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Taxonomy and Diversity of the Sponge Fauna from Walters Shoal, a Shallow Seamount in the Western Indian Ocean Region
Taxonomy and diversity of the sponge fauna from Walters Shoal, a shallow seamount in the Western Indian Ocean region By Robyn Pauline Payne A thesis submitted in partial fulfilment of the requirements for the degree of Magister Scientiae in the Department of Biodiversity and Conservation Biology, University of the Western Cape. Supervisors: Dr Toufiek Samaai Prof. Mark J. Gibbons Dr Wayne K. Florence The financial assistance of the National Research Foundation (NRF) towards this research is hereby acknowledged. Opinions expressed and conclusions arrived at, are those of the author and are not necessarily to be attributed to the NRF. December 2015 Taxonomy and diversity of the sponge fauna from Walters Shoal, a shallow seamount in the Western Indian Ocean region Robyn Pauline Payne Keywords Indian Ocean Seamount Walters Shoal Sponges Taxonomy Systematics Diversity Biogeography ii Abstract Taxonomy and diversity of the sponge fauna from Walters Shoal, a shallow seamount in the Western Indian Ocean region R. P. Payne MSc Thesis, Department of Biodiversity and Conservation Biology, University of the Western Cape. Seamounts are poorly understood ubiquitous undersea features, with less than 4% sampled for scientific purposes globally. Consequently, the fauna associated with seamounts in the Indian Ocean remains largely unknown, with less than 300 species recorded. One such feature within this region is Walters Shoal, a shallow seamount located on the South Madagascar Ridge, which is situated approximately 400 nautical miles south of Madagascar and 600 nautical miles east of South Africa. Even though it penetrates the euphotic zone (summit is 15 m below the sea surface) and is protected by the Southern Indian Ocean Deep- Sea Fishers Association, there is a paucity of biodiversity and oceanographic data. -
A Freshwater Sponge Misunderstood for a Marine New Genus and Species
Zootaxa 3974 (3): 447–450 ISSN 1175-5326 (print edition) www.mapress.com/zootaxa/ Correspondence ZOOTAXA Copyright © 2015 Magnolia Press ISSN 1175-5334 (online edition) http://dx.doi.org/10.11646/zootaxa.3974.3.12 http://zoobank.org/urn:lsid:zoobank.org:pub:63265F5C-F70E-48D7-B7C8-7073C5243DA8 An example of the importance of labels and fieldbooks in scientific collections: A freshwater sponge misunderstood for a marine new genus and species ULISSES PINHEIRO1,4, GILBERTO NICACIO1,2 & GUILHERME MURICY3 1Universidade Federal de Pernambuco, Centro de Ciências Biológicas, Departamento de Zoologia, Av. Nelson Chaves, s/n Cidade Universitária CEP 50373-970, Recife, PE, Brazil 2Graduate Program in Zoology, Museu Paraense Emílio Goeldi, Av. Perimetral 1901, Terra Firme, Belém, PA, Brazil 3Universidade Federal do Rio de Janeiro, Museu Nacional, Departamento de Invertebrados, 20940-040, Rio de Janeiro, RJ, Brazil 4Corresponding author. E-mail: [email protected] The demosponge genus Crelloxea Hechtel, 1983 was created to allocate a single species, Crelloxea spinosa Hechtel, 1983, described based on specimens collected by Jacques Laborel in northeastern Brazil in 1964 and deposited at the Porifera Collection of the Yale Peabody Museum. The genus Crelloxea was originally defined as "Crellidae with dermal and interstitial acanthoxeas and acanthostrongyles, with skeletal oxea and without microscleres or echinators" (Hechtel, 1983). Crelloxea was allocated in the marine sponge family Crellidae (Order Poecilosclerida), which is characterized by a tangential crust of spined ectosomal spicules (oxeas, anisoxeas or styles), a choanosomal plumose skeleton of smooth tornotes, sometimes a basal skeleton of acanthostyles erect on the substrate, microscleres usually arcuate chelae or absent, and surface with areolated pore fields (van Soest, 2002). -
Transcriptome Sequencing, Characterization and Overview of the Gene Expression Along Three Life Cycle Stages
