, spanner; red frog, Hawaiian CLASS Insecta ORDER Coleoptera FAMILY Tenebrionidae Tenebrio molitor mealworm, -
Canestro 06Evodev Retinoic Acid Machinery in Non-Chordates.Pdf
EVOLUTION & DEVELOPMENT 8:5, 394–406 (2006) Is retinoic acid genetic machinery a chordate innovation? Cristian Can˜estro,a John H. Postlethwait,a Roser Gonza`lez-Duarte,b and Ricard Albalatb,Ã aInstitute of Neuroscience, University of Oregon, Eugene, OR 97403, USA bDepartament de Gene`tica, Universitat de Barcelona, Av. Diagonal 645, 08028 Barcelona, Spain ÃAuthor for correspondence (email: [email protected]) SUMMARY Development of many chordate features and showed for the first time that RA genetic machineryF depends on retinoic acid (RA). Because the action of RA that is Aldh1a, Cyp26, and Rar orthologsFis present in during development seems to be restricted to chordates, it had nonchordate deuterostomes. This finding implies that RA been previously proposed that the ‘‘invention’’ of RA genetic genetic machinery was already present during early machinery, including RA-binding nuclear hormone receptors deuterostome evolution, and therefore, is not a chordate (Rars), and the RA-synthesizing and RA-degrading enzymes innovation. This new evolutionary viewpoint argues against Aldh1a (Raldh) and Cyp26, respectively, was an important the hypothesis that the acquisition of gene families under- step for the origin of developmental mechanisms leading lying RA metabolism and signaling was a key event for to the chordate body plan. We tested this hypothesis the origin of chordates. We propose a new hypothesis in by conducting an exhaustive survey of the RA machinery which lineage-specific duplication and loss of RA machinery in genomic databases for twelve deuterostomes. We genes could be related to the morphological radiation of reconstructed the evolution of these genes in deuterostomes deuterostomes. INTRODUCTION which appears to be the sister group of chordates (Cameron et al. -
Helminth Parasites in Two Populations of Astronotus
Original article ISSN 1984-2961 (Electronic) www.cbpv.org.br/rbpv Braz. J. Vet. Parasitol., Jaboticabal, v. 28, n. 3, p. 425-431, july.-sept. 2019 Doi: https://doi.org/10.1590/S1984-29612019052 Helminth parasites in two populations of Astronotus ocellatus (Cichliformes: Cichlidae) from the eastern Amazon, Northern Brazil Helmintos parasitos em duas populações de Astronotus ocellatus (Cichliformes: Cichlidae) da Amazônia oriental, Norte do Brasil Raul Henrique da Silva Pinheiro1,2 ; Marcos Tavares-Dias3 ; Elane Guerreiro Giese1,2* 1 Programa de Pós-graduação em Biologia de Agentes Infecciosos e Parasitários, Instituto de Ciências Biológicas, Universidade Federal do Pará – UFPA, Belém, PA, Brasil 2 Laboratório de Histologia e Embriologia Animal, Instituto da Saúde e Produção Animal, Universidade Federal Rural da Amazônia – UFRA, Belém, PA, Brasil 3 Empresa Brasileira de Pesquisa Agropecuária – EMBRAPA, Macapá, AP, Brasil Received March 15, 2019 Accepted May 31, 2019 Abstract This study compared the structure of helminth parasite communities in two populations ofAstronotus ocellatus from two localities in Pará State, eastern Amazon (Brazil). Hosts from the Tapajós River were infected by Posthodiplostomum sp. metacercarie, larvae of Contracaecum sp. and Pseudoproleptus sp., with predominance of Contracaecum sp. Hosts from Iara Lake were infected by Procamallanus spiculastriatus, Proteocephalus sp. and Acanthocephala gen. sp., with predominance of P. spiculastriatus. Parasites had an aggregated dispersion and there were differences in Shannon diversity index and the evenness between both host populations, because the parasite component community showed no similarity. The existence of variation in infracommunity and community of parasites for A. ocellatus from different localities indicates the presence of an uneven distribution in terms of species and density of parasites, as well as of intermediate hosts in the localities surveyed. -
A Preliminary Global Assessment of the Status of Exploited Marine Fish and Invertebrate Populations
