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Assessing Species Diversity of Coral Triangle Artisanal Fisheries: a DNA Barcode Reference Library for the Shore Fishes Retailed at Ambon Harbor (Indonesia)
Received: 19 September 2019 | Revised: 30 January 2020 | Accepted: 3 February 2020 DOI: 10.1002/ece3.6128 ORIGINAL RESEARCH Assessing species diversity of Coral Triangle artisanal fisheries: A DNA barcode reference library for the shore fishes retailed at Ambon harbor (Indonesia) Gino Limmon1 | Erwan Delrieu-Trottin2,3 | Jesaya Patikawa1 | Frederik Rijoly1 | Hadi Dahruddin4 | Frédéric Busson2,5 | Dirk Steinke6 | Nicolas Hubert2 1Pusat Kemaritiman dan Kelautan, Universitas Pattimura (Maritime and Marine Abstract Science Center of Excellence), Ambon, The Coral Triangle (CT), a region spanning across Indonesia and Philippines, is home Indonesia to about 4,350 marine fish species and is among the world's most emblematic re- 2Institut de Recherche pour le Développement, UMR 226 ISEM (UM- gions in terms of conservation. Threatened by overfishing and oceans warming, the CNRS-IRD-EPHE), Montpellier, France CT fisheries have faced drastic declines over the last decades. Usually monitored 3Museum für Naturkunde, Leibniz-Institut für Evolutions-und Biodiversitätsforschung through a biomass-based approach, fisheries trends have rarely been characterized an der Humboldt-Universität zu Berlin, at the species level due to the high number of taxa involved and the difficulty to Berlin, Germany accurately and routinely identify individuals to the species level. Biomass, however, 4Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences is a poor proxy of species richness, and automated methods of species identifica- (LIPI), Cibinong, Indonesia tion are required to move beyond biomass-based approaches. Recent meta-analyses 5UMR 7208 BOREA (MNHN-CNRS-UPMC- have demonstrated that species richness peaks at intermediary levels of biomass. IRD-UCBN), Muséum National d’Histoire Naturelle, Paris, France Consequently, preserving biomass is not equal to preserving biodiversity. -
Reef Fishes of the Bird's Head Peninsula, West
Check List 5(3): 587–628, 2009. ISSN: 1809-127X LISTS OF SPECIES Reef fishes of the Bird’s Head Peninsula, West Papua, Indonesia Gerald R. Allen 1 Mark V. Erdmann 2 1 Department of Aquatic Zoology, Western Australian Museum. Locked Bag 49, Welshpool DC, Perth, Western Australia 6986. E-mail: [email protected] 2 Conservation International Indonesia Marine Program. Jl. Dr. Muwardi No. 17, Renon, Denpasar 80235 Indonesia. Abstract A checklist of shallow (to 60 m depth) reef fishes is provided for the Bird’s Head Peninsula region of West Papua, Indonesia. The area, which occupies the extreme western end of New Guinea, contains the world’s most diverse assemblage of coral reef fishes. The current checklist, which includes both historical records and recent survey results, includes 1,511 species in 451 genera and 111 families. Respective species totals for the three main coral reef areas – Raja Ampat Islands, Fakfak-Kaimana coast, and Cenderawasih Bay – are 1320, 995, and 877. In addition to its extraordinary species diversity, the region exhibits a remarkable level of endemism considering its relatively small area. A total of 26 species in 14 families are currently considered to be confined to the region. Introduction and finally a complex geologic past highlighted The region consisting of eastern Indonesia, East by shifting island arcs, oceanic plate collisions, Timor, Sabah, Philippines, Papua New Guinea, and widely fluctuating sea levels (Polhemus and the Solomon Islands is the global centre of 2007). reef fish diversity (Allen 2008). Approximately 2,460 species or 60 percent of the entire reef fish The Bird’s Head Peninsula and surrounding fauna of the Indo-West Pacific inhabits this waters has attracted the attention of naturalists and region, which is commonly referred to as the scientists ever since it was first visited by Coral Triangle (CT). -
Training Manual Series No.15/2018
