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Free-Living Marine Nematodes from San Antonio Bay (Río Negro, Argentina)
A peer-reviewed open-access journal ZooKeys 574: 43–55Free-living (2016) marine nematodes from San Antonio Bay (Río Negro, Argentina) 43 doi: 10.3897/zookeys.574.7222 DATA PAPER http://zookeys.pensoft.net Launched to accelerate biodiversity research Free-living marine nematodes from San Antonio Bay (Río Negro, Argentina) Gabriela Villares1, Virginia Lo Russo1, Catalina Pastor de Ward1, Viviana Milano2, Lidia Miyashiro3, Renato Mazzanti3 1 Laboratorio de Meiobentos LAMEIMA-CENPAT-CONICET, Boulevard Brown 2915, U9120ACF, Puerto Madryn, Argentina 2 Universidad Nacional de la Patagonia San Juan Bosco, sede Puerto Madryn. Boulevard Brown 3051, U9120ACF, Puerto Madryn, Argentina 3Centro de Cómputos CENPAT-CONICET, Boulevard Brown 2915, U9120ACF, Puerto Madryn, Argentina Corresponding author: Gabriela Villares ([email protected]) Academic editor: H-P Fagerholm | Received 18 November 2015 | Accepted 11 February 2016 | Published 28 March 2016 http://zoobank.org/3E8B6DD5-51FA-499D-AA94-6D426D5B1913 Citation: Villares G, Lo Russo V, Pastor de Ward C, Milano V, Miyashiro L, Mazzanti R (2016) Free-living marine nematodes from San Antonio Bay (Río Negro, Argentina). ZooKeys 574: 43–55. doi: 10.3897/zookeys.574.7222 Abstract The dataset of free-living marine nematodes of San Antonio Bay is based on sediment samples collected in February 2009 during doctoral theses funded by CONICET grants. A total of 36 samples has been taken at three locations in the San Antonio Bay, Santa Cruz Province, Argentina on the coastal littoral at three tidal levels. This presents a unique and important collection for benthic biodiversity assessment of Patagonian nematodes as this area remains one of the least known regions. -
131 Nematode Fauna of Costa Rican Protected Areas
NEMATODE FAUNA OF COSTA RICAN PROTECTED AREAS Alejandro Esquivel Universidad Nacional de Heredia (U.N.A), Apdo postal 86-3000 Heredia, Costa Rica. ABSTRACT Esquivel, A. 2003. Nematode fauna of Costa Rican protected areas. Nematropica 33:131-145. The Instituto Nacional de Biodiversidad (INBio), in collaboration with the Nematology Laborato- ry at Universidad Nacional (U.N.A) of Costa Rica, conducted a nematode inventory of Costa Rican wild lands. Hundreds of samples were randomly collected for nematode analyses and thousands of specimens were permanently mounted on Cobb slides. A total of 74 families, 231 genera and 105 spe- cies has been detected so far. Dorylaimida was the dominant order both in number of specimens and genera, while the least dominant orders were Aphelenchida, Monhysterida and Desmocolecida. Some nematodes were widely distributed across all microhabitats, others appeared be restricted to a specific microhabitat or ecosystem. Basic and advanced reports regarding nematode inventory in Cos- ta Rican protected areas can be requested through the web page of INBio (http://atta.inbio.ac.cr). Key words: biodiversity, conservation areas, inventory, nematodes, survey. RESUMEN Esquivel, A. 2003. Nematofauna de las áreas protegidas de Costa Rica. Nematropica 33:131-145. El Instituto Nacional de Biodiversidad (INBio) en colaboración con el laboratorio de nematología de la Universidad Nacional (U.N.A), llevó a cabo el inventario de nematodos en áreas protegidas de Costa Rica. Cientos de muestras fueron colectadas al azar para análisis nematológicos y miles de es- pecimenes fueron montados permanentemente en laminillas de Cobb. Un total de 74 familias, 231 géneros y 105 especies han sido detectados. -
Nematode Taxonomic Diversity and Community Structure: Indicators of Environmental Conditions at Keetham Lake, Agra
NEMATODE TAXONOMIC DIVERSITY AND COMMUNITY STRUCTURE: INDICATORS OF ENVIRONMENTAL CONDITIONS AT KEETHAM LAKE, AGRA THESIS SUBMITTED FOR THE AWARD OF THE DEGREE OF DOCTOR OF PHILOSOPHY IN ZOOLOGY BY MALKA MUSTAQIM UNDER THE SUPERVISION OF PROF. QUDSIA TAHSEEN DEPARTMENT OF ZOOLOGY ALIGARH MUSLIM UNIVERSITY ALIGARH-202002 (INDIA) 2017 1 Dedicated to my Beloved Parents and Brothers 2 Qudsia Tahseen, Professor Department of Zoology, PhD, FASc, FNASc Aligarh Muslim University, Aligarh-202002, India Tel: +91 9319624196 E-mail: [email protected] Certificate This is to certify that the entire work presented in the thesis entitled, ‘‘Nematode taxonomic diversity and community structure: