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Mitochondrial Genomes of African Pangolins and Insights Into Evolutionary Patterns and Phylogeny of the Family Manidae Zelda Du Toit1,2, Morné Du Plessis2, Desiré L
du Toit et al. BMC Genomics (2017) 18:746 DOI 10.1186/s12864-017-4140-5 RESEARCH ARTICLE Open Access Mitochondrial genomes of African pangolins and insights into evolutionary patterns and phylogeny of the family Manidae Zelda du Toit1,2, Morné du Plessis2, Desiré L. Dalton1,2,3*, Raymond Jansen4, J. Paul Grobler1 and Antoinette Kotzé1,2,4 Abstract Background: This study used next generation sequencing to generate the mitogenomes of four African pangolin species; Temminck’s ground pangolin (Smutsia temminckii), giant ground pangolin (S. gigantea), white-bellied pangolin (Phataginus tricuspis) and black-bellied pangolin (P. tetradactyla). Results: The results indicate that the mitogenomes of the African pangolins are 16,558 bp for S. temminckii, 16,540 bp for S. gigantea, 16,649 bp for P. tetradactyla and 16,565 bp for P. tricuspis. Phylogenetic comparisons of the African pangolins indicated two lineages with high posterior probabilities providing evidence to support the classification of two genera; Smutsia and Phataginus. The total GC content between African pangolins was observed to be similar between species (36.5% – 37.3%). The most frequent codon was found to be A or C at the 3rd codon position. Significant variations in GC-content and codon usage were observed for several regions between African and Asian pangolin species which may be attributed to mutation pressure and/or natural selection. Lastly, a total of two insertions of 80 bp and 28 bp in size respectively was observed in the control region of the black-bellied pangolin which were absent in the other African pangolin species. Conclusions: The current study presents reference mitogenomes of all four African pangolin species and thus expands on the current set of reference genomes available for six of the eight extant pangolin species globally and represents the first phylogenetic analysis with six pangolin species using full mitochondrial genomes. -
Petition to List Eight Species of Pomacentrid Reef Fish, Including the Orange Clownfish and Seven Damselfish, As Threatened Or Endangered Under the U.S
BEFORE THE SECRETARY OF COMMERCE PETITION TO LIST EIGHT SPECIES OF POMACENTRID REEF FISH, INCLUDING THE ORANGE CLOWNFISH AND SEVEN DAMSELFISH, AS THREATENED OR ENDANGERED UNDER THE U.S. ENDANGERED SPECIES ACT Orange Clownfish (Amphiprion percula) photo by flickr user Jan Messersmith CENTER FOR BIOLOGICAL DIVERSITY SUBMITTED SEPTEMBER 13, 2012 Notice of Petition Rebecca M. Blank Acting Secretary of Commerce U.S. Department of Commerce 1401 Constitution Ave, NW Washington, D.C. 20230 Email: [email protected] Samuel Rauch Acting Assistant Administrator for Fisheries NOAA Fisheries National Oceanographic and Atmospheric Administration 1315 East-West Highway Silver Springs, MD 20910 E-mail: [email protected] PETITIONER Center for Biological Diversity 351 California Street, Suite 600 San Francisco, CA 94104 Tel: (415) 436-9682 _____________________ Date: September 13, 2012 Shaye Wolf, Ph.D. Miyoko Sakashita Center for Biological Diversity Pursuant to Section 4(b) of the Endangered Species Act (“ESA”), 16 U.S.C. § 1533(b), Section 553(3) of the Administrative Procedures Act, 5 U.S.C. § 553(e), and 50 C.F.R.§ 424.14(a), the Center for Biological Diversity hereby petitions the Secretary of Commerce and the National Oceanographic and Atmospheric Administration (“NOAA”), through the National Marine Fisheries Service (“NMFS” or “NOAA Fisheries”), to list eight pomacentrid reef fish and to designate critical habitat to ensure their survival. The Center for Biological Diversity (“Center”) is a non-profit, public interest environmental organization dedicated to the protection of imperiled species and their habitats through science, policy, and environmental law. The Center has more than 350,000 members and online activists throughout the United States. -
You Are What You Eat: a Genomic Analysis of the Gut Microbiome of Captive and Wild Octopus Vulgaris Paralarvae and Their Zooplankton Prey
