Amphipod Newsletter 34
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Complete Transcriptome Assembly and Annotation of a Critically Important
Environment International 137 (2020) 105319 Contents lists available at ScienceDirect Environment International journal homepage: www.elsevier.com/locate/envint Complete transcriptome assembly and annotation of a critically important amphipod species in freshwater ecotoxicological risk assessment: Gammarus T fossarum ⁎ Domenico R. Caputoa,1, Samuel C. Robsonb,1, Inge Wernerc, Alex T. Forda, a Institute of Marine Sciences, School of Biological Sciences, University of Portsmouth, Ferry Road, Portsmouth PO4 9LY, UK b Centre for Enzyme Innovation, St. Michael's Building, University of Portsmouth, White Swan Road, Portsmouth PO1 2DT, UK c Swiss Centre for Applied Ecotoxicology, Eawag - EPFL, Überlandstrasse 133, 8600 Dübendorf, Switzerland ARTICLE INFO ABSTRACT Handling Editor: Hefa Cheng Because of their crucial role in ecotoxicological risk assessment, amphipods (Crustacea) are commonly employed Keywords: as model species in a wide range of studies. However, despite their ecological importance, their genome has not Gammarus fossarum yet been completely annotated and molecular mechanisms underlying key pathways, such as the serotonin RNA sequencing pathway, in development of ecotoxicological biomarkers of exposure to neuroactive pharmaceuticals are still De novo assembly poorly understood. Furthermore, genetic similarities and discrepancies with other model arthropods (e.g., Serotonin pathway Drosophila melanogaster) have not been completely clarified. In this report, we present a new transcriptome assembly of Gammarus fossarum, an important amphipod species, widespread in Central Europe. RNA-Seq with Illumina HiSeq technology was used to analyse samples extracted from total internal tissues. We used the Trinity and Trinotate software suites for transcriptome assembly and annotation, respectively. The quality of this as- sembly and the affiliated targeted homology searches greatly enrich the molecular knowledge on this species. -
Phylogeny and Phylogeography of the Family Hyalidae (Crustacea: Amphipoda) Along the Northeast Atlantic Coasts
ALMA MATER STUDIORUM UNIVERSITÀ DI BOLOGNA SCUOLA DI SCIENZE - CAMPUS DI RAVENNA CORSO DI LAUREA MAGISTRALE IN BIOLOGIA MARINA Phylogeny and phylogeography of the family Hyalidae (Crustacea: Amphipoda) along the northeast Atlantic coasts Tesi di laurea in Alterazione e Conservazione degli Habitat Marini Relatore Presentata da Prof. Marco Abbiati Andrea Desiderato Correlatore Prof. Henrique Queiroga II sessione Anno accademico 2014/2015 “...Nothing at first can appear more difficult to believe than that the more complex organs and instincts should have been perfected, not by means superior to, though analogous with, human reason, but by the accumulation of innumerable slight variations, each good for the individual possessor…” (Darwin 1859) 1 1) Index 1) Index ------------------------------------------------------------------------------------------------ 2 2) Abstract ------------------------------------------------------------------------------------------- 3 3) Introduction ------------------------------------------------------------------------------------- 4 a) Hyalidae Bulycheva, 1957 ----------------------------------------------------------------- 4 b) Phylogeny -------------------------------------------------------------------------------------- 6 i) Phylogeny of Hyalidae -------------------------------------------------------------------- 7 c) The DNA barcode --------------------------------------------------------------------------- 8 d) Apohyale prevostii (Milne Edwars, 1830) --------------------------------------------- 9 -
Improving the Utilization of Data for Environmental Risk Assessment
