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Reef Fish Biodiversity in the Florida Keys National Marine Sanctuary Megan E
University of South Florida Scholar Commons Graduate Theses and Dissertations Graduate School November 2017 Reef Fish Biodiversity in the Florida Keys National Marine Sanctuary Megan E. Hepner University of South Florida, [email protected] Follow this and additional works at: https://scholarcommons.usf.edu/etd Part of the Biology Commons, Ecology and Evolutionary Biology Commons, and the Other Oceanography and Atmospheric Sciences and Meteorology Commons Scholar Commons Citation Hepner, Megan E., "Reef Fish Biodiversity in the Florida Keys National Marine Sanctuary" (2017). Graduate Theses and Dissertations. https://scholarcommons.usf.edu/etd/7408 This Thesis is brought to you for free and open access by the Graduate School at Scholar Commons. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Scholar Commons. For more information, please contact [email protected]. Reef Fish Biodiversity in the Florida Keys National Marine Sanctuary by Megan E. Hepner A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science Marine Science with a concentration in Marine Resource Assessment College of Marine Science University of South Florida Major Professor: Frank Muller-Karger, Ph.D. Christopher Stallings, Ph.D. Steve Gittings, Ph.D. Date of Approval: October 31st, 2017 Keywords: Species richness, biodiversity, functional diversity, species traits Copyright © 2017, Megan E. Hepner ACKNOWLEDGMENTS I am indebted to my major advisor, Dr. Frank Muller-Karger, who provided opportunities for me to strengthen my skills as a researcher on research cruises, dive surveys, and in the laboratory, and as a communicator through oral and presentations at conferences, and for encouraging my participation as a full team member in various meetings of the Marine Biodiversity Observation Network (MBON) and other science meetings. -
Identification Guide to the Common Coatal Food Fishes of the Pacific Region-48-53
YDX Myripristis adusta Holocentridae / Soldierfish and Squirrelfish Shadowfin soldierfish Silvery-salmon pink with 1 dark 3 1 scale margins, particularly on upper body. 2 Reddish-black spot on rear margin of gill covers and 3 reddish-black margins on soft dorsal, anal and caudal fins. Max length: 30 cm FL AS CK FJ FM GU KI 2 MH MP NC NR NU PF PG PN PW SB TK TO TV VU WF WS YDX Myripristis amaena Holocentridae / Soldierfish and Squirrelfish Brick soldierfish Silvery-red with 1 dark scale 1 margins and 2 dark red band on margin of gill covers. 3 Dorsal, anal and caudal fins red without white margins. Max length: 27 cm FL AS CK FJ FM GU KI MH MP NC NR NU PF 2 3 PG PN PW SB TK TO TV VU WF WS Similar to Myripristis violacea but without white margins on soft dorsal, anal and caudal fins. YJW Myripristis berndti Holocentridae / Soldierfish and Squirrelfish Blotcheye soldierfish, bigscale soldierfish 4 White with red tints and 1 red 1 scale margins. 2 Dark margin on gill covers and 3 white margins on soft dorsal, pelvic, anal and caudal fins.4 Outer part of spiny dorsal fin orange-yellow. Max length: 28 cm FL AS CK FJ FM GU KI 2 MH MP NC NR NU PF PG PN PW SB TK TO 3 TV VU WF WS Similar to Myripristis kuntee but with much larger scales and a redder overall appearance. 48 Holocentridae / Soldierfish and Squirrelfish Myripristis kuntee YJZ Shoulderbar soldierfish 2 Silvery orange-red with 1 darker scale margins. -
1 Exon Probe Sets and Bioinformatics Pipelines for All Levels of Fish Phylogenomics
bioRxiv preprint doi: https://doi.org/10.1101/2020.02.18.949735; this version posted February 19, 2020. 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. 1 Exon probe sets and bioinformatics pipelines for all levels of fish phylogenomics 2 3 Lily C. Hughes1,2,3,*, Guillermo Ortí1,3, Hadeel Saad1, Chenhong Li4, William T. White5, Carole 4 C. Baldwin3, Keith A. Crandall1,2, Dahiana Arcila3,6,7, and Ricardo Betancur-R.7 5 6 1 Department of Biological Sciences, George Washington University, Washington, D.C., U.S.A. 7 2 Computational Biology Institute, Milken Institute of Public Health, George Washington 8 University, Washington, D.C., U.S.A. 9 3 Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian 10 Institution, Washington, D.C., U.S.A. 11 4 College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China 12 5 CSIRO Australian National Fish Collection, National Research Collections of Australia, 13 Hobart, TAS, Australia 14 6 Sam Noble Oklahoma Museum of Natural History, Norman, O.K., U.S.A. 15 7 Department of Biology, University of Oklahoma, Norman, O.K., U.S.A. 16 17 *Corresponding author: Lily C. Hughes, [email protected]. 