ORIGINAL RESEARCH published: 31 May 2017 doi: 10.3389/fphys.2017.00362 You Are What You Eat: A Genomic Analysis of the Gut Microbiome of Captive and Wild Octopus vulgaris Paralarvae and Their Zooplankton Prey Álvaro Roura 1, 2*, Stephen R. Doyle 1, 3, Manuel Nande 4, 5 and Jan M. Strugnell 1, 6 1 Department of Ecology, Environment and Evolution, La Trobe University, Melbourne, VIC, Australia, 2 Ecología y Biodiversidad Marina, Instituto de Investigaciones Marinas (CSIC), Vigo, Spain, 3 Parasite Genomic Group, Wellcome Trust Sanger Institute, Cambridge, United Kingdom, 4 Grupo de Acuicultura Marina, Instituto Español de Oceanografía, Vigo, Spain, 5 Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, Vigo, Spain, 6 Marine Biology and Aquaculture, James Cook University, Townsville, QLD, Australia The common octopus (Octopus vulgaris) is an attractive species for aquaculture, however, several challenges inhibit sustainable commercial production. Little is known Edited by: about the early paralarval stages in the wild, including diet and intestinal microbiota, Giovanna Ponte, CephRes and SZN, Italy which likely play a significant role in development and vitality of this important life stage. Reviewed by: High throughput sequencing was used to characterize the gastrointestinal microbiome Muthugounder S. Shivakumar, of wild O. vulgaris paralarvae collected from two different upwelling regions off the coast Periyar University, India Andrea Tarallo, of North West Spain (n = 41) and Morocco (n = 35). These were compared to that Stazione Zoologica Anton Dohrn, Italy of paralarvae reared with Artemia for up to 25 days in captivity (n = 29). In addition, *Correspondence: the gastrointestinal microbiome of zooplankton prey (crabs, copepod and krill) was Álvaro Roura also analyzed to determine if the microbial communities present in wild paralarvae are [email protected] derived from their diet. -
MARINE LIFE PROFILE: HAWAIIAN LIMPET SNAIL Classification
Waikïkï Aquarium Education Department MARINE LIFE PROFILE: HAWAIIAN LIMPET SNAIL Hawaiian name: ‘opihi Scientific name: Cellana exarata and others Distribution: Hawaiian Islands Size: up to 3 inches (7.5 cm) Diet: algae Limpets are common snails found on rocky shores throughout the world. But the four species which occur in Hawaii are endemic, found here and no where else! The most common species is the "blackfoot" ‘opihi (Cellana exarata) which occurs on basalt shorelines, from the splash zone high on the shore, seaward to the level of the mean low tide where crust-like pink calcareous algae forms a band on the rocks. Like other snails, limpets have: (1) a head with eyes and tentacles, a mouth on a protrusible proboscis (mouth tube); (2) a broad muscular foot for clinging and crawling; and (3) a soft body mass (containing the internal organs) which is protected by their shell. Living on this part of the shore, the ‘opihi must withstand periods of drying exposure during low tides, as well as heavy surge and pounding waves at high tide. They cling firmly to the rock surface with the muscular foot that acts like a suction cup to keep them from being torn off the rocks. The cap-shaped shell has a low profile and low center of gravity so that the snail presents little resistance to the water as it pounds and pours over the shore. The ribs and grooves in the shell help spread the force of the crashing waves by channeling water down the sides of the shell. Each ‘opihi lives in a shallow depression on the rock that it makes itself, possibly by rasping at the rock with its radula. -
California Saltwater Sport Fishing Regulations
2017–2018 CALIFORNIA SALTWATER SPORT FISHING REGULATIONS For Ocean Sport Fishing in California Effective March 1, 2017 through February 28, 2018 13 2017–2018 CALIFORNIA SALTWATER SPORT FISHING REGULATIONS Groundfish Regulation Tables Contents What’s New for 2017? ............................................................. 4 24 License Information ................................................................ 5 Sport Fishing License Fees ..................................................... 8 Keeping Up With In-Season Groundfish Regulation Changes .... 11 Map of Groundfish Management Areas ...................................12 Summaries of Recreational Groundfish Regulations ..................13 General Provisions and Definitions ......................................... 