indicators of environmental conditions at Keetham Lake, Agra’’ by Ms. Malka Mustaqim is original and was carried out under my supervision. I have permitted Ms. Mustaqim to submit the thesis to Aligarh Muslim University, Aligarh for the award of degree of Doctor of Philosophy in Zoology. (Qudsia Tahseen) Supervisor 3 ANNEXURE-Ι CANDIDATE’S DECLARATION I, Malka Mustaqim, Department of Zoology, certify that the work embodied in this Ph.D. thesis is my own bonafide work carried out by me under the supervision of Prof. Qudsia Tahseen at Aligarh Muslim University, Aligarh. The matter embodied in this Ph.D. thesis has not been submitted for the award of any other degree. I declare that I have faithfully acknowledged, given credit to and referred to the research workers wherever their works have been cited in the text and the body of the thesis. I further certify that I have not willfully lifted up some others work, para, text, data, results, etc. -
(Stsm) Scientific Report
SHORT TERM SCIENTIFIC MISSION (STSM) SCIENTIFIC REPORT This report is submitted for approval by the STSM applicant to the STSM coordinator Action number: CA15219-45333 STSM title: Free-living marine nematodes from the eastern Mediterranean deep sea - connecting COI and 18S rRNA barcodes to structure and function STSM start and end date: 06/02/2020 to 18/3/2020 (short than the planned two months due to the Co-Vid 19 virus pandemic) Grantee name: Zoya Garbuzov PURPOSE OF THE STSM: My Ph.D. thesis is devoted to the population ecology of free-living nematodes inhabiting deep-sea soft substrates of the Mediterranean Levantine Basin. The success of the study largely depends on my ability to accurately identify collected nematodes at the species level, essential for appropriate environmental analysis. Morphological identification of nematodes at the species level is fraught with difficulties, mainly because of their relatively simple body shape and the absence of distinctive morphological characters. Therefore, a combination of morphological identification to genus level and the use of molecular markers to reach species identification is assumed to provide a better distinction of species in this difficult to identify group. My STSM host, Dr. Nikolaos Lampadariou, is an experienced taxonomist and nematode ecologist. In addition, I will have access to the molecular laboratory of Dr. Panagiotis Kasapidis. Both researchers are based at the Hellenic Center for Marine Research (HCMR) in Crete and this STSM is aimed at combining morphological taxonomy, under the supervision of Dr. Lampadariou, with my recently acquired experience in nematode molecular taxonomy for relating molecular identifiers to nematode morphology. -
Taxonomy Assignment Approach Determines the Efficiency of Identification of Metabarcodes in Marine Nematodes
Taxonomy assignment approach determines the efficiency of identification of metabarcodes in marine nematodes Oleksandr Holovachov1, Quiterie Haenel2, Sarah J. Bourlat3 and Ulf Jondelius1 1Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden 2Zoological Institute, University of Basel, Switzerland 3Department of Marine Sciences, University of Gothenburg, Sweden Abstract: Precision and reliability of barcode-based biodiversity assessment can be affected at several steps during acquisition and analysis of the data. Identification of barcodes is one of the crucial steps in the process and can be accomplished using several different approaches, namely, alignment-based, probabilistic, tree-based and phylogeny-based. Number of identified sequences in the reference databases affects the precision of identification. This paper compares the identification of marine nematode barcodes using alignment-based, tree-based and phylogeny-based approaches. Because the nematode reference dataset is limited in its taxonomic scope, barcodes can only be assigned to higher taxonomic categories, families. Phylogeny-based approach using Evolutionary Placement Algorithm provided the largest number of positively assigned metabarcodes and was least affected by erroneous sequences and limitations of reference data, comparing to alignment- based and tree-based approaches. Key words: biodiversity, identification, barcode, nematodes, meiobenthos. 1 1. Introduction Metabarcoding studies based on high throughput sequencing of amplicons from marine samples have reshaped our understanding of the biodiversity of marine microscopic eukaryotes, revealing a much higher diversity than previously known [1]. Early metabarcoding of the slightly larger sediment-dwelling meiofauna have mainly focused on scoring relative diversity of taxonomic groups [1-3]. The next step in metabarcoding: identification of species, is limited by the available reference database, which is sparse for most marine taxa, and by the matching algorithms. -
