Zootaxa, Talitridae
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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. -
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. -
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. -
Lake Wells Potash Project Subterranean Fauna Assessment
Lake Wells Potash Project Subterranean Fauna Assessment Prepared for: Australian Potash Limited June 2020 Final Report Three rounds of field survey were undertaken Lake Wells Subterranean Fauna Australian Potash Limited Lake Wells Potash Project Subterranean Fauna Assessment Bennelongia Pty Ltd 5 Bishop Street Jolimont WA 6014 P: (08) 9285 8722 F: (08) 9285 8811 E: [email protected] ABN: 55 124 110 167 Report Number: 329 Report Version Prepared by Reviewed by Submitted to Client Method Date Draft Anton Mittra Stuart Halse Email 19-11-2018 Final 1 Anton Mittra Michael Curran Email 21-12-2018 Final 2 Stuart Halse Email 1-11-2019 Final 3 Stuart Halse Email 4-6-2020 BEC_Lake Wells subterranean fauna _final_1xi2019.docx This document has been prepared to the requirements of the Client and is for the use by the Client, its agents, and Bennelongia Environmental Consultants. Copyright and any other Intellectual Property associated with the document belongs to Bennelongia Environmental Consultants and may not be reproduced without written permission of the Client or Bennelongia. No liability or responsibility is accepted in respect of any use by a third party or for purposes other than for which the document was commissioned. Bennelongia has not attempted to verify the accuracy and completeness of information supplied by the Client. © Copyright 2018 Bennelongia Pty Ltd. i Lake Wells Subterranean Fauna Australian Potash Limited ii Lake Wells Subterranean Fauna Australian Potash Limited EXECUTIVE SUMMARY Australian Potash Limited proposes to develop the Lake Wells Potash Project (the Project) at Lake Wells in the northeastern Yilgarn region of Western Australia. -
Zootaxa, the Biogeography of Indo-West Pacific Tropical
Zootaxa 2260: 109–127 (2009) ISSN 1175-5326 (print edition) www.mapress.com/zootaxa/ Article ZOOTAXA Copyright © 2009 · Magnolia Press ISSN 1175-5334 (online edition) The biogeography of Indo-West Pacific tropical amphipods with particular reference to Australia* A.A. MYERS1 & J.K. LOWRY2 1Department of Zoology, Ecology and Plant Science, National University of Ireland, Cork, Ireland ([email protected]) 2Australian Museum, 6, College Street, Sydney, New South Wales 2010, Australia ([email protected]) *In: Lowry, J.K. & Myers, A.A. (Eds) (2009) Benthic Amphipoda (Crustacea: Peracarida) of the Great Barrier Reef, Australia. Zootaxa, 2260, 1–930. Abstract The extant distribution of amphipods in the tropical Indo-Pacific can be understood only by reference to the positions of shallow seas during the past two hundred million years. Amphipods attributable to extant families, even genera, were in existence in Mesozoic times. A number of amphipod families can be recognized as Gondwanan in origin, but Laurasian families, except in fresh waters, are more difficult to identify. The tropical amphipod fauna of Australia/New Guinea is thought to have evolved in situ until at least 15 Ma, when the continent reached proximity with Asia. Parsimony Analysis of Endemicity of Indo-Pacific amphipod families supports this hypothesis. Key words: Crustacea, Amphipoda, Biogeography, Indo-West Pacific, Great Barrier Reef, Australia, biogeography Introduction Using the paradigm of ‘dispersal and founder principle’ to explain modern marine distributions, is not tenable (Myers 1994, 1996; Heads 2005). We must attempt to understand sequences of vicariant events in earth history, if we are to understand species distributions in tropical areas. -
Modes of Speciation in Subterranean Diving Beetles from a Single Calcrete Aquifer in Central Western Australia
Modes of Speciation in Subterranean Diving Beetles from a Single Calcrete Aquifer in Central Western Australia Paroster macrosturtensis (Dytiscidae) TESSA BRADFORD Presented for the degree of Doctor of Philosophy School of Earth and Environmental Sciences The University of Adelaide, South Australia December 2009 This page has been left blank intentionally II This work contains no material which has been accepted for the award of any other degree or diploma in any university or other tertiary institution to Tessa Bradford and, to the best of my knowledge and belief, contains no material previously published or written by another person, except where due reference has been made in the text. I give consent to this copy of my thesis when deposited in the University Library, being made available for loan and photocopying, subject to the provisions of the Copyright Act 1968. The author acknowledges that copyright of published work contained within this thesis (as listed below) resides with the copyright holder of this work (Wiley-Blackwell). I also give permission for the digital version of my thesis to be made available on the web, via the University‘s digital research repository, the Library catalogue, the Australasian Digital Theses Program (ADTP) and also through web search engines, unless permission has been granted by the University to restrict access for a period of time. This study was funded by a University of Adelaide Divisional Scholarship awarded to Tessa Bradford and an ARC Discovery grant (DP0663675) awarded to Associate Professor Steve Cooper and Dr William Humphreys. Tessa Bradford Published work Bradford T, Adams M, Humphreys WF, Austin AD, Cooper SJB (2010) DNA barcoding of stygofauna uncovers cryptic amphipod diversity in a calcrete aquifer in Western Australia'a arid zone. -