20 General Ocean Fishing Regulations ��������������������������������������� 24 Fin Fish — General ................................................................ 24 General Ocean Fishing Fin Fish — Minimum Size Limits, Bag and Possession Limits, and Seasons ......................................................... 24 Fin Fish—Gear Restrictions ................................................... 33 Invertebrates ........................................................................ 34 34 Mollusks ............................................................................34 Crustaceans .......................................................................36 Non-commercial Use of Marine Plants .................................... 38 Marine Protected Areas and Other -
Global Seagrass Distribution and Diversity: a Bioregional Model ⁎ F
Journal of Experimental Marine Biology and Ecology 350 (2007) 3–20 www.elsevier.com/locate/jembe Global seagrass distribution and diversity: A bioregional model ⁎ F. Short a, , T. Carruthers b, W. Dennison b, M. Waycott c a Department of Natural Resources, University of New Hampshire, Jackson Estuarine Laboratory, Durham, NH 03824, USA b Integration and Application Network, University of Maryland Center for Environmental Science, Cambridge, MD 21613, USA c School of Marine and Tropical Biology, James Cook University, Townsville, 4811 Queensland, Australia Received 1 February 2007; received in revised form 31 May 2007; accepted 4 June 2007 Abstract Seagrasses, marine flowering plants, are widely distributed along temperate and tropical coastlines of the world. Seagrasses have key ecological roles in coastal ecosystems and can form extensive meadows supporting high biodiversity. The global species diversity of seagrasses is low (b60 species), but species can have ranges that extend for thousands of kilometers of coastline. Seagrass bioregions are defined here, based on species assemblages, species distributional ranges, and tropical and temperate influences. Six global bioregions are presented: four temperate and two tropical. The temperate bioregions include the Temperate North Atlantic, the Temperate North Pacific, the Mediterranean, and the Temperate Southern Oceans. The Temperate North Atlantic has low seagrass diversity, the major species being Zostera marina, typically occurring in estuaries and lagoons. The Temperate North Pacific has high seagrass diversity with Zostera spp. in estuaries and lagoons as well as Phyllospadix spp. in the surf zone. The Mediterranean region has clear water with vast meadows of moderate diversity of both temperate and tropical seagrasses, dominated by deep-growing Posidonia oceanica. -
Recent Trends in Marine Phycotoxins from Australian Coastal Waters
Review Recent Trends in Marine Phycotoxins from Australian Coastal Waters Penelope Ajani 1,*, D. Tim Harwood 2 and Shauna A. Murray 1 1 Climate Change Cluster (C3), University of Technology Sydney, Sydney, NSW 2007, Australia; [email protected] 2 Cawthron Institute, The Wood, Nelson 7010, New Zealand; [email protected] * Correspondence: [email protected]; Tel.: +61‐02‐9514‐7325 Academic Editor: Lucio G. Costa Received: 6 December 2016; Accepted: 29 January 2017; Published: 9 February 2017 Abstract: Phycotoxins, which are produced by harmful microalgae and bioaccumulate in the marine food web, are of growing concern for Australia. These harmful algae pose a threat to ecosystem and human health, as well as constraining the progress of aquaculture, one of the fastest growing food sectors in the world. With better monitoring, advanced analytical skills and an increase in microalgal expertise, many phycotoxins have been identified in Australian coastal waters in recent years. The most concerning of these toxins are ciguatoxin, paralytic shellfish toxins, okadaic acid and domoic acid, with palytoxin and karlotoxin increasing in significance. The potential for tetrodotoxin, maitotoxin and palytoxin to contaminate seafood is also of concern, warranting future investigation. The largest and most significant toxic bloom in Tasmania in 2012 resulted in an estimated total economic loss of ~AUD$23M, indicating that there is an imperative to improve toxin and organism detection methods, clarify the toxin profiles of species of phytoplankton and carry out both intra‐ and inter‐species toxicity comparisons. Future work also includes the application of rapid, real‐time molecular assays for the detection of harmful species and toxin genes. -