18 Current address: Department of Organismal Biology and Anatomy, University of Chicago, 19 Chicago, IL. 20 21 Keywords: Actinopterygii, Protein coding, Systematics, Phylogenetics, Evolution, Target 22 capture 23 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.02.18.949735; this version posted February 19, 2020. -
DEEP SEA LEBANON RESULTS of the 2016 EXPEDITION EXPLORING SUBMARINE CANYONS Towards Deep-Sea Conservation in Lebanon Project
DEEP SEA LEBANON RESULTS OF THE 2016 EXPEDITION EXPLORING SUBMARINE CANYONS Towards Deep-Sea Conservation in Lebanon Project March 2018 DEEP SEA LEBANON RESULTS OF THE 2016 EXPEDITION EXPLORING SUBMARINE CANYONS Towards Deep-Sea Conservation in Lebanon Project Citation: Aguilar, R., García, S., Perry, A.L., Alvarez, H., Blanco, J., Bitar, G. 2018. 2016 Deep-sea Lebanon Expedition: Exploring Submarine Canyons. Oceana, Madrid. 94 p. DOI: 10.31230/osf.io/34cb9 Based on an official request from Lebanon’s Ministry of Environment back in 2013, Oceana has planned and carried out an expedition to survey Lebanese deep-sea canyons and escarpments. Cover: Cerianthus membranaceus © OCEANA All photos are © OCEANA Index 06 Introduction 11 Methods 16 Results 44 Areas 12 Rov surveys 16 Habitat types 44 Tarablus/Batroun 14 Infaunal surveys 16 Coralligenous habitat 44 Jounieh 14 Oceanographic and rhodolith/maërl 45 St. George beds measurements 46 Beirut 19 Sandy bottoms 15 Data analyses 46 Sayniq 15 Collaborations 20 Sandy-muddy bottoms 20 Rocky bottoms 22 Canyon heads 22 Bathyal muds 24 Species 27 Fishes 29 Crustaceans 30 Echinoderms 31 Cnidarians 36 Sponges 38 Molluscs 40 Bryozoans 40 Brachiopods 42 Tunicates 42 Annelids 42 Foraminifera 42 Algae | Deep sea Lebanon OCEANA 47 Human 50 Discussion and 68 Annex 1 85 Annex 2 impacts conclusions 68 Table A1. List of 85 Methodology for 47 Marine litter 51 Main expedition species identified assesing relative 49 Fisheries findings 84 Table A2. List conservation interest of 49 Other observations 52 Key community of threatened types and their species identified survey areas ecological importanc 84 Figure A1. -
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. -
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). -
Factors Influencing Community Structure of Riverine
FACTORS INFLUENCING COMMUNITY STRUCTURE OF RIVERINE ORGANISMS: IMPLICATIONS FOR IMPERILED SPECIES MANAGEMENT by David S. Ruppel, M.S. A dissertation submitted to the Graduate Council of Texas State University in partial fulfillment of the requirements for the degree of Doctor of Philosophy with a Major in Aquatic Resources and Integrative Biology May 2019 Committee Members: Timothy H. Bonner, Chair Noland H. Martin Joseph A. Veech Kenneth G. Ostrand James A. Stoeckel COPYRIGHT by David S. Ruppel 2019 FAIR USE AND AUTHOR’S PERMISSION STATEMENT Fair Use This work is protected by the Copyright Laws of the United States (Public Law 94-553, section 107). Consistent with fair use as defined in the Copyright Laws, brief quotations from this material are allowed with proper acknowledgement. Use of this material for financial gain without the author’s express written permission is not allowed. Duplication Permission As the copyright holder of this work I, David S. Ruppel, authorize duplication of this work, in whole or in part, for educational or scholarly purposes only. ACKNOWLEDGEMENTS First, I thank my major advisor, Timothy H. Bonner, who has been a great mentor throughout my time at Texas State University. He has passed along his vast knowledge and has provided exceptional professional guidance and support with will benefit me immensely as I continue to pursue an academic career. I also thank my committee members Dr. Noland H. Martin, Dr. Joseph A. Veech, Dr. Kenneth G. Ostrand, and Dr. James A. Stoeckel who provided great comments on my dissertation and have helped in shaping manuscripts that will be produced in the future from each one of my chapters. -
