Zootaxa, the Biogeography of Indo-West Pacific Tropical
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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 -
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. -
Crustacea: Amphipoda: Dogielinotidae) from the Nipa Palm in Thailand, with an Updated Key to the Genera
RESEARCH ARTICLE Discovery of a new genus and species of dogielinotid amphipod (Crustacea: Amphipoda: Dogielinotidae) from the Nipa palm in Thailand, with an updated key to the genera 1,2 3 4 Koraon WongkamhaengID *, Pongrat Dumrongrojwattana , Myung-Hwa Shin a1111111111 a1111111111 1 Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand, 2 Coastal Oceanography and Climate Change Research Center, Prince of Songkla University, Hatyai, Songkhla, a1111111111 Thailand, 3 Department of Biology, Faculty of Science, Burapha University, Bangsaen, Chonburi, Thailand, a1111111111 4 National Marine Biodiversity Institute of Korea, Seocheon, South Korea a1111111111 * [email protected] Abstract OPEN ACCESS Citation: Wongkamhaeng K, Dumrongrojwattana During a scientific survey, a new genus of the dogielinotid amphipoda was found in the Nipa P, Shin M (2018) Discovery of a new genus and palm (Nypa fruticans) in Bang Krachao Urban Oasis, Samut Prakan Province, Thailand. We species of dogielinotid amphipod (Crustacea: placed this new genus, Allorchestoides gen. nov., within the family Dogielinotidae. The new Amphipoda: Dogielinotidae) from the Nipa palm in Thailand, with an updated key to the genera. PLoS taxa can be easily distinguished from the remaining genera by differences in the incisor of ONE 13(10): e0204299. https://doi.org/10.1371/ the left and right mandibles, apical robust setae of the maxilla 1, and the large coxa and journal.pone.0204299 strong obtuse palm in the female gnathopod 1. The type species of Allorchestoides gen. Editor: Feng Zhang, Nanjing Agricultural University, nov., Allorchestoides rosea n. sp., is described here in, with an updated key to the genera of CHINA the family Dogielinotidae. -
Figueroa Et Al Chile Mediterranean Re-Submitted
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Diposit Digital de la Universitat de Barcelona 1 Freshwater biodiversity and conservation in mediterranean climate streams of 2 Chile 3 4 1 Ricardo Figueroa* 5 2 Núria Bonada 6 1 Meyer Guevara 7 1 Pablo Pedreros 8 1 Francisco Correa-Araneda 9 1 María E. Díaz 10 3 Victor H. Ruiz 11 12 *1Corresponding author: [email protected] Center of Environmental Sciences EULA- 13 Chile, University of Concepcion, Casilla 160-C, Concepcion, Chile 14 2Grup de Recerca Freshwater Ecology and Management (FEM), Departament 15 d’Ecologia, Facultat de Biologia, Universitat de Barcelona (UB), Diagonal 643, 08028 16 Barcelona, Catalonia/Spain 17 3Department of Zoology, University of Concepcion, P.O. Box 160-C, Concepción, 18 Chile 19 20 21 Keywords: Central Chile, diversity, endemism, fauna, flora, streams and rivers 22 23 1 24 Abstract 25 26 In Chile, mediterranean climate conditions only occur in the Central Zone (ChMZ). 27 Despite its small area, this mediterranean climate region (med-region) has been 28 recognised as a hotspot for biodiversity. However, in contrast to the rivers of other med- 29 regions, the rivers in the ChMZ have been studied infrequently, and knowledge of their 30 freshwater biodiversity is scarce and fragmented. We gathered information on the 31 freshwater biodiversity of ChMZ, and present a review of the current knowledge of the 32 principal floral and faunal groups. Existing knowledge indicates that the ChMZ has high 33 levels of endemism, with many primitive species being of Gondwanan origin. -
New Zealand Freshwater Sciences Society Newsletter Number 41