Morpho-Chronological Variations and Primary Production in Posidonia
Morpho-chronological variations and primary production in Posidonia sea grass from Western Australia Gérard Pergent, Christine Pergent-Martini, Catherine Fernandez, Pasqualini Vanina, Diana Walker To cite this version: Gérard Pergent, Christine Pergent-Martini, Catherine Fernandez, Pasqualini Vanina, Diana Walker. Morpho-chronological variations and primary production in Posidonia sea grass from Western Aus- tralia. Journal of the Marine Biological Association of the United Kingdom, Cambridge University Press, 2004, 84 (5), pp.895-899. 10.1017/S0025315404010161h. hal-01768985 HAL Id: hal-01768985 https://hal.archives-ouvertes.fr/hal-01768985 Submitted on 17 Apr 2018 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. J. Mar. Biol. Ass. U.K. (2004), 84, 895^899 Printed in the United Kingdom Morpho-chronological variations and primary production in Posidonia sea grass from Western Australia P Ge¤rard Pergent* , Christine Pergent-Martini*, Catherine Fernandez*, O Vanina Pasqualini* and Diana Walker O *Equipe Ecosyste' mes Littoraux, Faculty of Sciences, -
E Urban Sanctuary Algae and Marine Invertebrates of Ricketts Point Marine Sanctuary
!e Urban Sanctuary Algae and Marine Invertebrates of Ricketts Point Marine Sanctuary Jessica Reeves & John Buckeridge Published by: Greypath Productions Marine Care Ricketts Point PO Box 7356, Beaumaris 3193 Copyright © 2012 Marine Care Ricketts Point !is work is copyright. Apart from any use permitted under the Copyright Act 1968, no part may be reproduced by any process without prior written permission of the publisher. Photographs remain copyright of the individual photographers listed. ISBN 978-0-9804483-5-1 Designed and typeset by Anthony Bright Edited by Alison Vaughan Printed by Hawker Brownlow Education Cheltenham, Victoria Cover photo: Rocky reef habitat at Ricketts Point Marine Sanctuary, David Reinhard Contents Introduction v Visiting the Sanctuary vii How to use this book viii Warning viii Habitat ix Depth x Distribution x Abundance xi Reference xi A note on nomenclature xii Acknowledgements xii Species descriptions 1 Algal key 116 Marine invertebrate key 116 Glossary 118 Further reading 120 Index 122 iii Figure 1: Ricketts Point Marine Sanctuary. !e intertidal zone rocky shore platform dominated by the brown alga Hormosira banksii. Photograph: John Buckeridge. iv Introduction Most Australians live near the sea – it is part of our national psyche. We exercise in it, explore it, relax by it, "sh in it – some even paint it – but most of us simply enjoy its changing modes and its fascinating beauty. Ricketts Point Marine Sanctuary comprises 115 hectares of protected marine environment, located o# Beaumaris in Melbourne’s southeast ("gs 1–2). !e sanctuary includes the coastal waters from Table Rock Point to Quiet Corner, from the high tide mark to approximately 400 metres o#shore. -
For the Determination of Diarrhetic Shellfish Toxins In
toxins Article A Comparative Analysis of Methods (LC-MS/MS, LC-MS and Rapid Test Kits) for the Determination of Diarrhetic Shellfish Toxins in Oysters, Mussels and Pipis Penelope A. Ajani 1,* , Chowdhury Sarowar 2, Alison Turnbull 3 , Hazel Farrell 4, Anthony Zammit 4, Stuart Helleren 5, Gustaaf Hallegraeff 3 and Shauna A. Murray 1 1 School of Life Sciences, University of Technology Sydney, P.O. Box 123, Broadway, NSW 2007, Australia; [email protected] 2 Sydney Institute of Marine Science, 19 Chowder Bay Road, Mosman, NSW 2088, Australia; [email protected] 3 Institute for Marine and Antarctic Science, University of Tasmania, 15-21 Nubeena Crescent, Taroona, TAS 7053, Australia; [email protected] (A.T.); [email protected] (G.H.) 4 NSW Food Authority, NSW Department of Primary Industries, P.O. Box 232, Taree, NSW 2430, Australia; [email protected] (H.F.); [email protected] (A.Z.) 5 Dalcon Environmental, Building 38, 3 Baron-Hay Ct, South Perth, WA 6151, Australia; [email protected] * Correspondence: [email protected] Abstract: Rapid methods for the detection of biotoxins in shellfish can assist the seafood industry and safeguard public health. Diarrhetic Shellfish Toxins (DSTs) are produced by species of the dinoflagellate genus Dinophysis, yet the comparative efficacy of their detection methods has not been systematically determined. Here, we examined DSTs in spiked and naturally contaminated shellfish– Citation: Ajani, P.A.; Sarowar, C.; Sydney Rock Oysters (Saccostrea glomerata), Pacific Oysters (Magallana gigas/Crassostrea gigas), Blue Turnbull, A.; Farrell, H.; Zammit, A.; Mussels (Mytilus galloprovincialis) and Pipis (Plebidonax deltoides/Donax deltoides), using LC-MS/MS Helleren, S.; Hallegraeff, G.; Murray, and LC-MS in 4 laboratories, and 5 rapid test kits (quantitative Enzyme-Linked Immunosorbent S.A. -
