Amphipod Newsletter 27
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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 -
BIOPAPUA Expedition Highlighting Deep-Sea Benthic Biodiversity of Papua New- Guinea
Biopapua Expedition – Progress report MUSÉUM NATIONAL D'HISTOIRE NATURELLE 57 rue Cuvier 75005 PARIS‐ France BIOPAPUA Expedition Highlighting deep-sea benthic Biodiversity of Papua New- Guinea Submitted by: Muséum National d'Histoire Naturelle (MNHN) Represented by (co‐PI): Dr Sarah Samadi (Researcher, IRD) Dr Philippe Bouchet (Professor, MNHN) Dr Laure Corbari (Research associate, MNHN) 1 Biopapua Expedition – Progress report Contents Foreword 3 1‐ Our understanding of deep‐sea biodiversity of PNG 4 2 ‐ Tropical Deep‐Sea Benthos program 5 3‐ Biopapua Expedition 7 4‐ Collection management 15 5‐ Preliminary results 17 6‐ Outreach and publications 23 7‐ Appendices 26 Appendix 1 27 NRI, note n°. 302/2010 on 26th march, 2010, acceptance of Biopapua reseach programme Appendix 2 28 Biopapua cruise Report, submitted by Ralph MANA (UPNG) A Report Submitted to School of Natural and Physical Sciences, University of Papua New Guinea Appendix 3 39 Chan, T.Y (2012) A new genus of deep‐sea solenocerid shrimp (Crustacea: Decapoda: Penaeoidea) from the Papua New Guinea. Journal of Crustacean Biology, 32(3), 489‐495. Appendix 4 47 Pante E, Corbari L., Thubaut J., Chan TY, Mana R., Boisselier MC, Bouchet P., Samadi S. (In Press). Exploration of the deep‐sea fauna of Papua New Guinea. Oceanography Appendix 5 60 Richer de Forges B. & Corbari L. (2012) A new species of Oxypleurodon Miers, 1886 (Crustacea Brachyura, Majoidea) from the Bismark Sea, Papua New Guinea. Zootaxa. 3320: 56–60 Appendix 6 66 Taxonomic list: Specimens in MNHN and Taiwan collections 2 Biopapua Expedition – Progress report Foreword Biopapua cruise was a MNHN/IRD deep‐sea cruise in partnership with the School of Natural and Physical Sciences, University of Papua New Guinea. -
Benthic Amphipod (Crustacea) Fauna of the Bandırma and Erdek Gulfs and Some Environmental Factors Affecting Their Distribution
ISSN: 0001-5113 ACTA ADRIAT., ORIGINAL SCIENTIFIC PAPER AADRAY 56(2): 171 - 188, 2015 Benthic amphipod (Crustacea) fauna of the Bandırma and Erdek Gulfs and some environmental factors affecting their distribution Ayşegül MÜLAYİM*1, Hüsamettin BALKIS1 and Murat SEZGİN2 1 Istanbul University, Faculty of Science, Department of Biology, 34134 Istanbul,Turkey 2Sinop University, Fisheries Faculty, Department of Hydrobiology 57000 Sinop, Turkey *Corresponding author, e-mail: [email protected] This study aims to determine the environmental factors affecting the fauna and distribution of benthic amphipod species inhabiting in the Bandırma and Erdek Gulfs which are located on the south of the Marmara Sea. Total of 66 species belonging to 22 families were identified after analyzing the samples collected seasonally from the depths ranging between 1 and 30 m between 2007- 2008. According to the data gathered from the literature, it was determined that one species (Bathyporeia elegans Watkin, 1938) was a new record for the Turkish seas and 37 species for the Marmara Sea. In the Bandırma Gulf, of the ecological variables of the environment temperature was determined to range between 6.6-27°C, salinity between 21.32-36.03 psu, dissolved oxygen between 4.04-11.26 mg l-1and pH between 8.00-8.38. In the Erdek Gulf, temperature ranged between 6.7 and 27°C, salinity between 21.93-35.54‰, dissolved oxygen between 3.67-13.26 mg l-1and pH between 8.06-8.36. In the surface sediment at the sampling stations of the Bandırma Gulf, total organic carbon values were between 0.07-4.42%, total calcium carbonate between 0.88-84.82%, total phosphorus between 609-12740 μg g-1 and mud percentage between 1.38-79.93%. -
Zoogeography of Epigean Freshwater Amphipoda (Crustacea) in Romania: Fragmented Distributions and Wide Altitudinal Variability
Zootaxa 3893 (2): 243–260 ISSN 1175-5326 (print edition) www.mapress.com/zootaxa/ Article ZOOTAXA Copyright © 2014 Magnolia Press ISSN 1175-5334 (online edition) http://dx.doi.org/10.11646/zootaxa.3893.2.5 http://zoobank.org/urn:lsid:zoobank.org:pub:8336FFDA-F1A5-4026-A5B6-CCEBFF84F40A Zoogeography of epigean freshwater Amphipoda (Crustacea) in Romania: fragmented distributions and wide altitudinal variability DENIS COPILAȘ-CIOCIANU1, MICHAŁ GRABOWSKI2, LUCIAN PÂRVULESCU3 & ADAM PETRUSEK1 1Charles University in Prague, Faculty of Science, Department of Ecology, Viničná 7, 12844, Prague, Czech Republic. E-mail: [email protected], [email protected] 2University of Łódź, Faculty of Biology and Environmental Protection, Department of Invertebrate Zoology & Hydrobiology, Banacha 12/16, 90-237, Łódź, Poland. E-mail: [email protected] 3West University of Timișoara, Faculty of Chemistry, Biology, Geography, Department of Biology