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Digital.CSIC Molecular Ecology Resources (2013) doi: 10.1111/1755-0998.12085 A NGS approach to the encrusting Mediterranean sponge Crella elegans (Porifera, Demospongiae, Poecilosclerida): transcriptome sequencing, characterization and overview of the gene expression along three life cycle stages A. R. PEREZ-PORRO,*† D. NAVARRO-GOMEZ,† M. J. URIZ* and G. GIRIBET† *Center for Advanced Studies of Blanes (CEAB-CSIC), c/Acces a la Cala St. Francesc 14, Girona, Blanes 17300, Spain, †Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA Abstract Sponges can be dominant organisms in many marine and freshwater habitats where they play essential ecological roles. They also represent a key group to address important questions in early metazoan evolution. Recent approaches for improving knowledge on sponge biological and ecological functions as well as on animal evolution have focused on the genetic toolkits involved in ecological responses to environmental changes (biotic and abiotic), development and reproduction. These approaches are possible thanks to newly available, massive sequencing tech- nologies–such as the Illumina platform, which facilitate genome and transcriptome sequencing in a cost-effective manner. Here we present the first NGS (next-generation sequencing) approach to understanding the life cycle of an encrusting marine sponge. For this we sequenced libraries of three different life cycle stages of the Mediterranean sponge Crella elegans and generated de novo transcriptome assemblies. Three assemblies were based on sponge tissue of a particular life cycle stage, including non-reproductive tissue, tissue with sperm cysts and tissue with larvae. -
The Global Invertebrate Genomics Alliance
Journal of Heredity 2014:105(1):1–18 © The American Genetic Association 2013. All rights reserved. doi:10.1093/jhered/est084 For permissions, please e-mail: [email protected] The Global Invertebrate Genomics Alliance (GIGA): Developing Community Resources to Study Downloaded from https://academic.oup.com/jhered/article-abstract/105/1/1/858593 by University of Florida, Joseph Ryan on 28 May 2019 Diverse Invertebrate Genomes GIGA COMMUNiTY OF SciENTisTs* Address correspondence to Dr. Jose V. Lopez, Oceanographic Center, Nova Southeastern University, 8000 North Ocean Drive, Dania Beach, FL 33004, or e-mail: [email protected]. *Authors are listed in the Appendix Abstract Over 95% of all metazoan (animal) species comprise the “invertebrates,” but very few genomes from these organisms have been sequenced. We have, therefore, formed a “Global Invertebrate Genomics Alliance” (GIGA). Our intent is to build a collaborative network of diverse scientists to tackle major challenges (e.g., species selection, sample collection and storage, sequence assembly, annotation, analytical tools) associated with genome/transcriptome sequencing across a large taxonomic spectrum. We aim to promote standards that will facilitate comparative approaches to invertebrate genomics and collabora- tions across the international scientific community. Candidate study taxa include species from Porifera, Ctenophora, Cnidaria, Placozoa, Mollusca, Arthropoda, Echinodermata, Annelida, Bryozoa, and Platyhelminthes, among others. GIGA will target 7000 noninsect/nonnematode species, with an emphasis on marine taxa because of the unrivaled phyletic diversity in the oceans. Priorities for selecting invertebrates for sequencing will include, but are not restricted to, their phylogenetic placement; relevance to organismal, ecological, and conservation research; and their importance to fisheries and human health. -
Transcriptome Sequencing, Characterization and Overview of the Gene Expression Along Three Life Cycle Stages
Molecular Ecology Resources (2013) doi: 10.1111/1755-0998.12085 A NGS approach to the encrusting Mediterranean sponge Crella elegans (Porifera, Demospongiae, Poecilosclerida): transcriptome sequencing, characterization and overview of the gene expression along three life cycle stages A. R. PEREZ-PORRO,*† D. NAVARRO-GOMEZ,† M. J. URIZ* and G. GIRIBET† *Center for Advanced Studies of Blanes (CEAB-CSIC), c/Acces a la Cala St. Francesc 14, Girona, Blanes 17300, Spain, †Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA Abstract Sponges can be dominant organisms in many marine and freshwater habitats where they play essential ecological roles. They also represent a key group to address important questions in early metazoan evolution. Recent approaches for improving knowledge on sponge biological and ecological functions as well as on animal evolution have focused on the genetic toolkits involved in ecological responses to environmental changes (biotic and abiotic), development and reproduction. These approaches are possible thanks to newly available, massive sequencing tech- nologies–such as the Illumina platform, which facilitate genome and transcriptome sequencing in a cost-effective manner. Here we present the first NGS (next-generation sequencing) approach to understanding the life cycle of an encrusting marine sponge. For this we sequenced libraries of three different life cycle stages of the Mediterranean sponge Crella elegans and generated de novo transcriptome assemblies. Three assemblies were based on sponge tissue of a particular life cycle stage, including non-reproductive tissue, tissue with sperm cysts and tissue with larvae. The fourth assembly pooled the data from all three stages. -