A PRELIMINARY GLOBAL ASSESSMENT OF THE STATUS OF EXPLOITED MARINE FISH AND INVERTEBRATE POPULATIONS June 30 2018 A PRELIMINARY GLOBAL ASSESSMENT OF THE STATUS OF EXPLOITED MARINE FISH AND INVERTEBRATE POPULATIONS Maria. L.D. Palomares, Rainer Froese, Brittany Derrick, Simon-Luc Nöel, Gordon Tsui Jessika Woroniak Daniel Pauly A report prepared by the Sea Around Us for OCEANA June 30, 2018 A PRELIMINARY GLOBAL ASSESSMENT OF THE STATUS OF EXPLOITED MARINE FISH AND INVERTEBRATE POPULATIONS Maria L.D. Palomares1, Rainer Froese2, Brittany Derrick1, Simon-Luc Nöel1, Gordon Tsui1, Jessika Woroniak1 and Daniel Pauly1 CITE AS: Palomares MLD, Froese R, Derrick B, Nöel S-L, Tsui G, Woroniak J, Pauly D (2018) A preliminary global assessment of the status of exploited marine fish and invertebrate populations. A report prepared by the Sea Around Us for OCEANA. The University of British Columbia, Vancouver, p. 64. 1 Sea Around Us, Institute for the Oceans and Fisheries, University of British Columbia, 2202 Main Mall, Vancouver BC V6T1Z4 Canada 2 Helmholtz Centre for Ocean Research GEOMAR, Düsternbrooker Weg 20, 24105 Kiel, Germany TABLE OF CONTENTS Executive Summary 1 Introduction 2 Material and Methods 3 − Reconstructed catches vs official catches 3 − Marine Ecoregions vs EEZs 3 − The CMSY method 5 Results and Discussion 7 − Stock summaries reports 9 − Problematic stocks and sources of bias 14 − Stocks in the countries where OCEANA operates 22 − Stock assessments on the Sea Around Us website 31 − The next steps 32 Acknowledgements 33 References 34 Appendices I. List of marine ecoregions by EEZ 37 II. Summaries of number of stock by region and 49 by continent III. -
Adaptive Evolution of Low Salinity Tolerance and Hypoosmotic Regulation in a Euryhaline Teleost, Takifugu Obscurus
Adaptive evolution of low salinity tolerance and hypoosmotic regulation in a euryhaline teleost, Takifugu obscurus Hanyuan Zhang Key Laboratory of Aquatic Genomics, Ministry of Agriculture, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Fengtai, Beijing, China Jilun Hou Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao, Hebei, China Haijin Liu Breeding Laboratory, Dalian Tianzheng Industry Co. Ltd., Dalian, Liaoning, China Haoyong Zhu Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China Gangchun Xu Freshwater Fisheries Research Centre of Chinese Academy of Fishery Sciences, Wuxi, China Jian Xu ( [email protected] ) Chinese Academy of Fishery Sciences https://orcid.org/0000-0003-0274-4268 Research article Keywords: Takifugu, low salt-tolerance, hypoosmotic regulation, population genomics, genome re- sequencing Posted Date: October 30th, 2019 DOI: https://doi.org/10.21203/rs.2.16620/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 at Marine Biology on June 3rd, 2020. See the published version at https://doi.org/10.1007/s00227-020-03705-x. Page 1/20 Abstract Background The mechanism of osmoregulation is crucial for maintaining growth, development, and life activities in teleosts. Takifugu obscurus, the only euryhaline species in the genus Takifugu, is a proper model organism for studying the mechanism of low salt-tolerance and hypoosmotic regulation. Results In this study, whole genome sequencing data were obtained from 90 puffersh representing ve species within this genus, T. rubripes, T. obscurus, T. -
Summary Report of Freshwater Nonindigenous Aquatic Species in U.S
Summary Report of Freshwater Nonindigenous Aquatic Species in U.S. Fish and Wildlife Service Region 4—An Update April 2013 Prepared by: Pam L. Fuller, Amy J. Benson, and Matthew J. Cannister U.S. Geological Survey Southeast Ecological Science Center Gainesville, Florida Prepared for: U.S. Fish and Wildlife Service Southeast Region Atlanta, Georgia Cover Photos: Silver Carp, Hypophthalmichthys molitrix – Auburn University Giant Applesnail, Pomacea maculata – David Knott Straightedge Crayfish, Procambarus hayi – U.S. Forest Service i Table of Contents Table of Contents ...................................................................................................................................... ii List of Figures ............................................................................................................................................ v List of Tables ............................................................................................................................................ vi INTRODUCTION ............................................................................................................................................. 1 Overview of Region 4 Introductions Since 2000 ....................................................................................... 1 Format of Species Accounts ...................................................................................................................... 2 Explanation of Maps ................................................................................................................................ -
Integration of the Genetic Map and Genome Assembly of Fugu Facilitates Insights Into Distinct Features of Genome Evolution in Teleosts and Mammals