and Chemistry, Pestalozzi 16A, 300115, Timișoara, Romania. E-mail: [email protected] Abstract Inland epigean freshwater amphipods of Romania are diverse and abundant for this region has a favourable geographical position between the Balkans and the Black Sea. Excluding Ponto-Caspian species originating in brackish waters and freshwater subterranean taxa, there are 11 formally recognized epigean freshwater species recorded from this country. They belong to 3 genera, each representing a different family: Gammarus (Gammaridae, 8 species or species complexes), Niphargus (Niphargidae, 2 epigean species) and Synurella (Crangonyctidae, one species). Their large-scale distribution patterns nevertheless remain obscure due to insufficient data, consequently limiting biogeographical interpretations. We provide extensive new data with high resolution distribution maps, thus improving the knowledge of the ranges of these taxa. -
Pu'u Wa'awa'a Biological Assessment
PU‘U WA‘AWA‘A BIOLOGICAL ASSESSMENT PU‘U WA‘AWA‘A, NORTH KONA, HAWAII Prepared by: Jon G. Giffin Forestry & Wildlife Manager August 2003 STATE OF HAWAII DEPARTMENT OF LAND AND NATURAL RESOURCES DIVISION OF FORESTRY AND WILDLIFE TABLE OF CONTENTS TITLE PAGE ................................................................................................................................. i TABLE OF CONTENTS ............................................................................................................. ii GENERAL SETTING...................................................................................................................1 Introduction..........................................................................................................................1 Land Use Practices...............................................................................................................1 Geology..................................................................................................................................3 Lava Flows............................................................................................................................5 Lava Tubes ...........................................................................................................................5 Cinder Cones ........................................................................................................................7 Soils .......................................................................................................................................9 -
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. -
Differential Impacts of Shared Parasites on Fitness Components Among Competing Hosts
Received: 23 November 2016 | Revised: 13 April 2017 | Accepted: 19 April 2017 DOI: 10.1002/ece3.3062 ORIGINAL RESEARCH Differential impacts of shared parasites on fitness components among competing hosts Olwyn C. Friesen | Robert Poulin | Clément Lagrue Department of Zoology, University of Otago, Dunedin, New Zealand Abstract Effects of parasites on individual hosts can eventually translate to impacts on host Correspondence Olwyn C. Friesen, Department of Zoology, communities. In particular, parasitism can differentially affect host fitness among sym- University of Otago, Dunedin, New Zealand. patric and interacting host species. We examined whether the impact of shared para- Email: [email protected] sites varied among host species within the same community. Specifically, we looked at Funding information the impacts of the acanthocephalan Acanthocephalus galaxii, the trematodes Department of Zoology, University of Otago Coitocaecum parvum and Maritrema poulini, and the nematode Hedruris spinigera, on three host species: the amphipods, Paracalliope fluviatilis and Paracorophium excava- tum, and the isopod, Austridotea annectens. We assessed parasite infection levels in the three host species and tested for effects on host survival, behavior, probability of pairing, and fecundity. Maritrema poulini and C. parvum were most abundant in P. exca- vatum but had no effect on its survival, whereas they negatively affected the survival of P. fluviatilis, the other amphipod. Female amphipods carrying young had higher M. poulini and C. parvum abundance than those without, yet the number of young car- ried was not linked to parasite abundance. Behavior of the isopod A. annectens was affected by M. poulini infection; more heavily infected individuals were more active. Paracorophium excavatum moved longer distances when abundance of C. -
Luth Wfu 0248D 10922.Pdf