New Zealand Freshwater Sciences Society Newsletter Number 41 November 2005 New Zealand Freshwater Sciences Society Newsletter No. 41 November 2005 Contents Introduction to the Society ....................................................................... 3 Editorial ............................................................................................. 4 President’s comment ................................................................................ 5 Research news ...................................................................................... 6 Freshwater Sciences Society Conference, Rotorua, 26 – 30 November 2006 ...............34 S.I.L. 1987 Trust Fund Awards .................................................................35 New Zealand Freshwater Sciences Society Medal and Honorary Membership ...............38 Minutes of the 37th Annual General Meeting ....................................................39 of the New Zealand Limnological Society Inc. (2004) .........................................39 Conference prizes 2004...........................................................................47 Conference Prizes, 2005..........................................................................48 Special Publications................................................................................50 Publications and theses ...........................................................................50 Membership list....................................................................................61 How do I join?.....................................................................................78 -
Cladistic Revision of Talitroidean Amphipods (Crustacea, Gammaridea), with a Proposal of a New Classification
CladisticBlackwell Publishing, Ltd. revision of talitroidean amphipods (Crustacea, Gammaridea), with a proposal of a new classification CRISTIANA S. SEREJO Accepted: 8 December 2003 Serejo, C. S. (2004). Cladistic revision of talitroidean amphipods (Crustacea, Gammaridea), with a proposal of a new classification. — Zoologica Scripta, 33, 551–586. This paper reports the results of a cladistic analysis of the Talitroidea s.l., which includes about 400 species, in 96 genera distributed in 10 families. The analysis was performed using PAUP and was based on a character matrix of 34 terminal taxa and 43 morphological characters. Four most parsimonious trees were obtained with 175 steps (CI = 0.617, RI = 0.736). A strict consensus tree was calculated and the following general conclusions were reached. The superfamily Talitroidea is elevated herein as infraorder Talitrida, which is subdivided into three main branches: a small clade formed by Kuria and Micropythia (the Kurioidea), and two larger groups maintained as distinct superfamilies (Phliantoidea, including six families, and Talitroidea s.s., including four). Within the Talitroidea s.s., the following taxonomic changes are proposed: Hyalellidae and Najnidae are synonymized with Dogielinotidae, and treated as subfamilies; a new family rank is proposed for the Chiltoniinae. Cristiana S. Serejo, Museu Nacional/UFRJ, Quinta da Boa Vista s/n, 20940–040, Rio de Janeiro, RJ, Brazil. E-mail: [email protected] Introduction Table 1 Talitroidean classification following Barnard & Karaman The talitroideans include amphipods ranging in length from 1991), Bousfield (1996) and Bousfield & Hendrycks (2002) 3 to 30 mm, and are widely distributed in the tropics and subtropics. In marine and estuarine environments, they are Superfamily Talitroidea Rafinesque, 1815 Family Ceinidae Barnard, 1972 usually found in shallow water, intertidally or even in the supra- Family Dogielinotidae Gurjanova, 1953 littoral zone. -
A Dataset on the Species Composition of Amphipods (Crustacea) in a Mexican Marine National Park: Alacranes Reef, Yucatan
Biodiversity Data Journal 6: e22622 doi: 10.3897/BDJ.6.e22622 Data Paper A dataset on the species composition of amphipods (Crustacea) in a Mexican marine national park: Alacranes Reef, Yucatan Carlos E. Paz-Ríos‡, Nuno Simões §,|,¶, Daniel Pech‡ ‡ Laboratorio de Biodiversidad Marina y Cambio Climatico (BIOMARCCA), El Colegio de la Frontera Sur, Unidad Campeche, Lerma, Campeche, Mexico § Unidad Academica Sisal, Facultad de Ciencias, Universidad Nacional Autonoma de Mexico, Puerto de Abrigo, Sisal, Yucatan, Mexico | Laboratorio Nacional de Resiliencia Costera (LANRESC), Puerto de Abrigo, Sisal, Yucatan, Mexico ¶ International