1. Budorcas Taxicolor Tibetanus Milne-Edwards.- a Horn of an Adult and Skins and Skulls of Two Very Young Animals, Tai-Pa-Shiang, August 16 and October 25
59.9(51.4) Article XXIX.- MAMMALS FROM SHEN-SI PROVINCE, CHINA. By J. A. ALLEN. A small collection of mammals from Mount Tai-pai, Shen-si Province, China, recently acquired by the Museum through Mr. Alan Owston of Yokohama, contains several species of interest. It comprises 55 specimens, representing 16 species, some of which appear to be undescribed. The material is rather poorly prepared, the skulls having been left in the skins, and when removed were found to be more or less mutilated, some of them lacking the whole of the postorbital portion. The collection is of interest as coming from a hitherto unexplored locality, the Tai-pa-shiang mountains, on the western border of Shen-si, which are said to reach an altitude of about 11,000 feet. The specimens are mostly labeled simply "Tai-pa- shiang," with the sex of the specimen and date of collection, but a few are labeled as from "Yumonko, foot of Tai-pa-shiang," and others are marked "Si-Tai-pa-shiang." In no case is the altitude indicated. 1. Budorcas taxicolor tibetanus Milne-Edwards.- A horn of an adult and skins and skulls of two very young animals, Tai-pa-shiang, August 16 and October 25. The two specimens are respectively male and female, and differ much in color, the male having the body, except the ventral surface and the dorsal stripe, pale yellowish, the dorsal stripe, the ventral surface and limbs dark dull reddish brown; top of nose and edge of ears blackish. The other has the body nearly white, with the underparts and limbs dark brown; the dorsal stripe is dark brown only over the shoulders, and black mixed with white on the top of the neck and posterior two-thirds of the dorsal line; black hairs are also appearing on the limbs. -
Chemotyping the Lignin of Posidonia Seagrasses
APL001 Analytical Pyrolysis Letters 1 Chemotyping the lignin of Posidonia seagrasses JOERI KAAL1,O SCAR SERRANO 2,J OSÉ CARLOS DEL RÍO3, AND JORGE RENCORET3 1Pyrolyscience, Santiago de Compostela, Spain 2Edith Cowan University, Joondalup, Australia 3IRNAS, CSIC, Seville, Spain Compiled January 18, 2019 A recent paper in Organic Geochemistry entitled "Radi- cally different lignin composition in Posidonia species may link to differences in organic carbon sequestration capacity" discusses the remarkable difference in lignin chemistry between two kinds of “Neptune grass”, i.e. Posidonia oceanica and Posidonia australis. A recent paper in Organic Geochemistry entitled "Radically different lignin composition in Posidonia species may link to differences in organic carbon sequestration capacity" discusses the remarkable difference in lignin chemistry between two kinds of “Neptune grass”, i.e. Posidonia oceanica and Posidonia australis. Initial efforts using analytical pyrolysis techniques (Py-GC- MS and THM-GC-MS) showed that the endemic Mediterranean Fig. 1. Posidonia oceanica mat deposits in Portlligat (Western member of the Posidonia genus, P. oceanica, has abnormally Mediterranean). Photo: Kike Ballesteros high amounts of p-HBA (para-hydroxybenzoic acid) whereas the down-under variety does not. State-of-the-art lignin charac- terization in Seville (DFRC, 2D-NMR) showed that the p-HBA ranean high-carbon accumulator (see figure below), but it proba- is part of the lignin backbone, and not glycosylated as initially bly contains slightly more p-HBA than Posidonia australis. Posido- expected, and P. oceanica is now the producer of the most exten- nia sinuosa is not capable of producing big mat deposits neither, sively p-HBA-acylated lignin known in the Plant Kingdom.