STATISTICALECO(-TOXICO)LOGY IMPROVINGTHEUTILISATIONOFDATAFOR ENVIRONMENTALRISKASSESSMENT by eduard szöcs from zarneˇ ¸sti / romania Accepted Dissertation thesis for the partial fulfillment of the requirements for a Doctor of Natural Sciences Fachbereich 7: Natur- und Umweltwissenschaften Universität Koblenz-Landau Thesis examiners: Prof. Dr. Ralf B. Schäfer, University Koblenz-Landau Prof. Dr. Ralf Schulz, University Koblenz-Landau Assoc. Prof. Dr. Christian Ritz, University of Copenhagen Date of the oral examination: 25th January 2017 Galileo Few may hear Galileo’s song (calling) A tribulation Adversities Fuel for a living, feeds us all Spirit is fire Uncompromising Hidden hand, protect us from The dead and dying Echo his madness His heresy feeds us all Spirit is fire Uncompromising Hidden hand, protect us from The dead and dying Few may Spirit is fire Feed on the senseless ending Spirit is fire Feed on the senseless ending - Song by Maynard James Keenan ACKNOWLEDGMENTS I thank all the persons that supported me during my studies and this dissertation. My special thanks to my supervisor Prof. Dr. Ralf B. Schäfer for his support throughout the last six years. I am thankful for his openness to my ideas and the opportunities given to follow them, for organising funding throughout this dissertation, for pushing me to sound scientific writing and critical reading, for challenging discussions, not only on statistical eco(-toxico)logy but also outside of the subject area. Many thanks to Prof. Dr. Ralf Schulz for examining this thesis and his influence on me during my undergrad studies. Moreover, I thank Prof. Dr. Engelbert Niehaus for chairing the dissertation committee. Without the continuous support of my parents, Anca and Helmut, this thesis would not have been possible - Thank you! I am grateful to my colleagues, students and other people for asking me tough statistical questions. -
On the Current State of Taxonomy of the Baikal Lake Amphipods (Crustacea: Amphipoda) and the Typological Ways of Constructing Their System
Arthropoda Selecta 28(3): 374–402 © ARTHROPODA SELECTA, 2019 On the current state of taxonomy of the Baikal Lake amphipods (Crustacea: Amphipoda) and the typological ways of constructing their system Î ñîâðåìåííîì ñîñòîÿíèè òàêñîíîìèè áàéêàëüñêèõ àìôèïîä (Crustacea: Amphipoda) è òèïîëîãè÷åñêîì ñïîñîáå ïîñòðîåíèÿ èõ ñèñòåìû V.V. Takhteev1, 2 Â.Â. Òàõòååâ1, 2 1 Department of Biological and Soil Science at Irkutsk State University, Karl Marx St. 1, Irkutsk 664003, Russia. E-mail: [email protected] 1 Иркутский государственный университет, биолого-почвенный факультет, ул. К. Маркса, 1, Иркутск 664003, Россия. E-mail: [email protected] 2 Baikal Museum of Irkutsk Scientific Center SB RAS, Akademicheskaya St. 1, Listvyanka Settl., Irkutsk Region 664520, Russia. 2 Байкальский Музей Иркутского научного центра Сибирского отделения Российской академии наук, ул. Академическая, 1, пос. Листвянка Иркутской обл. 664520, Россия. KEY WORDS: amphipods, Lake Baikal, taxonomy, taxonomic inflation, archetype, core, deviations, estab- lishment of families. КЛЮЧЕВЫЕ СЛОВА: амфиподы, озеро Байкал, таксономия, таксономическая инфляция, архетип, ядро, отклонения, установление семейств. Editorial note On the publication “On the current state of taxonomy of the Baikal Lake amphipods (Crustacea, Amphipoda) and the typological ways of constructing their system” by V.V. Takhteev In this issue we present an extensive article prepared by Prof. Vadim V. Takhteev, which is based on his long time effort in the study of diversity of amphipods in Lake Baikal and its watershed. This paper is highly polemical and may even seem either archaic or heretical in the time of domination of the phylogenetic paradigms in systematics. The author advocates classical morphological taxonomy, which own tradition, methods (disregarding whether we call it typology or not) and the language are significantly older than the modern phylogenetic approach. -
Additions to and Revisions of the Amphipod (Crustacea: Amphipoda) Fauna of South Africa, with a List of Currently Known Species from the Region