Molecular Phylogenies Confirm the Presence of Two Cryptic Hemimycale
Molecular phylogenies confirm the presence of two cryptic Hemimycale species in the Mediterranean and reveal the polyphyly of the genera Crella and Hemimycale (Demospongiae: Poecilosclerida) Maria J. Uriz, Leire Garate and Gemma Agell Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB-CSIC), Blanes, Girona, Spain ABSTRACT Background: Sponges are particularly prone to hiding cryptic species as their paradigmatic plasticity often favors species phenotypic convergence as a result of adaptation to similar habitat conditions. Hemimycale is a sponge genus (Family Hymedesmiidae, Order Poecilosclerida) with four formally described species, from which only Hemimycale columella has been recorded in the Atlanto-Mediterranean basin, on shallow to 80 m deep bottoms. Contrasting biological features between shallow and deep individuals of Hemimycale columella suggested larger genetic differences than those expected between sponge populations. To assess whether shallow and deep populations indeed belong to different species, we performed a phylogenetic study of Hemimycale columella across the Mediterranean. We also included other Hemimycale and Crella species from the Red Sea, with the additional aim of clarifying the relationships of the genus Hemimycale. Methods: Hemimycale columella was sampled across the Mediterranean, and Adriatic Seas. Hemimycale arabica and Crella cyathophora were collected from Submitted 19 November 2016 the Red Sea and Pacific. From two to three specimens per species and locality Accepted 4 January 2017 were extracted, amplified for Cytochrome C Oxidase I (COI) (M1–M6 partition), Published 7 March 2017 18S rRNA, and 28S (D3–D5 partition) and sequenced. Sequences were aligned using Corresponding author Clustal W v.1.81. Phylogenetic trees were constructed under neighbor joining (NJ), Maria J. -
Demosponge Distribution in the Eastern Mediterranean: a NW–SE Gradient
Helgol Mar Res (2005) 59: 237–251 DOI 10.1007/s10152-005-0224-8 ORIGINAL ARTICLE Eleni Voultsiadou Demosponge distribution in the eastern Mediterranean: a NW–SE gradient Received: 25 October 2004 / Accepted: 26 April 2005 / Published online: 22 June 2005 Ó Springer-Verlag and AWI 2005 Abstract The purpose of this paper was to investigate total number of species was an exponential negative patterns of demosponge distribution along gradients of function of depth. environmental conditions in the biogeographical subz- ones of the eastern Mediterranean (Aegean and Levan- Keywords Demosponges Æ Distribution Æ Faunal tine Sea). The Aegean Sea was divided into six major affinities Æ Mediterranean Sea Æ Aegean Sea Æ areas on the basis of its geomorphology and bathymetry. Levantine Sea Two areas of the Levantine Sea were additionally con- sidered. All available data on demosponge species numbers and abundance in each area, as well as their Introduction vertical and general geographical distribution were ta- ken from the literature. Multivariate analysis revealed a It is generally accepted that the Mediterranean Sea is NW–SE faunal gradient, showing an apparent dissimi- one of the world’s most oligotrophic seas. Conspicu- larity among the North Aegean, the South Aegean and ously, it harbors somewhat between 4% and 18% of the the Levantine Sea, which agrees with the differences in known world marine species, while representing only the geographical, physicochemical and biological char- 0.82% in surface area and 0.32% in volume of the world acteristics of the three areas. The majority of demo- ocean (Bianchi and Morri 2000). The eastern Mediter- sponge species has been recorded in the North Aegean, ranean, and especially the Levantine basin, is considered while the South Aegean is closer, in terms of demo- as the most oligotrophic Mediterranean region, having a sponge diversity, to the oligotrophic Levantine Sea. -
Cytonuclear Interactions in the Evolution of Animal Mitochondrial Trna Metabolism
