(Nordlig Sølvtorsk), Gadiculus Thori
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And Interspecific Variation in the Intestinal Microbiomes Of
bioRxiv preprint doi: https://doi.org/10.1101/864439; this version posted December 5, 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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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. 1 Metagenomic shotgun analyses reveal complex patterns of 2 intra- and interspecific variation in the intestinal 3 microbiomes of codfishes 4 5 6 Even Sannes Riiser1*, Thomas H.A. Haverkamp1,2, Srinidhi Varadharajan1, 7 Ørnulf Borgan3, Kjetill S. Jakobsen1, Sissel Jentoft1 and Bastiaan Star1* 8 9 1Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, 10 University of Oslo, PO Box 1066, Blindern, N-0316 Oslo, Norway. 11 12 2Present Address: Department of Epidemiology, Norwegian Veterinary Institute, 13 Oslo, Norway 14 15 3Department of Mathematics, University of Oslo, PO Box 1053, Blindern, N- 16 0316 Oslo, Norway. 17 18 19 * Correspondence 20 Even Sannes Riiser*: [email protected] 21 Bastiaan Star*: [email protected] 22 23 24 Abstract 25 The relative importance of host-specific selection or environmental factors in 26 determining the composition of the intestinal microbiome in wild vertebrates 27 remains poorly understood. Here, we use metagenomic shotgun sequencing of 28 individual specimens to compare the intra- and interspecific variation of 29 intestinal microbiome communities in two ecotypes (NEAC and NCC) of 30 Atlantic cod (Gadus morhua) –that have distinct behavior and habitats– and 31 three Gadidae species that occupy a range of ecological niches. Interestingly, we 32 find significantly diverged microbiomes amongst the two Atlantic cod ecotypes. -
Updated Checklist of Marine Fishes (Chordata: Craniata) from Portugal and the Proposed Extension of the Portuguese Continental Shelf
European Journal of Taxonomy 73: 1-73 ISSN 2118-9773 http://dx.doi.org/10.5852/ejt.2014.73 www.europeanjournaloftaxonomy.eu 2014 · Carneiro M. et al. This work is licensed under a Creative Commons Attribution 3.0 License. Monograph urn:lsid:zoobank.org:pub:9A5F217D-8E7B-448A-9CAB-2CCC9CC6F857 Updated checklist of marine fishes (Chordata: Craniata) from Portugal and the proposed extension of the Portuguese continental shelf Miguel CARNEIRO1,5, Rogélia MARTINS2,6, Monica LANDI*,3,7 & Filipe O. COSTA4,8 1,2 DIV-RP (Modelling and Management Fishery Resources Division), Instituto Português do Mar e da Atmosfera, Av. Brasilia 1449-006 Lisboa, Portugal. E-mail: [email protected], [email protected] 3,4 CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal. E-mail: [email protected], [email protected] * corresponding author: [email protected] 5 urn:lsid:zoobank.org:author:90A98A50-327E-4648-9DCE-75709C7A2472 6 urn:lsid:zoobank.org:author:1EB6DE00-9E91-407C-B7C4-34F31F29FD88 7 urn:lsid:zoobank.org:author:6D3AC760-77F2-4CFA-B5C7-665CB07F4CEB 8 urn:lsid:zoobank.org:author:48E53CF3-71C8-403C-BECD-10B20B3C15B4 Abstract. The study of the Portuguese marine ichthyofauna has a long historical tradition, rooted back in the 18th Century. Here we present an annotated checklist of the marine fishes from Portuguese waters, including the area encompassed by the proposed extension of the Portuguese continental shelf and the Economic Exclusive Zone (EEZ). The list is based on historical literature records and taxon occurrence data obtained from natural history collections, together with new revisions and occurrences. -
Marine Fishes of the Azores: an Annotated Checklist and Bibliography
MARINE FISHES OF THE AZORES: AN ANNOTATED CHECKLIST AND BIBLIOGRAPHY. RICARDO SERRÃO SANTOS, FILIPE MORA PORTEIRO & JOÃO PEDRO BARREIROS SANTOS, RICARDO SERRÃO, FILIPE MORA PORTEIRO & JOÃO PEDRO BARREIROS 1997. Marine fishes of the Azores: An annotated checklist and bibliography. Arquipélago. Life and Marine Sciences Supplement 1: xxiii + 242pp. Ponta Delgada. ISSN 0873-4704. ISBN 972-9340-92-7. A list of the marine fishes of the Azores is presented. The list is based on a review of the literature combined with an examination of selected specimens available from collections of Azorean fishes deposited in museums, including the collection of fish at the Department of Oceanography and Fisheries of the University of the Azores (Horta). Personal