GBE Integration of the Genetic Map and Genome Assembly of Fugu Facilitates Insights into Distinct Features of Genome Evolution in Teleosts and Mammals Wataru Kai1, Kiyoshi Kikuchi*,1, Sumanty Tohari2, Ah Keng Chew2, Alice Tay2, Atushi Fujiwara3, Sho Hosoya1, Hiroaki Suetake1, Kiyoshi Naruse4, Sydney Brenner2, Yuzuru Suzuki1, and Downloaded from https://academic.oup.com/gbe/article-abstract/doi/10.1093/gbe/evr041/582998 by guest on 22 April 2019 Byrappa Venkatesh2 1Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, University of Tokyo, Hamamatsu, Shizuoka, Japan 2Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore, Singapore 3National Research Institute of Fisheries Science, Fisheries Research Agency, Yokohama, Kanagawa, Japan 4Laboratory of Bioresources, National Institute for Basic Biology, Okazaki, Aichi, Japan *Corresponding author: E-mail: [email protected]. Accepted: 21 April 2011 Abstract The compact genome of fugu (Takifugu rubripes) has been used widely as a reference genome for understanding the evolution of vertebrate genomes. However, the fragmented nature of the fugu genome assembly has restricted its use for comparisons of genome architecture in vertebrates. To extend the contiguity of the assembly to the chromosomal level, we have generated a comprehensive genetic map of fugu and anchored the scaffolds of the assembly to the 22 chromosomes of fugu. The map consists of 1,220 microsatellite markers that provide anchor points to 697 scaffolds covering 86% of the genome assembly (http://www.fugu-sg.org/). The integrated genome map revealed a higher recombination rate in fugu compared with other vertebrates and a wide variation in the recombination rate between sexes and across chromosomes of fugu. -
99. Annual Meeting of the German Zoological Society 16
99. Annual Meeting of the German Zoological Society 16. – 20. September 2006 Münster 1 Welcome address Dear colleagues: Welcome to Münster and thank you very much for your participation! The 99th Annual Meeting of the German Zoological Society has attracted many participants from all over Europe. We are glad to present you a program that covers the broad spectrum of modern Zoology. The Program Committee has put together a well balanced selection of Plenary Lectures, Symposia, and Regular Scientific Sessions. In addition, the program will provide plenty of room for discussing more specialized issues during the breaks and the social events. The Poster Sessions represent an essential part of the conference where scientific results from more specific investigations will be presented. There will be ample time for discussion with the authors at the posters. Hopefully, this program will stimulate vivid discussions, new ideas and fruitful collaborations. We are pleased to act as host to you here in Münster for the next few days. For the organizers, Wolf-Michael Weber 2 General information Conference venue: Universität Münster, Auditorium Hindenburgplatz 10-12, Lecture rooms of the department biology Registration: Congress documents and badges will be handed out at the registration desk (Auditorium Hindenburgplatz 10-12) The desk is open: Saturday, September 16: 16:00 – 20:00 Sunday, September 17: from 8:00 Monday, September 18: from 8:00 Tuesday, September 19: from 8:00 Wedbesday, September 20: 8:00 – 10:00 Congress Secretariat: Institute of Animal Physiology Westfalian Wilhelms University Hindenburgplatz 55, 48143 Muenster Phone: +49 (0) 251 – 83 217 83 Fax: +49 (0) 251 – 83 217 85 E-Mail: [email protected] Oral presentations: Audio-visual equipment (Windows PC with CD-ROM drive and USB-port, video beamer) will be provided for Powerpoint presentations (preferably on USB stick or CD) in every lecture hall. -
Species Composition and Invasion Risks of Alien Ornamental Freshwater
www.nature.com/scientificreports OPEN Species composition and invasion risks of alien ornamental freshwater fshes from pet stores in Klang Valley, Malaysia Abdulwakil Olawale Saba1,2, Ahmad Ismail1, Syaizwan Zahmir Zulkifi1, Muhammad Rasul Abdullah Halim3, Noor Azrizal Abdul Wahid4 & Mohammad Noor Azmai Amal1* The ornamental fsh trade has been considered as one of the most important routes of invasive alien fsh introduction into native freshwater ecosystems. Therefore, the species composition and invasion risks of fsh species from 60 freshwater fsh pet stores in Klang Valley, Malaysia were studied. A checklist of taxa belonging to 18 orders, 53 families, and 251 species of alien fshes was documented. Fish Invasiveness Screening Test (FIST) showed that seven (30.43%), eight (34.78%) and eight (34.78%) species were considered to be high, medium and low invasion risks, respectively. After the calibration of the Fish Invasiveness Screening Kit (FISK) v2 using the Receiver Operating Characteristics, a threshold value of 17 for distinguishing between invasive and non-invasive fshes was identifed. As a result, nine species (39.13%) were of high invasion risk. In this study, we found that non-native fshes dominated (85.66%) the freshwater ornamental trade in Klang Valley, while FISK is a more robust tool in assessing the risk of invasion, and for the most part, its outcome was commensurate with FIST. This study, for the frst time, revealed the number of high-risk ornamental fsh species that give an awareness of possible future invasion if unmonitored in Klang Valley, Malaysia. As a global hobby, fshkeeping is cherished by both young and old people. -
Humboldt Bay Fishes
Humboldt Bay Fishes ><((((º>`·._ .·´¯`·. _ .·´¯`·. ><((((º> ·´¯`·._.·´¯`·.. ><((((º>`·._ .·´¯`·. _ .·´¯`·. ><((((º> Acknowledgements The Humboldt Bay Harbor District would like to offer our sincere thanks and appreciation to the authors and photographers who have allowed us to use their work in this report. Photography and Illustrations We would like to thank the photographers and illustrators who have so graciously donated the use of their images for this publication. Andrey Dolgor Dan Gotshall Polar Research Institute of Marine Sea Challengers, Inc. Fisheries And Oceanography [email protected] [email protected] Michael Lanboeuf Milton Love [email protected] Marine Science Institute [email protected] Stephen Metherell Jacques Moreau [email protected] [email protected] Bernd Ueberschaer Clinton Bauder [email protected] [email protected] Fish descriptions contained in this report are from: Froese, R. and Pauly, D. Editors. 2003 FishBase. Worldwide Web electronic publication. http://www.fishbase.org/ 13 August 2003 Photographer Fish Photographer Bauder, Clinton wolf-eel Gotshall, Daniel W scalyhead sculpin Bauder, Clinton blackeye goby Gotshall, Daniel W speckled sanddab Bauder, Clinton spotted cusk-eel Gotshall, Daniel W. bocaccio Bauder, Clinton tube-snout Gotshall, Daniel W. brown rockfish Gotshall, Daniel W. yellowtail rockfish Flescher, Don american shad Gotshall, Daniel W. dover sole Flescher, Don stripped bass Gotshall, Daniel W. pacific sanddab Gotshall, Daniel W. kelp greenling Garcia-Franco, Mauricio louvar -
Metaphylogeny of 82 Gene Families Sheds a New Light on Chordate Evolution
Int. J. Biol. Sci. 2006, 2 32 International Journal of Biological Sciences ISSN 1449-2288 www.biolsci.org 2006 2(2):32-37 ©2006 Ivyspring International Publisher. All rights reserved Research paper Metaphylogeny of 82 gene families sheds a new light on chordate evolution Alexandre Vienne and Pierre Pontarotti Phylogenomics Laboratory, EA 3781 Evolution Biologique, Université de Provence, 13331 MARSEILLE CEDEX 03, FRANCE Corresponding to: Alexandre Vienne, Phylogenomics Laboratory, EA 3781 Evolution Biologique, Place V. HUGO, Université de Provence, 13331 MARSEILLE CEDEX 03, France. Email: [email protected]. Phone: (33) 4 91 10 64 89 Received: 2006.01.15; Accepted: 2006.03.31; Published: 2006.04.10 Achieving a better comprehension of the evolution of species has always been an important matter for evolutionary biologists. The deuterostome phylogeny has been described for many years, and three phyla are distinguishable: Echinodermata (including sea stars, sea urchins, etc…), Hemichordata (including acorn worms and pterobranchs), and Chordata (including urochordates, cephalochordates and extant vertebrates). Inside the Chordata phylum, the position of vertebrate species is quite unanimously accepted. Nonetheless, the position of urochordates in regard with vertebrates is still the subject of debate, and has even been suggested by some authors to be a separate phylum from cephalochordates and vertebrates. It was also the case for agnathans species –myxines and hagfish– for which phylogenetic evidence was recently given for a controversial monophyly. This raises the following question: which one of the cephalochordata or urochordata is the sister group of vertebrates and what are their relationships? In the present work, we analyzed 82 protein families presenting homologs between urochordata and other deuterostomes and focused on two points: 1) testing accurately the position of urochordata and cephalochordata phyla in regard with vertebrates as well as chordates monophyly, 2) performing an estimation of the rate of gene loss in the Ciona intestinalis genome.