And Unexpected Placement of the Genus Molgolaimus Ditlevsen, 1921
Marine Biodiversity (2019) 49:2267–2280 https://doi.org/10.1007/s12526-019-00961-z ORIGINAL PAPER New nematode species from the continental slope of New Zealand (Chromadorea, Microlaimida, and Chromadorida), and unexpected placement of the genus Molgolaimus Ditlevsen, 1921 Daniel Leduc1 & Sujing Fu2 & Zeng Qi Zhao3 Received: 20 February 2019 /Revised: 3 April 2019 /Accepted: 16 April 2019 /Published online: 8 June 2019 # Senckenberg Gesellschaft für Naturforschung 2019 Abstract The current nematode classification comprises three primarily marine basal Chromadorean orders: the Microlaimida Leduc et al., 2018; Desmodorida De Coninck, 1965; and Chromadorida Chitwood, 1933. The phylogenetic placement of several taxa within these orders, however, is unclear due to the paucity of taxonomically informative morphological characters for high-level classification and is yet to be tested by molecular phylogenetic analyses due to the absence of molecular sequences. Here, we describe Molgolaimus kaikouraensis sp.nov.andAponema pseudotorosum sp. nov. from the continental slope of New Zealand and investigate phylogenetic relationships of these species and that of the rare desmodorid genera Onepunema and Pseudonchus, using SSU phylogenetic analyses for the first time. Whilst our analyses provided support for the current classification of Aponema within the family Microlaimidae and of Pseudonchus within the Desmodorida, we could not confirm relationships of Onepunema. We found no support for the placement of Molgolaimus with either the Desmodorida or Microlaimidae/ Microlaimida as in the current and previous classifications. Instead, Molgolaimus was classified with the Chromadorida with moderate and strong support in maximum likelihood and Bayesian analyses, respectively. Congruence analysis suggests that in some cases at least, the structure of the female reproductive system is a more taxonomically informative trait for marine nematode classification than the male reproductive system or cuticle. -
Nematoda, Monhysterida
ZOBODAT - www.zobodat.at Zoologisch-Botanische Datenbank/Zoological-Botanical Database Digitale Literatur/Digital Literature Zeitschrift/Journal: European Journal of Taxonomy Jahr/Year: 2015 Band/Volume: 0158 Autor(en)/Author(s): Leduc Daniel Artikel/Article: New species of Thelonema, Metasphaerolaimus, and Monhystrella (Nematoda, Monhysterida) from Kermadec Trench, Southwest Pacific 1-19 European Journal of Taxonomy 158: 1–19 ISSN 2118-9773 http://dx.doi.org/10.5852/ejt.2015.158 www.europeanjournaloftaxonomy.eu 2015 · Leduc D. This work is licensed under a Creative Commons Attribution 3.0 License. Research article urn:lsid:zoobank.org:pub:16E64AF8-518C-47F0-B3CF-6BA707C222FA New species of Thelonema, Metasphaerolaimus, and Monhystrella (Nematoda, Monhysterida) from Kermadec Trench, Southwest Pacifi c Daniel LEDUC National Institute of Water and Atmospheric Research, Private Bag 14-901, Wellington, New Zealand; +64 4 386 0379. Email: [email protected] urn:lsid:zoobank.org:author:9393949F-3426-4EE2-8BDE-DEFFACE3D9BC Abstract. Three new species of the order Monhysterida are described based on specimens obtained at depths of 8081 and 9177 m in the Kermadec Trench. Thelonema clarki sp. nov. is characterised by a large body size (3230–4461 μm), short cylindrical buccal cavity, gubernaculum without apophyses, and long conico-cylindrical tail. This is the fi rst record of the genus since its original description over two decades ago from the Peru Basin. Metasphaerolaimus constrictus sp. nov. is characterised by a relatively long body (1232–1623 -
Position of Pharyngeal Gland Outlets in Monhysteridae (Nemata)