information collected over several years is also incorporated. The geographic area considered is the Economic Exclusive Zone of the Azores. The list is organised in Classes, Orders and Families according to Nelson (1994). The scientific names are, for the most part, those used in Fishes of the North-eastern Atlantic and the Mediterranean (FNAM) (Whitehead et al. 1989), and they are organised in alphabetical order within the families. Clofnam numbers (see Hureau & Monod 1979) are included for reference. Information is given if the species is not cited for the Azores in FNAM. Whenever available, vernacular names are presented, both in Portuguese (Azorean names) and in English. Synonyms, misspellings and misidentifications found in the literature in reference to the occurrence of species in the Azores are also quoted. The 460 species listed, belong to 142 families; 12 species are cited for the first time for the Azores. -
Length–Weight Relationships of 216 North Sea Benthic Invertebrates
Journal o f the Marine Biological Association o f the United 2010, Kingdom, 90(1), 95-104. © Marine Biological Association of the United Kingdom, 2010 doi:io.ioi7/Soo25 315409991408 Length-weight relationships of 216 North Sea benthic invertebrates and fish L.A. ROBINSON1, S.P.R. GREENSTREET2, H. REISS3, R. CALLAWAY4, J. CRAEYMEERSCH5, I. DE BOOIS5, S. DEGRAER6, S. EHRICH7, H.M. FRASER2, A. GOFFIN6, I. KRÖNCKE3, L. LINDAL JORGENSON8, M.R. ROBERTSON2 AND J. LANCASTER4 School of Biological Sciences, Ecosystem Dynamics Group, University of Liverpool, Liverpool, L69 7ZB, UK, fish eries Research Services, Marine Laboratory, PO Box 101, Aberdeen, AB11 9DB, UK, 3Senckenberg Institute, Department of Marine Science, Südstrand 40,26382 Wilhelmshaven, Germany, 4University of Wales, Swansea, Singleton Park, Swansea, SA2 8PP, UK, Netherlands Institute for Fisheries Research (IMARES), PO Box 77, 4400 AB Yerseke, The Netherlands, sGhent University, Department of Biology, Marine Biology Section, K.L. Ledeganckstraat 35, B 9000, Gent, Belgium, 7Federal Research Institute for Rural Areas, Forestry and Fisheries, Institute of Sea Fisheries, Palmaille 9, 22767 Hamburg, Germany, institute of Marine Research, Box 1870, 5817 Bergen, Norway Size-based analyses of marine animals are increasingly used to improve understanding of community structure and function. However, the resources required to record individual body weights for benthic animals, where the number of individuals can reach several thousand in a square metre, are often prohibitive. Here we present morphometric (length-weight) relationships for 216 benthic species from the North Sea to permit weight estimation from length measurements. These relationships were calculated using data collected over two years from 283 stations. -
Mediterranean Sea
OVERVIEW OF THE CONSERVATION STATUS OF THE MARINE FISHES OF THE MEDITERRANEAN SEA Compiled by Dania Abdul Malak, Suzanne R. Livingstone, David Pollard, Beth A. Polidoro, Annabelle Cuttelod, Michel Bariche, Murat Bilecenoglu, Kent E. Carpenter, Bruce B. Collette, Patrice Francour, Menachem Goren, Mohamed Hichem Kara, Enric Massutí, Costas Papaconstantinou and Leonardo Tunesi MEDITERRANEAN The IUCN Red List of Threatened Species™ – Regional Assessment OVERVIEW OF THE CONSERVATION STATUS OF THE MARINE FISHES OF THE MEDITERRANEAN SEA Compiled by Dania Abdul Malak, Suzanne R. Livingstone, David Pollard, Beth A. Polidoro, Annabelle Cuttelod, Michel Bariche, Murat Bilecenoglu, Kent E. Carpenter, Bruce B. Collette, Patrice Francour, Menachem Goren, Mohamed Hichem Kara, Enric Massutí, Costas Papaconstantinou and Leonardo Tunesi The IUCN Red List of Threatened Species™ – Regional Assessment Compilers: Dania Abdul Malak Mediterranean Species Programme, IUCN Centre for Mediterranean Cooperation, calle Marie Curie 22, 29590 Campanillas (Parque Tecnológico de Andalucía), Málaga, Spain Suzanne R. Livingstone Global Marine Species Assessment, Marine Biodiversity Unit, IUCN Species Programme, c/o Conservation International, Arlington, VA 22202, USA David Pollard Applied Marine Conservation Ecology, 7/86 Darling Street, Balmain East, New South Wales 2041, Australia; Research Associate, Department of Ichthyology, Australian Museum, Sydney, Australia Beth A. Polidoro Global Marine Species Assessment, Marine Biodiversity Unit, IUCN Species Programme, Old Dominion University, Norfolk, VA 23529, USA Annabelle Cuttelod Red List Unit, IUCN Species Programme, 219c Huntingdon Road, Cambridge CB3 0DL,UK Michel Bariche Biology Departement, American University of Beirut, Beirut, Lebanon Murat Bilecenoglu Department of Biology, Faculty of Arts and Sciences, Adnan Menderes University, 09010 Aydin, Turkey Kent E. Carpenter Global Marine Species Assessment, Marine Biodiversity Unit, IUCN Species Programme, Old Dominion University, Norfolk, VA 23529, USA Bruce B. -