Patterns of Population Genetic Variation in Sympatric Chiltoniid Amphipods Within a Calcrete Aquifer Reveal a Dynamic Subterranean Environment
Heredity (2013) 111, 77–85 & 2013 Macmillan Publishers Limited All rights reserved 0018-067X/13 www.nature.com/hdy ORIGINAL ARTICLE Patterns of population genetic variation in sympatric chiltoniid amphipods within a calcrete aquifer reveal a dynamic subterranean environment TM Bradford1,2, M Adams2,3, MT Guzik2, WF Humphreys2,4,5, AD Austin2 and SJB Cooper2,3 Calcrete aquifers from the Yilgarn region of arid central Western Australia contain an assemblage of obligate groundwater invertebrate species that are each endemic to single aquifers. Fine-scale phylogeographic and population genetic analyses of three sympatric and independently derived species of amphipod (Chiltoniidae) were carried out to determine whether there were common patterns of population genetic structure or evidence for past geographic isolation of populations within a single calcrete aquifer. Genetic diversity in amphipod mitochondrial DNA (cytochrome c oxidase subunit I gene) and allozymes were examined across a 3.5 km2 region of the Sturt Meadows calcrete, which contains a grid of 115 bore holes ( ¼ wells). Stygobiont amphipods were found to have high levels of mitochondrial haplotype diversity coupled with low nucleotide diversity. Mitochondrial phylogeographic structuring was found between haplogroups for one of the chiltoniid species, which also showed population structuring for nuclear markers. Signatures of population expansion in two of the three species, match previous findings for diving beetles at the same site, indicating that the system is dynamic. We propose isolation of populations in refugia within the calcrete, followed by expansion events, as the most likely source of intraspecific genetic diversity, due to changes in water level influencing gene flow across the calcrete. -
Reproductive Biology in Quadrivisio Lutzi Medeiros And
Medeiros and Weber Reproductive biology in Quadrivisio lutzi Supplementary Material. Amphipod data used for comparisons and for PCA analysis. For those species with more than one information, the mean value across populations was used for PCA. PCA was only possible for those species with all three reproductive parameters available (HMFBLr, BS/BL and EggD-%FS). Female 1st size Brood Egg Species Name (Abbr) Family Habitat HMFBLr BS/BL EggD-%FS Source BodyLength maturity Size Size Ampelisca abdita (Aab) Ampeliscidae MW 6.6 26.0 0.166 3.9 0.43 6.5 Mills (1967)a Ampelisca araucana (Aar) Ampeliscidae MW 4.8 4.7 0.312 1.0 0.45 9.4 Carrasco and Arcos (1984)a Ampelisca vadorum (Ava) Ampeliscidae MW 6.0 9.1 0.250 1.5 0.51 8.5 Van Dolah and Bird (1980)a Gitanopsis squamosa (Gsq) Amphilochidae MW 3.6 5.9 0.194 1.6 0.40 11.1 Thurston (1974)a Ampithoe laxipodus (Ala) Ampithoidae MW 5.7 4.2 8.0 0.122 0.9 Appadoo and Myers (2004) Ampithoe longimana (Alo) Ampithoidae MW 5.8 2.4 9.4 1.6 0.42 7.2 Nelson (1978)b Ampithoe ramondi (Ara) Ampithoidae MW 8.0 21.0 0.375 2.6 0.31 3.9 Gilat (1962)a Cymadusa compta (Cco) Ampithoidae MW 5.8 3.5 13.5 1.6 0.41 7.1 Nelson (1978)b Grandidierella bonnieroides (Gbo) Aoridae MW 5.4 28.9 0.389 5.3 Thömke (1979)a Lembos websteri (Lwe) Aoridae MW 4.7 2.5 8.0 1.7 0.43 9.1 Nelson (1978)b Leptocheirus pilosus (Lpil) Aoridae BW 3.5 11.0 0.143 3.1 Goodhart (1939)a Microdeutopus gryllotalpa (Mgr) Aoridae MW 6.3 21.0 0.270 3.3 Myers (1971)a Atylus guttatus (Agu) Atylidae MW 5.5 26.0 0.273 4.7 0.40 7.3 Ivanov (1961)a Amphiporeia virginiana -
Amphipod Newsletter 27
1 AMPHIPOD NEWSLETTER 27 Produced by Wim Vader, Tromsø Museum, N-9037 Tromsø, Norway ([email protected]) in May 2005. INTRODUCTION This newsletter mainly covers the amphipod literature for 2004, but as I have prepared files about all amphipods described since 1990 (to be published in Amphipod Newsletter 28 before long) I have here included a number of articles which I had earlier overlooked and which contain descriptions of new amphipod taxa (pp 34-38). I shall be very grateful, if colleagues could notify me of any omissions in and corrections to these lists. As I have done in the latest newsletters, I have again taken the liberty to copy an important revised classification in this newsletter; after the Baikal amphipods by Kamaltynov and the Corophiidea by Myers and Lowry this time the entirely revised classification of the Talitrida, resulting from the cladistic analysis of this group by Cristiana Serejo (2004), is written out on pp 39-40. As usual, I have also provided alphabetical and systematic indexes to the new amphipod taxa, that are described in the papers listed in this bibliography. In view of the state of flux in which amphipod systematics and classification finds itself these days, this is a complicated task and one where it will be impossible to please all colleagues. I have used a number of informal groups, where I have not been able to find formalized family names as yet. This is especially the case within the Lysianassoidea, where we eagerly await the magnum opus of Lowry & Stoddart, but also in some freshwater groups, where maybe mainly my own insufficient knowledge is to blame.