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by CMFRI Digital Repository DBTR-H D Indian Council of Agricultural Research Ministry of Science and Technology Central Marine Fisheries Research Institute Department of Biotechnology CMFRI Training Manual Series No.15/2018 Training Manual In the frame work of the project: DBT sponsored Three Months National Training in Molecular Biology and Biotechnology for Fisheries Professionals 2015-18 Training Manual In the frame work of the project: DBT sponsored Three Months National Training in Molecular Biology and Biotechnology for Fisheries Professionals 2015-18 Training Manual This is a limited edition of the CMFRI Training Manual provided to participants of the “DBT sponsored Three Months National Training in Molecular Biology and Biotechnology for Fisheries Professionals” organized by the Marine Biotechnology Division of Central Marine Fisheries Research Institute (CMFRI), from 2nd February 2015 - 31st March 2018. Principal Investigator Dr. P. Vijayagopal Compiled & Edited by Dr. P. Vijayagopal Dr. Reynold Peter Assisted by Aditya Prabhakar Swetha Dhamodharan P V ISBN 978-93-82263-24-1 CMFRI Training Manual Series No.15/2018 Published by Dr A Gopalakrishnan Director, Central Marine Fisheries Research Institute (ICAR-CMFRI) Central Marine Fisheries Research Institute PB.No:1603, Ernakulam North P.O, Kochi-682018, India. 2 Foreword Central Marine Fisheries Research Institute (CMFRI), Kochi along with CIFE, Mumbai and CIFA, Bhubaneswar within the Indian Council of Agricultural Research (ICAR) and Department of Biotechnology of Government of India organized a series of training programs entitled “DBT sponsored Three Months National Training in Molecular Biology and Biotechnology for Fisheries Professionals”. -
Reef Fishes of the Bird's Head Peninsula, West Papua, Indonesia
Check List 5(3): 587–628, 2009. ISSN: 1809-127X LISTS OF SPECIES Reef fishes of the Bird’s Head Peninsula, West Papua, Indonesia Gerald R. Allen 1 Mark V. Erdmann 2 1 Department of Aquatic Zoology, Western Australian Museum. Locked Bag 49, Welshpool DC, Perth, Western Australia 6986. E-mail: [email protected] 2 Conservation International Indonesia Marine Program. Jl. Dr. Muwardi No. 17, Renon, Denpasar 80235 Indonesia. Abstract A checklist of shallow (to 60 m depth) reef fishes is provided for the Bird’s Head Peninsula region of West Papua, Indonesia. The area, which occupies the extreme western end of New Guinea, contains the world’s most diverse assemblage of coral reef fishes. The current checklist, which includes both historical records and recent survey results, includes 1,511 species in 451 genera and 111 families. Respective species totals for the three main coral reef areas – Raja Ampat Islands, Fakfak-Kaimana coast, and Cenderawasih Bay – are 1320, 995, and 877. In addition to its extraordinary species diversity, the region exhibits a remarkable level of endemism considering its relatively small area. A total of 26 species in 14 families are currently considered to be confined to the region. Introduction and finally a complex geologic past highlighted The region consisting of eastern Indonesia, East by shifting island arcs, oceanic plate collisions, Timor, Sabah, Philippines, Papua New Guinea, and widely fluctuating sea levels (Polhemus and the Solomon Islands is the global centre of 2007). reef fish diversity (Allen 2008). Approximately 2,460 species or 60 percent of the entire reef fish The Bird’s Head Peninsula and surrounding fauna of the Indo-West Pacific inhabits this waters has attracted the attention of naturalists and region, which is commonly referred to as the scientists ever since it was first visited by Coral Triangle (CT). -
Annotated Checklist of the Fish Species (Pisces) of La Réunion, Including a Red List of Threatened and Declining Species
Stuttgarter Beiträge zur Naturkunde A, Neue Serie 2: 1–168; Stuttgart, 30.IV.2009. 1 Annotated checklist of the fish species (Pisces) of La Réunion, including a Red List of threatened and declining species RONALD FR ICKE , THIE rr Y MULOCHAU , PA tr ICK DU R VILLE , PASCALE CHABANE T , Emm ANUEL TESSIE R & YVES LE T OU R NEU R Abstract An annotated checklist of the fish species of La Réunion (southwestern Indian Ocean) comprises a total of 984 species in 164 families (including 16 species which are not native). 65 species (plus 16 introduced) occur in fresh- water, with the Gobiidae as the largest freshwater fish family. 