Additions to and revisions of the amphipod (Crustacea: Amphipoda) fauna of South Africa, with a list of currently known species from the region Rebecca Milne Department of Biological Sciences & Marine Research Institute, University of CapeTown, Rondebosch, 7700 South Africa & Charles L. Griffiths* Department of Biological Sciences & Marine Research Institute, University of CapeTown, Rondebosch, 7700 South Africa E-mail: [email protected] (with 13 figures) Received 25 June 2013. Accepted 23 August 2013 Three species of marine Amphipoda, Peramphithoe africana, Varohios serratus and Ceradocus isimangaliso, are described as new to science and an additional 13 species are recorded from South Africa for the first time. Twelve of these new records originate from collecting expeditions to Sodwana Bay in northern KwaZulu-Natal, while one is an introduced species newly recorded from Simon’s Town Harbour. In addition, we collate all additions and revisions to the regional amphipod fauna that have taken place since the last major monographs of each group and produce a comprehensive, updated faunal list for the region. A total of 483 amphipod species are currently recognized from continental South Africa and its Exclusive Economic Zone . Of these, 35 are restricted to freshwater habitats, seven are terrestrial forms, and the remainder either marine or estuarine. The fauna includes 117 members of the suborder Corophiidea, 260 of the suborder Gammaridea, 105 of the suborder Hyperiidea and a single described representative of the suborder Ingolfiellidea. -
Report of the Working Group on the Biology and Life History of Crabs (WGCRAB)
ICES WGCRAB REPORT 2012 SCICOM STEERING GROUP ON ECOSYSTEM FUNCTIONS ICES CM 2012/SSGEF:08 REF. SSGEF, SCICOM, ACOM Report of the Working Group on the Biology and Life History of Crabs (WGCRAB) 14–18 May 2012 Port Erin, Isle of Man, UK International Council for the Exploration of the Sea Conseil International pour l’Exploration de la Mer H. C. Andersens Boulevard 44–46 DK-1553 Copenhagen V Denmark Telephone (+45) 33 38 67 00 Telefax (+45) 33 93 42 15 www.ices.dk [email protected] Recommended format for purposes of citation: ICES. 2012. Report of the Working Group on the Biology and Life History of Crabs (WGCRAB), 14–18 May 2012. ICES CM 2012/SSGEF:08 80pp. For permission to reproduce material from this publication, please apply to the Gen- eral Secretary. The document is a report of an Expert Group under the auspices of the International Council for the Exploration of the Sea and does not necessarily represent the views of the Council. © 2012 International Council for the Exploration of the Sea ICES WGCRAB Report 2012 | i Contents Executive summary ................................................................................................................ 1 1 Introduction .................................................................................................................... 2 2 Adoption of the agenda ................................................................................................ 2 3 Terms of reference 2011 ................................................................................................ 2 4 -
Recreational Boating As a Major Vector of Spread of Nonindigenous Species Around the Mediterranean Aylin Ulman
Recreational boating as a major vector of spread of nonindigenous species around the Mediterranean Aylin Ulman To cite this version: Aylin Ulman. Recreational boating as a major vector of spread of nonindigenous species around the Mediterranean. Ecosystems. Sorbonne Université, 2018. English. NNT : 2018SORUS222. tel- 02483397 HAL Id: tel-02483397 https://tel.archives-ouvertes.fr/tel-02483397 Submitted on 18 Feb 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. Sorbonne Université Università di Pavia Ecole doctorale CNRS, Laboratoire d'Ecogeochimie des Environments Benthiques, LECOB, F-66650 Banyuls-sur-Mer, France Recreational boating as a major vector of spread of non- indigenous species around the Mediterranean La navigation de plaisance, vecteur majeur de la propagation d’espèces non-indigènes autour des marinas Méditerranéenne Par Aylin Ulman Thèse de doctorat de Philosophie Dirigée par Agnese Marchini et Jean-Marc Guarini Présentée et soutenue publiquement le 6 Avril, 2018 Devant un jury composé de : Anna Occhipinti (President, University -
Congolli (Pseudaphritis Urvillii) and Australian Salmon (Arripis Truttaceus and A