Journal of Nematology 28(2): 169-176. 1996. © The Society of Nematologists 1996. Position of Pharyngeal Gland Outlets in Monhysteridae (Nemata) A. COOMANS, I A. EYUALEM, 1'2 AND M. C. VAN DE VELDE 1 Abstract: In this study an attempt was made to determine the position of the outlets and nuclei of the pharyngeal glands in four monhysterid genera. Five Eumonhystera spp., seven Monhystera spp., and eight Monhystrella spp. were studied under the light microscope. Longitudinal sections of an undescribed Monhystera sp. and cross sections of Geomonhystera ckisjuncta were also studied under the scanning and transmission electron microscope, respectively. The results of the light microscopic studies were inconclusive about the position of the outlets but showed a number of nuclei in the basal part of the pharynx. The scanning and transmission electron microscopic studies revealed five pharyngeal glands and their outlets; their position was as follows: dorsal gland outlet at the base of buccal tooth, first pair of ventrosublateral gland outlets halfway along the pharynx, and second pair of ventrosublateral gland outlets close to the base of the pharynx. It is concluded that at least three, and possibly five, nuclei are in the basal part of the pharynx. This pattern, in the position of the outlets and nuclei, is similar to that in Caenorhabditi6 elegans (Maupas, 1900) Dougherty, 1953 and may well be the basic plan in the Class Chromadorea (including Secernentia as a subclass). Key words: Geomonhystera, Monhystera, Monhysterida, morphology, nematode systematics, pharyn- geal gland outlet, pharynx, scanning electron microscopy, transmission electron microscopy, ultra- structure. The number, shape, and position of near the base of the stoma; the ventrosub- pharyngeal glands, and especially the po- lateral (="subventral") glands never open sition of their nuclei and outlets, are im- at the anterior end of the pharynx. -
Thesis Outline
UNIVERSITY OF SOUTHAMPTON Faculty of Engineering, Science, and Mathematics School of Ocean and Earth Science Resolving phylogenetic relationships within the order Enoplida (Phylum Nematoda) by Holly Marie Bik Thesis of the degree of Doctor of Philosophy January 2010 Graduate School of the National Oceanography Centre, Southampton This PhD Dissertation by Holly Marie Bik has been produced under the supervision of the following persons Supervisors Prof John Lambshead Dr Lawrence Hawkins Dr Alan Hughes Dr David Lunt Research Advisor Prof W. Kelley Thomas Chair of Advisory Panel Dr Martin Sheader 2 UNIVERSITY OF SOUTHAMPTON ABSTRACT FACULTY OF ENGINEERING, SCIENCE & MATHEMATICS SCHOOL OF OCEAN & EARTH SCIENCE Doctor of Philosophy RESOLVING PHYLOGENETIC RELATIONSHIPS WITHIN THE ORDER ENOPLIDA (PHYLUM NEMATODA) by Holly Marie Bik The Order Enoplida (Phylum Nematoda) has been proposed as a divergent nematode lineage—Enoplid nematodes are thought to exhibit morphological and developmental characteristics present in the ‘ancestral nematode’. However, previous molecular phylogenies have failed to unequivocally confirm the position of this group. The Enoplida is primarily comprised of free-living marine species; if these taxa represent close relatives of the nematode ancestor, this relationship would presumably imply a marine origin for the phylum. Prior to this investigation, few publically available gene sequences existed for Enoplid nematodes, and published sequences represented only shallow water fauna from Northwest Europe. This study has aimed to improve resolution at the base of the nematode tree, using drastically increased taxon-sampling within the previously neglected Enoplid clade. Morphological identifications, nuclear gene sequences (18S and 28S rRNA), and mitochondrial gene sequences (Cox1) were obtained from marine specimens representing a variety of deep-sea and intertidal habitats. -
ESTUDO DA NEMATOFAUNA NO BIOMA MATA ATLÂNTICA Carla
PONTIFÍCIA UNIVERSIDADE CATÓLICA DO RIO GRANDE DO SUL FACULDADE DE BIOCIÊNCIAS PROGRAMA DE PÓS-GRADUAÇÃO EM ZOOLOGIA ESTUDO DA NEMATOFAUNA NO BIOMA MATA ATLÂNTICA Carla Aristonara Müller DISSERTAÇÃO DE MESTRADO PONTIFÍCIA UNIVERSIDADE CATÓLICA DO RIO GRANDE DO SUL Av. Ipiranga 6681 - Caixa Postal 1429 Fone: (051) 320-3500 CEP 90619-900 Porto Alegre - RS Brasil 2017 i PONTIFÍCIA UNIVERSIDADE CATÓLICA DO RIO GRANDE DO SUL FACULDADE DE BIOCIÊNCIAS PROGRAMA DE PÓS-GRADUAÇÃO EM ZOOLOGIA ESTUDO DA NEMATOFAUNA NO BIOMA MATA ATLÂNTICA Carla Aristonara Müller Orientador: Dr. Carlos Graeff Teixeira DISSERTAÇÃO DE MESTRADO PORTO ALEGRE - RS - BRASIL 2017 ii SUMÁRIO Dedicatória................................................................................................................................iv