165 species (plus 16 introduced) live in transitional waters. In marine habitats, 965 species (plus two introduced) are found, with the Labridae, Serranidae and Gobiidae being the largest families; 56.7 % of these species live in shallow coral reefs, 33.7 % inside the fringing reef, 28.0 % in shallow rocky reefs, 16.8 % on sand bottoms, 14.0 % in deep reefs, 11.9 % on the reef flat, and 11.1 % in estuaries. 63 species are first records for Réunion. Zoogeographically, 65 % of the fish fauna have a widespread Indo-Pacific distribution, while only 2.6 % are Mascarene endemics, and 0.7 % Réunion endemics. The classification of the following species is changed in the present paper: Anguilla labiata (Peters, 1852) [pre- viously A. bengalensis labiata]; Microphis millepunctatus (Kaup, 1856) [previously M. brachyurus millepunctatus]; Epinephelus oceanicus (Lacepède, 1802) [previously E. fasciatus (non Forsskål in Niebuhr, 1775)]; Ostorhinchus fasciatus (White, 1790) [previously Apogon fasciatus]; Mulloidichthys auriflamma (Forsskål in Niebuhr, 1775) [previously Mulloidichthys vanicolensis (non Valenciennes in Cuvier & Valenciennes, 1831)]; Stegastes luteobrun- neus (Smith, 1960) [previously S. -
Deep Bottom ID
by par Lindsay Chapman, Aymeric Desurmont, Youngmi Choi, Lindsay Chapman, Aymeric Desurmont, Youngmi Choi, Pierre Boblin, William Sokimi and Steve Beverly Pierre Boblin, William Sokimi et Steve Beverly nzaid ii © Copyright Secretariat of the Pacific Community 2008 © Copyright Secrétariat général de la Communauté du Pacifique 2008 All rights for commercial / for profit reproduction or translation, in any Tous droits réservés de reproduction ou de traduction à des fins commer- form, reserved. SPC authorises the partial reproduction or translation of ciales/lucratives, sous quelque forme que ce soit. Le Secrétariat général de this material for scientific, educational or research purposes, provided SPC la Communauté du Pacifique autorise la reproduction ou la traduction par- and the source document are properly acknowledged. Permission to tielles de ce document à des fins scientifiques ou éducatives ou pour les reproduce the document and/or translate in whole, in any form, whether besoins de la recherche, à condition qu’il soit fait mention de la CPS et de for commercial / for profit or non-profit purposes, must be requested in la source. L’autorisation de la reproduction et/ou de la traduction intégrale writing. Original SPC artwork may not be altered or separately published ou partielle de ce document, sous quelque forme que ce soit, à des fins without permission. commerciales/lucratives ou à titre gratuit, doit être sollicitée au préalable par écrit. Il est interdit de modifier ou de publier séparément des Original text: English and French graphismes originaux de la CPS sans autorisation préalable. Texte original :anglais et français Secretariat of the Pacific Community Cataloguing-in-publication data Chapman, L. -
Using a Collaborative Data Collection Method to Update Life-History Values for Snapper And
bioRxiv preprint doi: https://doi.org/10.1101/655571; this version posted May 30, 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 4.0 International license. 1 Using a collaborative data collection method to update life-history values for snapper and 2 grouper in Indonesia’s deep-slope demersal fishery 3 4 Elle Wibisono1*, Peter Mous2, Austin Humphries1,3 5 1 Department of Fisheries, Animal and Veterinary Sciences, University of Rhode Island, 6 Kingston, Rhode Island, USA 7 2 The Nature Conservancy Indonesia Fisheries Conservation Program, Bali, Indonesia 8 3 Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, 9 USA 10 11 12 *Corresponding author 13 E-mail: [email protected] (EW) 14 15 1 bioRxiv preprint doi: https://doi.org/10.1101/655571; this version posted May 30, 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 4.0 International license. 16 Abstract 17 The deep-slope demersal fishery that targets snapper and grouper species is an important fishery 18 in Indonesia. Boats operate at depths between 50-500 m using drop lines and bottom long lines. 19 There are few data, however, on the basic characteristics of the fishery which impedes accurate 20 stock assessments and the establishment of harvest control rules. -