GBE Cytonuclear Interactions in the Evolution of Animal Mitochondrial tRNA Metabolism Walker Pett1,2 and Dennis V. Lavrov1,* 1Department of Ecology, Evolution and Organismal Biology, Iowa State University 2Present address: Laboratoire de Biome´trieetBiologieE´volutive CNRS UMR 5558, Universite´ Lyon 1, Villeurbanne, France *Corresponding author: E-mail: [email protected]. Accepted: June 22, 2015 Data deposition: Raw genomic sequencing data for Corticium candelabrum have been deposited at the NCBI Sequence Read Archive under the accession SRR2021567. The Corticium candelabrum genome assembly and phylogenetic profiling sequence alignments have been placed on FigShare, doi: 10.6084/m9.figshare.1412684. Mitochondrial DNA sequences from Crella elegans and Petrosia ficiformis have been deposited at GenBank under the accessions KR911862 and KR911863, respectively. Abstract The evolution of mitochondrial information processing pathways, including replication, transcription and translation, is characterized by the gradual replacement of mitochondrial-encoded proteins with nuclear-encoded counterparts of diverse evolutionary origins. Although the ancestral enzymes involved in mitochondrial transcription and replication have been replaced early in eukaryotic evolution, mitochondrial translation is still carried out by an apparatus largely inherited from the a-proteobacterial ancestor. However, variation in the complement of mitochondrial-encoded molecules involved in translation, including transfer RNAs (tRNAs), provides evidence for the ongoing evolution of mitochondrial protein synthesis. Here, we investigate the evolution of the mitochondrial translational machinery using recent genomic and transcriptomic data from animals that have experienced the loss of mt-tRNAs, including phyla Cnidaria and Ctenophora, as well as some representatives of all four classes of Porifera. We focus on four sets of mitochondrial enzymes that directly interact with tRNAs: Aminoacyl-tRNA synthetases, glutamyl-tRNA amidotransferase, tRNAIle lysidine synthetase, and RNase P. -
Phylum Porifera
www.nature.com/scientificreports OPEN Development of a multilocus- based approach for sponge (phylum Porifera) identification: refinement Received: 01 September 2016 Accepted: 19 December 2016 and limitations Published: 02 February 2017 Qi Yang1,2, Christopher M. M. Franco1,2, Shirley J. Sorokin1,2,3 & Wei Zhang1,2,4 For sponges (phylum Porifera), there is no reliable molecular protocol available for species identification. To address this gap, we developed a multilocus-based Sponge Identification Protocol (SIP) validated by a sample of 37 sponge species belonging to 10 orders from South Australia. The universal barcode COI mtDNA, 28S rRNA gene (D3–D5), and the nuclear ITS1-5.8S-ITS2 region were evaluated for their suitability and capacity for sponge identification. The highest Bit Score was applied to infer the identity. The reliability of SIP was validated by phylogenetic analysis. The 28S rRNA gene and COI mtDNA performed better than the ITS region in classifying sponges at various taxonomic levels. A major limitation is that the databases are not well populated and possess low diversity, making it difficult to conduct the molecular identification protocol. The identification is also impacted by the accuracy of the morphological classification of the sponges whose sequences have been submitted to the database. Re-examination of the morphological identification further demonstrated and improved the reliability of sponge identification by SIP. Integrated with morphological identification, the multilocus-based SIP offers an improved protocol for more reliable and effective sponge identification, by coupling the accuracy of different DNA markers. Sponges (phylum Porifera), the evolutionary oldest multicellular animals, are sessile, benthic filter-feeders1. -
3538665.Pdf (2.855Mb)
Comparative description of ten transcriptomes of newly sequenced invertebrates and efficiency estimation of genomic sampling in non-model taxa The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Riesgo, Ana, Sónia C S Andrade, Prashant P Sharma, Marta Novo, Alicia R Pérez-Porro, Varpu Vahtera, Vanessa L González, Gisele Y Kawauchi, and Gonzalo Giribet. 