Inland Waters and Catchment Ecology Diet and trophic characteristics of mulloway (Argyrosomus japonicus), congolli (Pseudaphritis urvillii) and Australian salmon (Arripis truttaceus and A. trutta) in the Coorong George Giatas and Qifeng Ye SARDI Publication No. F2015/000479-1 SARDI Research Report Series No. 858 SARDI Aquatics Sciences PO Box 120 Henley Beach SA 5022 September 2015 Giatas and Ye (2015) Diet of three fish species in the Coorong Diet and trophic characteristics of mulloway (Argyrosomus japonicus), congolli (Pseudaphritis urvillii) and Australian salmon (Arripis truttaceus and A. trutta) in the Coorong George Giatas and Qifeng Ye SARDI Publication No. F2015/000479-1 SARDI Research Report Series No. 858 September 2015 II Giatas and Ye (2015) Diet of three fish species in the Coorong This publication may be cited as: Giatas, G.C. and Ye, Q. (2015). Diet and trophic characteristics of mulloway (Argyrosomus japonicus), congolli (Pseudaphritis urvillii) and Australian salmon (Arripis truttaceus and A. trutta) in the Coorong. South Australian Research and Development Institute (Aquatic Sciences), Adelaide. SARDI Publication No. F2015/000479-1. SARDI Research Report Series No. 858. 81pp. South Australian Research and Development Institute SARDI Aquatic Sciences 2 Hamra Avenue West Beach SA 5024 Telephone: (08) 8207 5400 Facsimile: (08) 8207 5406 http://www.pir.sa.gov.au/research DISCLAIMER The authors warrant that they have taken all reasonable care in producing this report. The report has been through the SARDI internal review process, and has been formally approved for release by the Research Chief, Aquatic Sciences. Although all reasonable efforts have been made to ensure quality, SARDI does not warrant that the information in this report is free from errors or omissions. -
Freshwater Gammarus Species from Europe, North Africa and Adjacent Regions of Asia (Crustacea-Amphipoda)
FRESHWATER GAMMARUS SPECIES FROM EUROPE, NORTH AFRICA AND ADJACENT REGIONS OF ASIA (CRUSTACEA-AMPHIPODA) PART II. GAMMARUS ROESELI-GROUP AND RELATED SPECIES by GORDAN S. KARAMAN Biological Institute, Titograd, Yugoslavia & SJOUK PINKSTER Institute of Taxonomic Zoology, University of Amsterdam, The Netherlands FRESHWATER GAMMARUS SPECIES FROM EUROPE, NORTH AFRICA AND ADJACENT REGIONS OF ASIA (CRUSTACEA-AMPHIPODA) PART II. GAMMARUS ROESELI-GROUP AND RELATED SPECIES by GORDAN S. KARAMAN Biological Institute, Tito grad, Yugoslavia 8Z SJOUK PINKSTER Institute of Taxonomic Zoology, University of Amsterdam, The Netherlands ABSTRACT 9) For all species complete lists of all studied localities 1) This part of the revision of the freshwater Gammarus are given (except for G. roeseli, for economical reasons), species deals with the G. roeseli-group. Members of this together with two maps in which the distribution is illus- artificial group are characterized by the presence of dorsal trated. processes (carinae) on the metasome segments. RESUME 2) A historical review is given from the first description of G. roeseli and the taxonomic confusion that followed, to 1) Cette deuxieme partie de la revision traite des Gam- the start of this study when 3 species and at least 15 sub- marus d'eau douce du groupe roeseli. Les membres de ce species were known. groupe artificiel sont caracterises par la presence de carenes 3) Where possible, the type material of all these taxa is dorsales sur les segments du metasome. re-examined and compared with hundreds of newly collected 2) Un apercu historique est donne des la premiere samples and material from all major museums in Europe. -
The 17Th International Colloquium on Amphipoda
Biodiversity Journal, 2017, 8 (2): 391–394 MONOGRAPH The 17th International Colloquium on Amphipoda Sabrina Lo Brutto1,2,*, Eugenia Schimmenti1 & Davide Iaciofano1 1Dept. STEBICEF, Section of Animal Biology, via Archirafi 18, Palermo, University of Palermo, Italy 2Museum of Zoology “Doderlein”, SIMUA, via Archirafi 16, University of Palermo, Italy *Corresponding author, email: [email protected] th th ABSTRACT The 17 International Colloquium on Amphipoda (17 ICA) has been organized by the University of Palermo (Sicily, Italy), and took place in Trapani, 4-7 September 2017. All the contributions have been published in the present monograph and include a wide range of topics. KEY WORDS International Colloquium on Amphipoda; ICA; Amphipoda. Received 30.04.2017; accepted 31.05.2017; printed 30.06.2017 Proceedings of the 17th International Colloquium on Amphipoda (17th ICA), September 4th-7th 2017, Trapani (Italy) The first International Colloquium on Amphi- Poland, Turkey, Norway, Brazil and Canada within poda was held in Verona in 1969, as a simple meet- the Scientific Committee: ing of specialists interested in the Systematics of Sabrina Lo Brutto (Coordinator) - University of Gammarus and Niphargus. Palermo, Italy Now, after 48 years, the Colloquium reached the Elvira De Matthaeis - University La Sapienza, 17th edition, held at the “Polo Territoriale della Italy Provincia di Trapani”, a site of the University of Felicita Scapini - University of Firenze, Italy Palermo, in Italy; and for the second time in Sicily Alberto Ugolini - University of Firenze, Italy (Lo Brutto et al., 2013). Maria Beatrice Scipione - Stazione Zoologica The Organizing and Scientific Committees were Anton Dohrn, Italy composed by people from different countries. -