Introduced Marine Species in Pago Pago Harbor, Fagatele Bay and the National Park Coast, American Samoa
INTRODUCED MARINE SPECIES IN PAGO PAGO HARBOR, FAGATELE BAY AND THE NATIONAL PARK COAST, AMERICAN SAMOA December 2003 COVER Typical views of benthic organisms from sampling areas (clockwise from upper left): Fouling organisms on debris at Pago Pago Harbor Dry Dock; Acropora hyacinthus tables in Fagetele Bay; Porites rus colonies in Fagasa Bay; Mixed branching and tabular Acropora in Vatia Bay INTRODUCED MARINE SPECIES IN PAGO PAGO HARBOR, FAGATELE BAY AND THE NATIONAL PARK COAST, AMERICAN SAMOA Final report prepared for the U.S. Fish and Wildlife Service, Fagetele Bay Marine Sanctuary, National Park of American Samoa and American Samoa Department of Marine and Natural Resources. S. L. Coles P. R. Reath P. A. Skelton V. Bonito R. C. DeFelice L. Basch Bishop Museum Pacific Biological Survey Bishop Museum Technical Report No 26 Honolulu Hawai‘i December 2003 Published by Bishop Museum Press 1525 Bernice Street Honolulu, Hawai‘i Copyright © 2003 Bishop Museum All Rights Reserved Printed in the United States of America ISSN 1085-455X Contribution No. 2003-007 to the Pacific Biological Survey EXECUTIVE SUMMARY The biological communities at ten sites around the Island of Tutuila, American Samoa were surveyed in October 2002 by a team of four investigators. Diving observations and collections of benthic observations using scuba and snorkel were made at six stations in Pago Pago Harbor, two stations in Fagatele Bay, and one station each in Vatia Bay and Fagasa Bay. The purpose of this survey was to determine the full complement of organisms greater than 0.5 mm in size, including benthic algae, macroinvertebrates and fishes, occurring at each site, and to evaluate the presence and potential impact of nonindigenous (introduced) marine species. -
Macolor Niger (Forsskål, 1775) Macolor Macularis Fowler, 1931
click for previous page 2898 Bony Fishes Macolor niger (Forsskål, 1775) Frequent synonyms / misidentifications: Macolor macolor (Lesson, 1827); M. typus Bleeker, 1860 / Macolor macularis Fowler, 1931. FAO names: En - Black-and-white snapper; Fr - Vivaneau plate; Sp - Pargo blanco y negro. Diagnostic characters: Body relatively deep, laterally com- pressed. Dorsal profile of head convex in adults, in oblique straight line in young. Lacrimal (suborbital region) relatively broad. Nostrils on each side of snout not very close together. Mouth large and terminal, lower jaw protruding slightly when mouth closed. Premaxillae protrusible. Maxilla reaching vertical slightly ante- rior to middle of eye. Row of conical teeth in each jaw, en- larged anteriorly, and inner bands of villiform teeth on sides adult of upper jaw and front of lower jaw; vomerine tooth patch broadly V-shaped. Maxilla without scales or longitudinal ridges. Preopercle with deep notch (or gash) receiving elongate interopercular spine which is absent in specimens less than about 16 cm stand- juvenile ard length. First gill arch with 26 to 38 gill rakers on upper limb, 60 to 71 on lower limb (total 89 to 107). Dorsal fin continuous, but spinous portion distinctly notched in young, notch shallower in large specimens. Dorsal and anal fins distinctly pointed posteriorly. Last soft ray of both dorsal and anal fins not produced, shorter than next to last ray. Caudal fin rounded and with central rays elongated in small juveniles, slightly notched at interme- diate sizes, and emarginate in adults. Pectoral fins fairly long; in specimens more than about 95 mm standard length, pectoral fins 90 to 110% head length. -
Checklist of the Shore Fishes of New Caledonia
Plates 15/1 & 15/2 Checklist of the shore fishes of New Caledonia Ronald FRICKE J & Michel KULBICKI 2 J Ichthyology, Staatliches Museumfiir Naturkunde, Rosenstein 1,70191 Stuttgart, Germany [email protected] 2IRD, UR128, Universite de Perpignan, 52, Avenue Paul Alduy, 66860 Perpignan Cedex, France michel.kulbicki@univ-perpJr The present checklist includes the fish species known from the upper 100 m of the New Caledonian seas. Some deep-sea fishes which are occasionally found in shallow water (e.g. Loyalty Islands), high sea species which only rarely enter coastal waters, or freshwater fish species which may be found in estuaries, are excluded