Chair for Ocean and Coastal Studies, Harte Research Institute, Texas A&M, Corpus Christi, Texas, United States of America Corresponding author: Carlos E. Paz-Ríos ([email protected]) Academic editor: Yasen Mutafchiev Received: 29 Nov 2017 | Accepted: 16 Jan 2018 | Published: 25 Jan 2018 Citation: Paz-Ríos C, Simões N, Pech D (2018) A dataset on the species composition of amphipods (Crustacea) in a Mexican marine national park: Alacranes Reef, Yucatan. Biodiversity Data Journal 6: e22622. https://doi.org/10.3897/BDJ.6.e22622 Abstract Background Alacranes Reef was declared as a National Marine Park in 1994. Since then, many efforts have been made to inventory its biodiversity. However, groups such as amphipods have been underestimated or not considered when benthic invertebrates were inventoried. Here we present a dataset that contributes to the knowledge of benthic amphipods (Crustacea, Peracarida) from the inner lagoon habitats from the Alacranes Reef National Park, the largest coral reef ecosystem in the Gulf of Mexico. The dataset contains information on records collected from 2009 to 2011. -
Strengthening Marine Amphipod DNA Barcode Libraries for Environmental Monitoring
bioRxiv preprint doi: https://doi.org/10.1101/2020.08.26.268896; this version posted October 15, 2020. 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. Strengthening marine amphipod DNA barcode libraries for environmental monitoring Chinnamani Prasannakumar1,2*, Ganesh Manikantan3, J. Vijaylaxmi4, Balakrishnan Gunalan3,5, Seerangan Manokaran6, S. R. Pugazhvendan7,8 1Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Panaji, Goa-403004, India. 2Institute of Marine Microbes and Ecosphere, State Key Laboratory for Marine Environmental Sciences, Xiamen University, Xiamen, Fujian, 361102, PR China. 3Centre of Advance studies in Marine Biology, Annamalai University, Parangipettai, Tamil Nadu- 608502, India. 4Department of Marine Sciences, Goa University, Taleigao Plateau, Goa-403206, India. 5Post Graduate and Research Department of Zoology, Thiru Kolanjiappar Government Arts College, Virudhachalam, Tamil Nadu- 606001, India. 6Center for Environment & Water, King Fahd University of Petroleum and Minerals, Dhahran-31261, Saudi Arabia. 7Department of Zoology, Arignar Anna Government Arts College, Cheyyar, Tamil Nadu- 604407, India. 8Department of Zoology, Annamalai University, Annamalai Nagar, Chidambaram, Tamil Nadu- 608002, India. *Corresponding author’s email id: [email protected] Abstract Environmental DNA barcoding technology is gaining innovative applications. The effectiveness of current DNA barcode reference libraries in identifying amphipod barcodes and/or strengthening the existing library was tested. From 2500 amphipod individuals we barcoded 22 amphipod species belonging to 17 genera, 13 families among which 13 species were first time barcoded. More than 80 percent of the species were new distributional records. -
Southeastern Regional Taxonomic Center South Carolina Department of Natural Resources
Southeastern Regional Taxonomic Center South Carolina Department of Natural Resources http://www.dnr.sc.gov/marine/sertc/ Southeastern Regional Taxonomic Center Invertebrate Literature Library (updated 9 May 2012, 4056 entries) (1958-1959). Proceedings of the salt marsh conference held at the Marine Institute of the University of Georgia, Apollo Island, Georgia March 25-28, 1958. Salt Marsh Conference, The Marine Institute, University of Georgia, Sapelo Island, Georgia, Marine Institute of the University of Georgia. (1975). Phylum Arthropoda: Crustacea, Amphipoda: Caprellidea. Light's Manual: Intertidal Invertebrates of the Central California Coast. R. I. Smith and J. T. Carlton, University of California Press. (1975). Phylum Arthropoda: Crustacea, Amphipoda: Gammaridea. Light's Manual: Intertidal Invertebrates of the Central California Coast. R. I. Smith and J. T. Carlton, University of California Press. (1981). Stomatopods. FAO species identification sheets for fishery purposes. Eastern Central Atlantic; fishing areas 34,47 (in part).Canada Funds-in