2012. Comparative description of ten transcriptomes of newly sequenced invertebrates and efficiency estimation of genomic sampling in non-model taxa. Frontiers in Zoology 9: 33. Published Version doi:10.1186/1742-9994-9-33 Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:11729510 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA Riesgo et al. Frontiers in Zoology 2012, 9:33 http://www.frontiersinzoology.com/content/9/1/33 RESEARCH Open Access Comparative description of ten transcriptomes of newly sequenced invertebrates and efficiency estimation of genomic sampling in non-model taxa Ana Riesgo1,2*, Sónia C S Andrade1, Prashant P Sharma1, Marta Novo1,3, Alicia R Pérez-Porro1,2, Varpu Vahtera1,4, Vanessa L González1, Gisele Y Kawauchi1 and Gonzalo Giribet1 Abstract Introduction: Traditionally, genomic or transcriptomic data have been restricted to a few model or emerging model organisms, and to a handful of species of medical and/or environmental importance. Next-generation sequencing techniques have the capability of yielding massive amounts of gene sequence data for virtually any species at a modest cost. -
Splendid Sponges (Intertidal)
about this guide | about sponges | colour index | species index | species pages | icons | glossary inspirational invertebrates splendid spongesa guide to the intertidal Version 1, 2017 sponges of New Zealand Nicola Rush Michelle Kelly with Blayne Herr 1 about this guide | about sponges | colour index | species index | species pages | icons | glossary about this guide Sponges are the most common marine invertebrates that inhabit the New Zealand coastline and harbours, from the intertidal zone down to the continental shelf, deep ocean trenches, and abyssal plains. They are a magnificent and very diverse group of sea creatures. We hope that you will enjoy reading about them here and use this guide to help identify these splendid creatures in the wild. SPLENDID SPONGES - A GUIDE TO THE INTERTIDAL SPONGES OF NEW ZEALAND is a fully illustrated working guide to the most commonly encountered sponges in intertidal habitats around the country, starting with Auckland, and adding more from other locations, over time. It is designed for New Zealanders like you who live near the sea, dive and snorkel, explore our coasts, make a living from it, and for those who educate and are charged with kaitiakitanga, conservation and management of our marine realm. This guide is part of a series of guides on New Zealand’s marine life that NIWA’s Coasts and Oceans group is presently developing. The guide starts with a simple introduction to living sponges and how to identify them, followed by a colour index and a species index, followed by detailed individual species pages and additional supporting information. The taxonomic names in this guide are the result of specimen-based identifications by Dr Michelle Kelly and budding spongologist Nicola Rush. -
Two New Species of Encrusting Sponge (Porifera, Family Crellidae) from Eastern Canada
Canadian Journal of Zoology Two new species of encrusting sponge (Porifera, Family Crellidae) from eastern Canada. Journal: Canadian Journal of Zoology Manuscript ID cjz-2021-0041.R1 Manuscript Type: Article Date Submitted by the 31-Mar-2021 Author: Complete List of Authors: Goodwin, Claire; Huntsman Marine Science Centre, Aquatic Biosciences; University of New Brunswick Saint John Dinn, Curtis; Fisheries and Oceans Canada Gulf Region, Nefedova, Ekaterina; Zoological Institute RAS Nijhof, Frauke;Draft Huntsman Marine Science Centre Murillo, Francisco; Fisheries and Oceans Canada Maritimes Region, Bedford Institute of Oceanography Nozères, Claude; Fisheries and Oceans Canada, Maurice Lamontagne Institute Is your manuscript invited for consideration in a Special Not applicable (regular submission) Issue?: PORIFERA < Taxon, <i>Crella</i>, <i>Crellomima</i>, Bay of Fundy, Keyword: Gulf of St. Lawrence, Scotian Shelf, new demosponges © The Author(s) or their Institution(s) Page 1 of 39 Canadian Journal of Zoology 1 Title: Two new species of encrusting sponge (Porifera, Family Crellidae) from eastern 2 Canada. 3 CLAIRE GOODWIN1,2, CURTIS DINN3, EKATERINA NEFEDOVA4, FRAUKE NIJHOF1, 4 FRANCISCO JAVIER MURILLO5, CLAUDE NOZÈRES6 5 1. Huntsman Marine Science Centre, St. Andrews, New Brunswick, Canada 6 2. University of New Brunswick, Saint John, New Brunswick, Canada 7 3. Fisheries and Oceans Canada, Gulf Fisheries Centre, Moncton, New Brunswick, Canada 8 4. Zoological Institute of the Russian Academy of Sciences, Saint Petersburg, Russia 9 5. Fisheries and Oceans Canada, Bedford Institute of Oceanography, Dartmouth, Nova Scotia, Canada 10 6. Fisheries and Oceans Canada, Maurice Lamontagne Institute, Mont-Joli, Quebec, Canada 11 * corresponding author: [email protected] 12 Draft 13 Competing interests: The authors declare there are no competing interests.