An Evolutionary Preserved Intergenic Spacer in Gadiform Mitogenomes
Jørgensen et al. BMC Evolutionary Biology 2014, 14:182 http://www.biomedcentral.com/1471-2148/14/182 RESEARCH ARTICLE Open Access An evolutionary preserved intergenic spacer in gadiform mitogenomes generates a long noncoding RNA Tor Erik Jørgensen1, Ingrid Bakke2, Anita Ursvik3, Morten Andreassen3, Truls Moum1 and Steinar D Johansen1,3* Abstract Background: Vertebrate mitogenomes are economically organized and usually lack intergenic sequences other than the control region. Intergenic spacers located between the tRNAThr and tRNAPro genes (“T-P spacers”) have been observed in several taxa, including gadiform species, but information about their biological roles and putative functions is still lacking. Results: Sequence characterization of the complete European hake Merluccius merluccius mitogenome identified a complex T-P spacer ranging in size from 223–532 bp. Further analyses of 32 gadiform species, representing 8 families and 28 genera, revealed the evolutionary preserved presence of T-P spacers across all taxa. Molecular complexity of the T-P spacers was found to be coherent with the phylogenetic relationships, supporting a common ancestral origin and gain of function during codfish evolution. Intraspecific variation of T-P spacer sequences was assessed in 225 Atlantic cod specimens and revealed 26 haplotypes. Pyrosequencing data representing the mito-transcriptome poly (A) fraction in Atlantic cod identified an abundant H-strand specific long noncoding RNA of about 375 nt. The T-P spacer corresponded to the 5’ part of this transcript, which terminated within the control region in a tail-to-tail configuration with the L-strand specific transcript (the 7S RNA). Conclusions: The T-P spacer is inferred to be evolutionary preserved in gadiform mitogenomes due to gain of function through a long noncoding RNA. -
399 4. Bibliography
click for previous page 399 4. BIBLIOGRAPHY Alcock, A., 1889. Natural history notes from H.M. Indian Marine Survey Steamer “Investigator”, Commander Alfred Carpenter, R.N., D.S.O., commanding No. 13. On the bathybial fishes of the Bay of Bengal and neighboring waters, obtained during the seasons 1885-1889. Ann.Mag.Nat.Hist., ser. 6,6(23):376-399 .................., 1891. On the deep-sea fishes collected by the “Investigator” in 1890-1891. Ann.Mag.Nat.Hist., ser. 6,8:16-34; 119-138, pls vii-viii .................., 1899. A descriptive catalogue of the Indian deep-sea fishes in the Indian Museum. Being a revised account of the deep-sea fishes collected by the Royal Indian Marine Survey ship Investigator. Calcutta, Indian Museum, 211 pp. Allen, M.J. & G.8. Smith, 1988. Atlas and zoogeography of common fishes in the Bering Sea and Northeastern Pacific. NOAA Tech.Rep. NMFS, 66: 151 pp. Altukhov, K.A., 1979. O razmnozheznii i razvitii saiki Boreogadus saida (Lepechin) v Belom More. (The reproduction and development of the Arctic cod, Boreogadus saida, in the White Sea.) Vopr.lkhtiol.. 19(5):874-82 (J.Ichthyol., 19(5):93-101) Amaoka, K. et al. (eds), 1983. Fishes from the north-eastern Sea of Japan and the Okhotsk Sea off Hokkaido. Japan Fisheries Resource Conservation Association. Tokyo. 371 pp. Andriashev, A.P., 1954. Fishes of the northern seas of the USSR. Keys to the fauna of the USSR. Zool.lnst.USSR Acad.Sci., 53. Moscow-Leningrad, 617 p. (Transl. for Smithsonian Inst. and Nat.Sci.Found., by Israel Program for Sci.Transl., 1964) ...................., 1965. -
Molecular Identification Methods of Fish Species