Agradecimentos..........................................................................................................................v Resumo......................................................................................................................................vi Abstract....................................................................................................................................vii Apresentação..............................................................................................................................8 Introdução Geral.........................................................................................................................9 Capítulo I..................................................................................................................................11 -
Patino L Evolution and Community
i Evolution and community structure of parasites in Galápagos giant tortoises Leandro Dario Patino Patino Submitted in accordance with the requirements for the degree of Doctor in Philosophy The University of Leeds Faculty of Biological Sciences December, 2016 ii The candidate confirms that the work submitted is his/her own, except where work which has formed part of jointly-authored publications has been included. The contribution of the candidate and the other authors to this work has been explicitly indicated below. The candidate confirms that appropriate credit has been given within the thesis where reference has been made to the work of others. The blood samples and ticks for the years 2005 and 2006, used for Chapters 2 and 3, were collected during my work in the Galápagos Genetics, Epidemiology & Pathology (GGEPL) and in partnership with the DMV Marilyn Cruz and the DMV Pamela Martinez, also other members of staff, volunteers and students working in the laboratory at that time. The microscope analysis of ~ 1000 blood films prepared for the years before 2013, were also conducted in collaboration with them. I was involved in microscope analysis of ~30% of samples including Isabela and Santiago. Dr Cruz and Dr Martinez, analysed the remaining samples collected across all the tortoise populations included in this study. The GGEPL operated in Galápagos from 2003 to 2010 as a collaboration among the Galápagos National Park Directorate, the University of Leeds, Zoological Society of London, the University of Guayaquil and the NGO Concepto Azul. During this time the Laboratory was supported by grants from the UK government’s Darwin Initiative scheme (reference numbers: 162-12- 17 & EIDPO15), awarded to Dr Simon Goodman, Dr Virna Cedeño, and Prof Andrew Cunningham. -
A Focus on the Enoplida and Early-Branching Clades
University of New Hampshire University of New Hampshire Scholars' Repository Hubbard Center for Genome Studies (HCGS) Research Institutes, Centers and Programs 11-12-2010 Moving towards a complete molecular framework of the Nematoda: a focus on the Enoplida and early-branching clades Holly M. Bik Natural History Museum, London P. John D. Lambshead National Oceanography Centre W. Kelley Thomas University of New Hampshire, [email protected] David H. Lunt University of Hull Follow this and additional works at: https://scholars.unh.edu/hubbard Part of the Ecology and Evolutionary Biology Commons Recommended Citation Bik et al.: Moving towards a complete molecular framework of the Nematoda: a focus on the Enoplida and early-branching clades. BMC Evolutionary Biology 2010 10:353. This Article is brought to you for free and open access by the Research Institutes, Centers and Programs at University of New Hampshire Scholars' Repository. It has been accepted for inclusion in Hubbard Center for Genome Studies (HCGS) by an authorized administrator of University of New Hampshire Scholars' Repository. For more information, please contact [email protected]. Bik et al. BMC Evolutionary Biology 2010, 10:353 http://www.biomedcentral.com/1471-2148/10/353 RESEARCH ARTICLE Open Access Moving towards a complete molecular framework of the Nematoda: a focus on the Enoplida and early-branching clades Holly M Bik1,2,3*, P John D Lambshead2, W Kelley Thomas3, David H Lunt4 Abstract Background: The subclass Enoplia (Phylum Nematoda) is purported to be the earliest branching clade amongst all nematode taxa, yet the deep phylogeny of this important lineage remains elusive.