Lobsters and Crabs As Potential Vectors for Tunicate Dispersal in the Southern Gulf of St. Lawrence, Canada
Aquatic Invasions (2009) Volume 4, Issue 1: 105-110 This is an Open Access article; doi: 10.3391/ai. 2009.4.1.11 © 2009 The Author(s). Journal compilation © 2009 REABIC Special issue “Proceedings of the 2nd International Invasive Sea Squirt Conference” (October 2-4, 2007, Prince Edward Island, Canada) Andrea Locke and Mary Carman (Guest Editors) Research article Lobsters and crabs as potential vectors for tunicate dispersal in the southern Gulf of St. Lawrence, Canada Renée Y. Bernier, Andrea Locke* and John Mark Hanson Fisheries and Oceans Canada, Gulf Fisheries Centre, P.O. Box 5030, Moncton, NB, E1C 9B6 Canada * Corresponding author E-mail: [email protected] Received 20 February 2008; accepted for special issue 5 June 2008; accepted in revised form 22 December 2008; published online 16 January 2009 Abstract Following anecdotal reports of tunicates on the carapaces of rock crab (Cancer irroratus) and American lobster (Homarus americanus), we evaluated the role of these species and northern lady crab Ovalipes ocellatus as natural vectors for the spread of invasive tunicates in the southern Gulf of St. Lawrence. Several hundred adult specimens of crabs and lobster from two tunicate- infested estuaries and Northumberland Strait were examined for epibionts. Small patches of Botrylloides violaceus were found on rock crabs examined from Savage Harbour and a small colony of Botryllus schlosseri was found on one lobster from St. Peters Bay. Lobster and lady crab collected in Northumberland Strait had no attached colonial tunicates but small sea grapes (Molgula sp.) were found attached on the underside of 5.5% of the rock crab and on 2.5% of lobster collected in Northumberland Strait in August 2006. -
Crustacea, Malacostraca) from the Bulgarian Black Sea Area
ISSN 1314-3379 CHECKLIST OF MARINE AMPHIPODA (CRUSTACEA, MALACOSTRACA) FROM THE BULGARIAN BLACK SEA AREA S. Uzunova СПИСЪК НА МОРСКИТЕ АМФИПОДИ (CRUSTACEA, MALACOSTRACA) ОТ БЪЛГАРСКИЯ СЕКТОР НА ЧЕРНО МОРЕ С. Узунова Резюме : В настоящата публикация е обобщена наличната информация за морски видове от Разред Amphipoda (Crustacea, Malacostraca ) от българския сектор на Черно море . Съобщени са общо 55 вида морски амфиподи , принадлежащи към 26 семейства от разред Amphipoda. Ключови думи : Amphipoda, Crustacea, Black Sea, checklist . Introduction First information about Amphipoda from the Bulgarian Black Sea area is available in CHICHKOFF [9] and CASPERS [8]. VALKANOV [47] created the first catalogue of the Black Sea fauna from Bulgarian coastal area. Later on KUNEVA -ABADJIEVA [15] reported 46 amphipod species for the Bulgarian waters and the region of Bosphorus. In 1968 KUNEVA -ABADJIEVA [17] described for first time the species Cheirocratus sundevalli (RATHKE , 1843) for the Black Sea. VALKANOV &M ARINOV [44] added new 9 amphipod species. Several works on amphipod distribution and ecology were published by KUNEVA -ABADJIEVA [13, 14, 16, 18, 19], KUNEVA -ABADJIEVA & MARINOV [21,22], MARINOV & KUNEVA -ABADJIEVA [25], MARINOV et al. [26], MARINOV &S TOYKOV [27] and UZUNOVA [36,37,38,39]. MARINOV [23] summarized the number of amphipod species to 62, brackish water ones included. UZUNOVA [39] reported total of 46 species from the sublittoral and mediolitoral zone. More recent information about the distribution of amphipoda in the upper sublittoral and Zostera beds is found in UZUNOVA [40, 41]. The aim of the present paper is to update the information for the marine Amphipoda from the Bulgaria Black Sea area, according to the recent taxonomic advances.