Rev Fish Biol Fisheries (2009) 19:265–293 DOI 10.1007/s11160-009-9107-4 RESEARCHPAPER Molecular identification methods of fish species: reassessment and possible applications Fabrice Teletchea Received: 19 August 2008 / Accepted: 7 January 2009 / Published online: 28 January 2009 Ó Springer Science+Business Media B.V. 2009 Abstract Fish species identification is traditionally in molecular biology in the past 10 years has based on external morphological features. Yet, in rendered possible the study of DNA from virtually many cases fishes and especially their diverse any substrates, offering new perspectives for the developmental stages are difficult to identify by development of various applications, which will morphological characters. DNA-based identification likely continue to increase in the future. methods offer an analytically powerful addition or even an alternative. This work intends to provide an Keywords Mitochondrial DNA updated and extensive overview on the PCR-methods DNA barcoding Taxonomy PCRÁ Á Á Á for fish species identification. Among the ten main Food products Forensic Á methods developed, three PCR-RFLP, PCR-FINS and PCR-specific primers have been the most used. Two other emerging methods, namely real-time PCR and microarray technology, offer new potential for Introduction quantification of DNA and simultaneous detection of numerous species, respectively. Almost 500 species Fish species identification is traditionally based on have been targeted in the past decade, among which external morphological features, including body the most studied belong to gadoids, scombroids, and shape, pattern of colors, scale size and count, number salmonids. The mitochondrial cytochrome b gene and relative position of fins, number and type of fin was by far the most targeted DNA markers. -
Taxonomy, Distribution and Evolution of Trisopterine Gadidae by Means of Otoliths and Other Characteristics
fishes Article Taxonomy, Distribution and Evolution of Trisopterine Gadidae by Means of Otoliths and Other Characteristics Pieter A. M. Gaemers Joost van den Vondelstraat 30, 7103 XW Winterswijk, The Netherlands; [email protected]; Tel.: +31-543-750383 Academic Editor: Eric Hallerman Received: 1 April 2016; Accepted: 7 July 2016; Published: 17 July 2017 Abstract: In a greater study of the recent fossil Gadidae, the object of this paper is to better define the trisopterine species and their relationships. The taxonomy of the four recent species usually included in the genus Trisopterus is further elaborated by means of published and new data on their otoliths, by published data on general external features and meristics of the fishes, and their genetics. Fossil otoliths, from the beginning of the Oligocene up to the present, reveal much of their evolution and throw more light on their relationships. Several succeeding and partly overlapping lineages representing different genera are recognized during this time interval. The genus Neocolliolus Gaemers, 1976, for Trisopterus esmarkii (Nilsson, 1855), is more firmly based. A new genus, Allotrisopterus, is introduced for Trisopterus minutus (Linnaeus, 1758). The similarity with Trisopterus capelanus (Lacepède, 1800) is an example of convergent evolution. The tribe Trisopterini Endo (2002) should only contain Trisopterus, Allotrisopterus and Neocolliolus as recent genera. Correct identification of otoliths from fisheries research and from sea bottom samples extends the knowledge of the present day geographical distribution of T. capelanus and T. luscus (Linnaeus, 1758). T. capelanus is also living along the Atlantic coast of Portugal and at least up to and including the Ría de Arosa, Galicia, Spain. -
HANDBOOK of FISH BIOLOGY and FISHERIES Volume 1 Also Available from Blackwell Publishing: Handbook of Fish Biology and Fisheries Edited by Paul J.B
HANDBOOK OF FISH BIOLOGY AND FISHERIES Volume 1 Also available from Blackwell Publishing: Handbook of Fish Biology and Fisheries Edited by Paul J.B. Hart and John D. Reynolds Volume 2 Fisheries Handbook of Fish Biology and Fisheries VOLUME 1 FISH BIOLOGY EDITED BY Paul J.B. Hart Department of Biology University of Leicester AND John D. Reynolds School of Biological Sciences University of East Anglia © 2002 by Blackwell Science Ltd a Blackwell Publishing company Chapter 8 © British Crown copyright, 1999 BLACKWELL PUBLISHING 350 Main Street, Malden, MA 02148‐5020, USA 108 Cowley Road, Oxford OX4 1JF, UK 550 Swanston Street, Carlton, Victoria 3053, Australia The right of Paul J.B. Hart and John D. Reynolds to be identified as the Authors of the Editorial Material in this Work has been asserted in accordance with the UK Copyright, Designs, and Patents Act 1988. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording or otherwise, except as permitted by the UK Copyright, Designs, and Patents Act 1988, without the prior permission of the publisher. First published 2002 Reprinted 2004 Library of Congress Cataloging‐in‐Publication Data has been applied for. Volume 1 ISBN 0‐632‐05412‐3 (hbk) Volume 2 ISBN 0‐632‐06482‐X (hbk) 2‐volume set ISBN 0‐632‐06483‐8 A catalogue record for this title is available from the British Library. Set in 9/11.5 pt Trump Mediaeval by SNP Best‐set Typesetter Ltd, Hong Kong Printed and bound in the United Kingdom by TJ International Ltd, Padstow, Cornwall. -
Otolith Stratigraphy of Late Weichselian and Holocene Sediments of Malangsdjupet, Off Northem Norway
Otolith stratigraphy of Late Weichselian and Holocene sediments of Malangsdjupet, off northem Norway PIETER A. M. GAEMERS & TORE O. VORREN Gaemers, P. A. M. & Vorren, T. 0.: Otolith stratigraphy of Late Weichselian and Holocene sediments of Malangsdjupet, off northern Norway. Norsk Geologisk Tidsskrift, Vol. 65, pp 187-199. Oslo 1985. ISSN 0029-196X. Otoliths of eleven fish species have been identified in cores recovered from the trough Malangsdjupet (dose to 70°N) on the Norwegian continental shelf. The codfish family (Gadidae) dominates with eight species. Three acmc-zones bclonging to the Mer/angius merlangus Lineage-Zone are establishcd: the Boreogadus sp. Acme-Zone (about 15,000 or 14,000 to 10,000 years B. P.), the Neocolliolus esmarki Acme-Zone (10,000 to 7,800 years B. P.) and the Micromesistius poutassou Acme-Zone (7,800B. P. to present). The Boreogadus sp. Acme-Zone reflects an arctic environment while the two others reflect boreal conditions. The M. poutassou Acme-Zone represents a more oceanic environment than the carly Holocene N. esmarki Acme-Zone. P. A. M. Gaemers, Rijksmuseum van Geologie en Mineralogie, Hooglandse Kerkgracht 17, 2312 HS Leiden, the Netherlands. T. O. Vorren, Institute of Biology and Geology, University of Tromsø, P. O. Box 3085 Guleng, N-9001 Tromsø, Norway. Studies of otoliths from the present sea floor and Material and methods the youngest Quaternary sediments are few in number. Jensen (1905) described otoliths from Twenty-seven gravity cores (diameter 100 mm) an area between Jan Mayen, Iceland and the from ten stations (Fig. lB) were investigated for Faroes, and many years later Wigley & Stinton otoliths. -
The Status of the Fishes Described from Sicily by Rafinesque
FishTaxa (2019) 4(1): 99-124 Journal homepage: www.fishtaxa.com © 2019 FISHTAXA. All rights reserved The status of the fishes described from Sicily by Rafinesque Paolo PARENTI Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza, 1 20126 Milano, Italy. E-mail: [email protected] Abstract Rafinesque described and named 241 species of fishes from Sicily, Mediterranean Sea. The descriptions are reported in four publications printed in the 1810 and 1814. Among these nominal species 30 represent valid species, 130 are recognized as junior synonyms, and the remnant 81 are unplaced, having no status on the Eschmeyer’s Catalog of Fishes (ECoF). This study reveals that most of these unplaced species can be synonymized with species that are well known from the area. In particular, it has been discovered that four nominal species predate well established fish name and are declared nomina oblita: they are Blennius juloides, Blennius lanceolatus, Blennius lupus and Gadus gardone. The corresponding junior synonym, Parablennius rouxi (Cocco, 1833), Gaidropsarus vulgaris (Cloquet, 1824), and Gadiculus argenteus Guichenot, 1850 are declared nomina protecta. The genus Nemochirus is here regarded as a new synonym of Trachypterus Goüan, 1770. Status of the genus Diepinotus is given in the appendix. Keywords: Parablennius rouxi, Gaidropsarus vulgaris, Gadiculus argenteus, Nomina oblita. Zoobank: urn:lsid:zoobank.org:pub:A982CEEC-6CAF-4F00-8BCF-06721D598C36 Introduction Constantine Samuel Rafinesque (22 October 1783-18 September 1840) was an eccentric self-taught naturalist, a passionate systematist and namer, an insatiable explorer and collector particular prodigal to describe new taxa, eager to publish his findings to gain priority of discovery of new genera and species.