SCALE-DEPENDENT VARIATION IN MOLECULAR AND ECOLOGICAL PATTERNS OF INFECTION FOR ENDOHELMINTHS FROM CENTRARCHID FISHES BY KYLE E. LUTH A Dissertation Submitted to the Graduate Faculty of WAKE FOREST UNIVERSITY GRADAUTE SCHOOL OF ARTS AND SCIENCES in Partial Fulfillment of the Requirements for the Degree of DOCTOR OF PHILOSOPHY Biology May 2016 Winston-Salem, North Carolina Approved By: Gerald W. Esch, Ph.D., Advisor Michael V. K. Sukhdeo, Ph.D., Chair T. Michael Anderson, Ph.D. Herman E. Eure, Ph.D. Erik C. Johnson, Ph.D. Clifford W. Zeyl, Ph.D. ACKNOWLEDGEMENTS First and foremost, I would like to thank my PI, Dr. Gerald Esch, for all of the insight, all of the discussions, all of the critiques (not criticisms) of my works, and for the rides to campus when the North Carolina weather decided to drop rain on my stubborn head. The numerous lively debates, exchanges of ideas, voicing of opinions (whether solicited or not), and unerring support, even in the face of my somewhat atypical balance of service work and dissertation work, will not soon be forgotten. I would also like to acknowledge and thank the former Master, and now Doctor, Michael Zimmermann; friend, lab mate, and collecting trip shotgun rider extraordinaire. Although his need of SPF 100 sunscreen often put our collecting trips over budget, I could not have asked for a more enjoyable, easy-going, and hard-working person to spend nearly 2 months and 25,000 miles of fishing filled days and raccoon, gnat, and entrail-filled nights. You are a welcome camping guest any time, especially if you do as good of a job attracting scorpions and ants to yourself (and away from me) as you did on our trips. -
Review and Meta-Analysis of the Environmental Biology and Potential Invasiveness of a Poorly-Studied Cyprinid, the Ide Leuciscus Idus
REVIEWS IN FISHERIES SCIENCE & AQUACULTURE https://doi.org/10.1080/23308249.2020.1822280 REVIEW Review and Meta-Analysis of the Environmental Biology and Potential Invasiveness of a Poorly-Studied Cyprinid, the Ide Leuciscus idus Mehis Rohtlaa,b, Lorenzo Vilizzic, Vladimır Kovacd, David Almeidae, Bernice Brewsterf, J. Robert Brittong, Łukasz Głowackic, Michael J. Godardh,i, Ruth Kirkf, Sarah Nienhuisj, Karin H. Olssonh,k, Jan Simonsenl, Michał E. Skora m, Saulius Stakenas_ n, Ali Serhan Tarkanc,o, Nildeniz Topo, Hugo Verreyckenp, Grzegorz ZieRbac, and Gordon H. Coppc,h,q aEstonian Marine Institute, University of Tartu, Tartu, Estonia; bInstitute of Marine Research, Austevoll Research Station, Storebø, Norway; cDepartment of Ecology and Vertebrate Zoology, Faculty of Biology and Environmental Protection, University of Lodz, Łod z, Poland; dDepartment of Ecology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia; eDepartment of Basic Medical Sciences, USP-CEU University, Madrid, Spain; fMolecular Parasitology Laboratory, School of Life Sciences, Pharmacy and Chemistry, Kingston University, Kingston-upon-Thames, Surrey, UK; gDepartment of Life and Environmental Sciences, Bournemouth University, Dorset, UK; hCentre for Environment, Fisheries & Aquaculture Science, Lowestoft, Suffolk, UK; iAECOM, Kitchener, Ontario, Canada; jOntario Ministry of Natural Resources and Forestry, Peterborough, Ontario, Canada; kDepartment of Zoology, Tel Aviv University and Inter-University Institute for Marine Sciences in Eilat, Tel Aviv, -
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. -
Ecotoxicology of Estuarine Amphipod Paracorophium Excavatum
E icolo fEstua ·ne Amphipod Paracorophium excavatum A thesis Submitted in partial fulfilment the requirements for Degree of Master of Science in Environmental Science at The University of Canterbury by Carol Wong Hee Ting University of Canterbury 1999 ABSTRACT The estuarine tube dwelling amphipod Paracorophium excavatum was investigated for its suitability as a bio-indicator and bio-monitor. Distribution patterns of P. excavatum were determined at 13 sites in the Canterbury region that differed in particle size distribution ranging from sandy to muddy sediment, with overall10w organic content. Low tide salinity ranged from 5 to 33 0/00 between sites and sediment moisture content ranged between 23 to 41 % moisture. Amphipods were absent from most sites within the Avon-Heathcote Estuary. The availability, life history and fecundity of P. excavatum were compared from intertidal mudflat sites in Brooklands Lagoon and Kairaki over a period of thirteen months. Four sediment core samples were collected at monthly intervals and P. excavatum IS population structure and life history pattern studied. The life history til· <: of P. excavatum can be characterised bY fast-growing, annual, iteroporous, bivoltine, females ovigerous throughout the year and thelygenous (female biased) population. P. excavatum showed relative consistency in abundance throughout the year with monthly densities ranging from 875.79 per 0.1 m-2 (July) to 1754.77 per 0.1 m-2 (December) at Brooklands Lagoon and 1031.83 per 0.1 m2 (November) to 1780.24 per 0.1 m2 (December) at Kairaki. There was a linear relationship between numbers of eggs per female and female length.