Some Biological Aspects of Lessepsian Sargocentron Rubrum (Forsskål, 1775) in the North Cyprus, Mediterranean
Scientific Papers. Series D. Animal Science. Vol. LX, 2017 products, Quality acces to success, Scientific Journal tation in the vegetable industry. Journal of Purchasing ISSN 2285-5750; ISSN CD-ROM 2285-5769; ISSN Online 2393-2260; ISSN-L 2285-5750 of Management Systems, 15(143):95-97. & Supply Management, 12:39-50. Nicolae Carmen Georgeta, Liliana Mihaela Moga, Resende-Filho M., 2007. A Principal-Agent Model for SOME BIOLOGICAL ASPECTS OF LESSEPSIAN Magda Ioana Nenciu, Gratziela Victoria Bahaciu, Investigating Traceability Systems Incentives on Monica Paula Marin, 2015. Particularities and Food Safety. 105th EAAE Seminar ‘International SARGOCENTRON RUBRUM (FORSSKÅL, 1775) management of the distribution chain for fish and Marketing and International Trade of Quality Food IN THE NORTH CYPRUS, MEDITERRANEAN SEA fishery products. Scientific Papers. Series "AgroLife Products’, Bologna, Italy, March 8-10. Journal", 4(1):111-116. Romanian parliament, The Romanian Aquaculture and Popa M., Niculiţă P., Miteluţ A., Geicu M., Drăghici M., Fishing Law, 2014, available at: Yaşar ÖZVAROL, Aysu TATLISES Popa A., Sterian A., Turcu D., 2010. Good Practice http://apepaduri.gov.ro/wp-content/uploads/2014/07/ Guide regarding the traceability on agro-food Legea-Acvaculturii-si-Pescuitului-24-04-2014.pdf pathway. Noua Publishing House, Bucharest. Van der Meulen, B., 2004. Food safety law in the Akdeniz University, Faculty of Fisheries, Pinarbaşı bulvarı, 07059 Antalya, Turkey Rabade L.A., Alfaro J.A., 2006. Buyer-supplier European Union: An Introduction. Wageningen Pers relationship’s influence on traceability implemen- Publisher, Wageningen. Corresponding author e-mail: [email protected] Abstract This study was carried out by trammel nets in the waters of North Cyprus, 0-50 m, between January - November 2016. -
The Marine Biodiversity and Fisheries Catches of the Pitcairn Island Group
The Marine Biodiversity and Fisheries Catches of the Pitcairn Island Group THE MARINE BIODIVERSITY AND FISHERIES CATCHES OF THE PITCAIRN ISLAND GROUP M.L.D. Palomares, D. Chaitanya, S. Harper, D. Zeller and D. Pauly A report prepared for the Global Ocean Legacy project of the Pew Environment Group by the Sea Around Us Project Fisheries Centre The University of British Columbia 2202 Main Mall Vancouver, BC, Canada, V6T 1Z4 TABLE OF CONTENTS FOREWORD ................................................................................................................................................. 2 Daniel Pauly RECONSTRUCTION OF TOTAL MARINE FISHERIES CATCHES FOR THE PITCAIRN ISLANDS (1950-2009) ...................................................................................... 3 Devraj Chaitanya, Sarah Harper and Dirk Zeller DOCUMENTING THE MARINE BIODIVERSITY OF THE PITCAIRN ISLANDS THROUGH FISHBASE AND SEALIFEBASE ..................................................................................... 10 Maria Lourdes D. Palomares, Patricia M. Sorongon, Marianne Pan, Jennifer C. Espedido, Lealde U. Pacres, Arlene Chon and Ace Amarga APPENDICES ............................................................................................................................................... 23 APPENDIX 1: FAO AND RECONSTRUCTED CATCH DATA ......................................................................................... 23 APPENDIX 2: TOTAL RECONSTRUCTED CATCH BY MAJOR TAXA ............................................................................ -
Fishery Conservation and Management § 665.221