Trust. Ottawa, Department of Fisheries and Oceans Canada, by arrangement with the Food and Agriculture Organization of the United Nations, vols. 1-7. W. Fischer, G. Bianchi and W. B. Scott. (1984). Taxonomic guide to the polychaetes of the northern Gulf of Mexico. Volume II. Final report to the Minerals Management Service. J. M. Uebelacker and P. G. Johnson. Mobile, AL, Barry A. Vittor & Associates, Inc. (1984). Taxonomic guide to the polychaetes of the northern Gulf of Mexico. Volume III. Final report to the Minerals Management Service. J. M. Uebelacker and P. G. Johnson. Mobile, AL, Barry A. Vittor & Associates, Inc. (1984). Taxonomic guide to the polychaetes of the northern Gulf of Mexico. -
Zootaxa, Ringanui (Amphipoda: Gammaridea: Paraleptamphopidae)
Zootaxa 1148: 1–25 (2006) ISSN 1175-5326 (print edition) www.mapress.com/zootaxa/ ZOOTAXA 1148 Copyright © 2006 Magnolia Press ISSN 1175-5334 (online edition) Ringanui, a new genus of stygobitic amphipod from New Zealand (Amphipoda: Gammaridea: Paraleptamphopidae) GRAHAM D. FENWICK National Institute of Water and Atmosphere, P.O. Box 8602, Christchurch, New Zealand. E-mail: [email protected] Abstract A new genus is established for two new species of paraleptamphopid amphipods. Both species are stygobites inhabiting alluvial aquifers up to at least 18 m beneath the Canterbury Plains in New Zealand. First collected by Charles Chilton in 1882, these two species became confused with Paraleptamphopus subterraneus. The new genus, Ringanui, is a significant step in resolving this confusion. Ringanui differs from Paraleptamphopus on several characters and is most easily recognised by diverse gnathopods, the first of which is enlarged relative to gnathopod 2. The two species are described and illustrated in detail. They differ in size and gnathopod characteristics, but other differences are small. Ringanui koonuiroa is the smaller species and is most easily recognised by the single, very long robust seta defining the palm of gnathopod 1. The second species, R. toonuiiti, is the larger, but its palmar defining spine is relatively short. Both species occur together at the same locations and apparently in the same habitat. Key words: Crustacea, Groundwater, new genus Introduction Groundwater amphipods from New Zealand intrigued the international scientific community when first described by Charles Chilton in 1882 (a, b). Amongst the first three species described was Chilton’s Calliope subterranea Chilton, 1882. -
AMPHIPOD Newsletter 35 (2011)
Amphipod Newsletter 35 ! ! 2011 AMPHIPOD newsletter 35 (2011) Introduction of the Bibliography In remembrance Meetings & info new AN-team The list of new amphipod George Crawford XIV ICA 2010 who will take over the literature since Amphipod Stella Vassilenko XV ICA 2013 Amphipod Newsletter? Newsletter 34 (2010) TCS summer 2012 Page 2 Pages 3 - 43 Pages 44 - 45 Pages 46 - 47 INTRODUCTION The Amphipod Newsletter was started up by me in 1971, and in 40 years I have, often with the help of colleagues, produced 35 issues, at first mimeographed, the later ones on the Amphipod Website on the Internet. I have retired from my position as curator of zoology at Tromsø Museum in Tromsø, N. Norway, 4 years ago on reaching 70, and at the latest amphipod conference, in Sevilla in Spain in September 2010, I have asked for more regular assistance in the production of the newsletter, even though I am willing to continue for the time being to assist in the compiling of a bibliography of recent amphipod literature. At the meeting help was indeed offered, and from this issue, AN 35, the newsletter will be produced in cooperation with Adam Baldinger (Harvard), Miranda Lowe (Natural History Museum, London) and Anne Helene S. Tandberg (Norwegian Institute of New Amphipod Web-Site Marine Research, Tromsø, Norway). They will, maybe unnecessarily for most of you, introduce themselves elsewhere in this newsletter. A new amphipod web-site is Also the Amphipod website will move from Tromsø to Harvard eventually and under construction at as soon as some practical difficulties have been overcome.