from this list. The geographical distribution of the shore fishes of New Caledonia is discussed by Kulbicki (in press). A detailed annotated checklist of all New Caledonian fish species including distribution data, litera ture references and material lists is in preparation by R. Fricke. In the present checklist of shore fish species, all records which are verified either by museum specimens or by confirmation by revising authors, are included. Families are arranged systematically according to Nelson (2006), and species alphabetically under the family names. Doubtful records are discussed after the family name. The names which have been applied to New Caledonian shore fish species in the literature are either list ed as valid species, or as synonyms or misidentifications in parentheses behind the species name. In the checklist, reference is given to materials in the collections of the Australian Museum Sydney (AMS), the Museum National d'Histoire Naturelle Paris (MNHN), and the Staatliches Museum flir Naturkunde Stuttgart (SMNS), in order to document new records. -
Fishes of the Fiji Islands
The University of the South Pacific Division of Marine Studies Technical Report No. 1/2010 A Checklist of the Fishes of Fiji and a Bibliography of Fijian Fish Johnson Seeto & Wayne J. Baldwin © Johnson Seeto 2010 All rights reserved No part to this publication may be reproduced or transmitted in any form or by any means without permission of the authors. Design and Layout: Posa A. Skelton, BioNET-PACINET ISBN: xxx USP Library Cataloguing in Publication Data Seeto, J., Baldwin, W.J. A Checklist of the Fishes of Fiji and a Bibliography of Fijian Fishes. Division of Marine Studies Technical Report 1/2010. The University of the South Pacific. Suva, Fiji. 2010 102 p.: col. ill.; 27.9 cm A Checklist of the Fishes of Fiji and a Bibliography of Fijian Fish Johnson Seeto & Wayne J. Baldwin Division of Marine Studies School of Islands and Oceans Faculty of Science, Technology & Environment The University of the South Pacific Suva Campus Fiji Technical Report 1/2010 February, 2010 Johnson Seeto & Wayne J. Baldwin I. INTRODUCTION May,1999. IRD collected deepsea fauna from Fiji 5 years ago. The first book that described the Fijian fish fauna was written Fish identification has also been made from fish bones and by Henry W. Fowler in 1959 and it covered 560 species. Carlson archaeological evidence (Gifford, 1951; Best, 1984). Ladd (1945) (1975) wrote a checklist of 575 Fijian fish species (107 families) also listed some fossil fish from Fiji. based on collections he made with Mike Gawel, while setting up the University of the South Pacific Marine Reference collection. -
Family-Lutjanidae-Overview-PDF-Update.Pdf
FAMILY Lutjanidae Gill 1861 - snappers [=Acanthopomes, Mesopriontes, Aphareoidei, Lutjaninae, Hoplopagrinae, Platyiniini, Etelinae, Aprioninae, Paradicichthyinae, Symphorinae, Neomaenidae, Apsilinae] GENUS Aphareus Cuvier, in Cuvier & Valeniennes, 1830 - snappers, jobfish [=Fares, Humefordia, Playtpodus, Sacrestinus, Ulapiscis] Species Aphareus furca (Lacepede, 1801) - smalltoothed jobfish [=caerulescens, elegans, flavivultus, pikea, sacrestinus] Species Aphareus rutilans Cuvier, in Cuvier & Valenciennes, 1830 - rusty jobfish [=thompsoni] GENUS Aprion Valenciennes, in Cuvier & Valenciennes, 1830 - snappers, jobfish [=Sparopsis] Species Aprion virescens Valenciennes, in Cuvier & Valenciennes, 1830 - green jobfish [=elongatus, kanekonis, latifrons, microchir, placidus] GENUS Apsilus Valenciennes, in Cuvier & Valenciennes, 1830 - snappers [=Tropidinius] Species Apsilus dentatus Guichenot, 1853 - black snapper [=arnillo] Species Apsilus fuscus Valenciennes, in Cuvier & Valenciennes, 1830 - African forktail snapper GENUS Etelis Cuvier, 1828 - snappers [=Elastoma, Erythrobussothen, Etelinus, Hesperanthias, Macrops] Species Etelis carbunculus Cuvier, in Cuvier & Valenciennes, 1828 - deepwater red snapper [=marshi] Species Etelis coruscans Valenciennes, 1862 - deepwater longtail red snapper [=evurus, lifuensis] Species Etelis oculatus (Valenciennes, 1828) - queen snapper [=gracilis] Species Etelis radiosus Anderson, 1981 - pale snapper GENUS Hoplopagrus Gill, 1861 - snapper [=Deuteracanthus] Species Hoplopagrus guentherii Gill, 1862 - Mexican