Fishery Conservation and Management § 665.221 § 665.210 Hawaii restricted bottomfish Bottomfish Species as specified in species. § 665.210 in the MHI management sub- area, except as otherwise allowed in Hawaii restricted bottomfish species means the following species: this section. (e) On and after the date specified in Local name English Scientific name § 665.211(c), no person may sell or offer common name for sale Hawaii Restricted Bottomfish lehi ........... silver jaw jobfish ....... Aphareus rutilans. Species as specified in § 665.210, except ehu ........... squirrelfish snapper .. Etelis carbunculus. as otherwise authorized by law. onaga ....... longtail snapper ........ Etelis coruscans. opakapaka Pink snapper............ Pristipomoides (f) Fishing for, and the resultant pos- filamentosus. session or sale of, Hawaii Restricted kalekale .... snapper .................... Pristipomoides sieboldii. Bottomfish Species by vessels legally gindai ....... snapper .................... Pristipomoides zonatus. hapu‘upu‘u sea bass................... Epinephelus quernus. registered to Mau Zone, Ho‘omalu Zone, or PRIA bottomfish fishing per- mits and conducted in compliance with § 665.211 Total Allowable Catch (TAC) all other laws and regulations, is ex- limit. empted from this section. (a) TAC limits will be set annually for the fishing year by NMFS, as rec- § 665.212 Non-commercial bag limits. ommended by the Council, based on the No more than a total of five fish (all best available scientific, commercial, species combined) identified as Hawaii and other information, and taking into Restricted Bottomfish Species as speci- account the associated risk of over- fied in § 665.210, may be harvested, pos- fishing. sessed, or landed by any individual par- (b) The Regional Administrator shall ticipating in a non-commercial vessel- publish a notice indicating the annual based fishing trip in the MHI manage- TAC limit in the FEDERAL REGISTER by ment subarea. -
A New Versatile Primer Set Targeting a Short Fragment of the Mitochondrial
A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents Matthieu Leray, Joy Y. Yang, Christopher P. Meyer, Suzanne C. Mills, Natalia Agudelo, Vincent Ranwez, Joel T. Boehm, Ryuji J. Machida To cite this version: Matthieu Leray, Joy Y. Yang, Christopher P. Meyer, Suzanne C. Mills, Natalia Agudelo, et al.. A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents. Frontiers in Zoology, BioMed Central, 2013, 10, 14 p. hal-01268031 HAL Id: hal-01268031 https://hal.archives-ouvertes.fr/hal-01268031 Submitted on 28 May 2020 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. Leray et al. Frontiers in Zoology 2013, 10:34 http://www.frontiersinzoology.com/content/10/1/34 RESEARCH Open Access A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: -
Evaluation of Genetic Relationship of Some Squirrelfishes Through DNA Barcode
Vol.64: e21210076, 2021 https://doi.org/10.1590/1678-4324-2021210076 ISSN 1678-4324 Online Edition Article - Biological and Applied Sciences Evaluation of Genetic Relationship of some Squirrelfishes through DNA Barcode Lamiaa Elsayed Mokhtar Deef1* https://orcid.org/0000-0002-4462-3432 1Damietta University, Faculty of Science, Department of Zoology, New Damietta, Damietta, Egypt. Editor-in-Chief: Alexandre Rasi Aoki Associate Editor: Marcelo Ricardo Vicari Received: 2021.02.13; Accepted: 2021.04.25. *Correspondence: [email protected] and [email protected]; Tel.: +201006796514 (L.E.M.D.). HIGHLIGHTS Confusion in the taxonomy of squirrelfishes was caused by the numerous nominal species. Our phylogeny provides a basis for evolutionary analyses of the Holocentridae. Silverspot squirrelfish was clustered as closest taxa to sabre squirrelfish. Abstract: Species of the subfamily Holocentrinae, family Holocentidae, commonly called, squirrelfishes, are widely distributed from tropical to warm temperate waters. In Egypt, no data are available on genetic and evolutionary relationships of the family Holocentridae. Therefore, the study of the genetic relationship among Holocentrids species is crucial for proper management and convenient strategies. The purpose of this study was to evaluate the genetic relationship among eight species belonging to the family Holocentridae from the Mediterranean Sea and the Red Sea in Egypt using DNA barcoding. Based on this molecular marker, a phylogenetic tree was constructed for the studied Holocentrids species. 12S rRNA sequences discovered that Sargocentron caudimaculatum was clustered as closest taxa to Sargocentron spiniferum, being a sister group to each other. Also, Sargocentron punctatissimum and Sargocentron macrosquamis were more related to each other and formed a sister group.