Quantification of Settlement and Recruitment Processes in Bivalve M Ollusks
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The History and Decline of Ostrea Lurida in Willapa Bay, Washington Author(S): Brady Blake and Philine S
The History and Decline of Ostrea Lurida in Willapa Bay, Washington Author(s): Brady Blake and Philine S. E. Zu Ermgassen Source: Journal of Shellfish Research, 34(2):273-280. Published By: National Shellfisheries Association DOI: http://dx.doi.org/10.2983/035.034.0208 URL: http://www.bioone.org/doi/full/10.2983/035.034.0208 BioOne (www.bioone.org) is a nonprofit, online aggregation of core research in the biological, ecological, and environmental sciences. BioOne provides a sustainable online platform for over 170 journals and books published by nonprofit societies, associations, museums, institutions, and presses. Your use of this PDF, the BioOne Web site, and all posted and associated content indicates your acceptance of BioOne’s Terms of Use, available at www.bioone.org/page/terms_of_use. Usage of BioOne content is strictly limited to personal, educational, and non-commercial use. Commercial inquiries or rights and permissions requests should be directed to the individual publisher as copyright holder. BioOne sees sustainable scholarly publishing as an inherently collaborative enterprise connecting authors, nonprofit publishers, academic institutions, research libraries, and research funders in the common goal of maximizing access to critical research. Journal of Shellfish Research, Vol. 34, No. 2, 273–280, 2015. THE HISTORY AND DECLINE OF OSTREA LURIDA IN WILLAPA BAY, WASHINGTON BRADY BLAKE1 AND PHILINE S. E. ZU ERMGASSEN2* 1Washington State Department of Fish and Wildlife, 375 Hudson Street, Port Townsend, WA 98368; 2Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom ABSTRACT With an annual production of 1500 metric tons of shucked oysters, Willapa Bay, WA currently produces more oysters than any other estuary in the United States. -
The Histopathology of Antique Ark's Mantle (Anadara Antiquata) Post
The histopathology of antique ark’s mantle (Anadara antiquata) post-depuration with the shells’ filtration Nabila A. Putri, Laksmi Sulmartiwi, Kustiawan T. Pursetyo Faculty of Fisheries and Marine, Universitas Airlangga, 60115, Surabaya, Indonesia. Corresponding author: L. Sulmartiwi, [email protected] Abstract. Cockles are marine organisms which have the character of filter feeders so that heavy metals can be neutralized naturally through their shells. However, not all heavy metals can be neutralized, so depuration needs to be done. After depuration, histopathological analysis is needed to determine the condition of the soft tissue of the shells so that the disease can be diagnosed through structural changes that occur in the organs that are the main target of pollutants. This study aims to determine the histopathology of antique ark’s mantle (Anadara antiquata) after post-depuration with the filtration of the cockles’ shells. This research method applies an experimental method with scoring histological damage to antique ark’s mantle that ranges from 0 to 3, depending on the level and extent of the changes that occur. After that, the distribution of normal and non-homogeneous data was obtained, and then the Kruskal-Wallis non-parametric test was conducted. The main parameter is the histopathology of the antique ark’s mantle. Supporting parameters include water quality, namely temperature, dissolved oxygen (DO), nitrate, nitrite, ammonia, salinity, levels of heavy metals Pb and Cd, total suspended solid (TSS) and total dissolved solid (TDS). The results of the Kruskal-Wallis statistical analysis shows no significant difference between treatments P0 (Control), P1 (Filter 25%), P2 (Filter 50%), P3 (Filter 75%), and P4 (Filter 100%). -
Analysis of Synonymous Codon Usage Patterns in Sixty-Four Different Bivalve Species
Analysis of synonymous codon usage patterns in sixty-four diVerent bivalve species Marco Gerdol1, Gianluca De Moro1, Paola Venier2 and Alberto Pallavicini1 1 Department of Life Sciences, University of Trieste, Trieste, Italy 2 Department of Biology, University of Padova, Padova, Italy ABSTRACT Synonymous codon usage bias (CUB) is a defined as the non-random usage of codons encoding the same amino acid across diVerent genomes. This phenomenon is common to all organisms and the real weight of the many factors involved in its shaping still remains to be fully determined. So far, relatively little attention has been put in the analysis of CUB in bivalve mollusks due to the limited genomic data available. Taking advantage of the massive sequence data generated from next generation sequencing projects, we explored codon preferences in 64 diVerent species pertaining to the six major evolutionary lineages in Bivalvia. We detected remarkable diVerences across species, which are only partially dependent on phylogeny. While the intensity of CUB is mild in most organisms, a heterogeneous group of species (including Arcida and Mytilida, among the others) display higher bias and a strong preference for AT-ending codons. We show that the relative strength and direction of mutational bias, selection for translational eYciency and for translational accuracy contribute to the establishment of synonymous codon usage in bivalves. Although many aspects underlying bivalve CUB still remain obscure, we provide for the first time an overview of this phenomenon -
Shell Classification – Using Family Plates
Shell Classification USING FAMILY PLATES YEAR SEVEN STUDENTS Introduction In the following activity you and your class can use the same techniques as Queensland Museum The Queensland Museum Network has about scientists to classify organisms. 2.5 million biological specimens, and these items form the Biodiversity collections. Most specimens are from Activity: Identifying Queensland shells by family. Queensland’s terrestrial and marine provinces, but These 20 plates show common Queensland shells some are from adjacent Indo-Pacific regions. A smaller from 38 different families, and can be used for a range number of exotic species have also been acquired for of activities both in and outside the classroom. comparative purposes. The collection steadily grows Possible uses of this resource include: as our inventory of the region’s natural resources becomes more comprehensive. • students finding shells and identifying what family they belong to This collection helps scientists: • students determining what features shells in each • identify and name species family share • understand biodiversity in Australia and around • students comparing families to see how they differ. the world All shells shown on the following plates are from the • study evolution, connectivity and dispersal Queensland Museum Biodiversity Collection. throughout the Indo-Pacific • keep track of invasive and exotic species. Many of the scientists who work at the Museum specialise in taxonomy, the science of describing and naming species. In fact, Queensland Museum scientists -
Phylogenetic Relationships of Serpulidae (Annelida: Polychaeta) Based on 18S Rdna Sequence Data, and Implications for Opercular Evolution Janina Lehrkea,Ã, Harry A
ARTICLE IN PRESS Organisms, Diversity & Evolution 7 (2007) 195–206 www.elsevier.de/ode Phylogenetic relationships of Serpulidae (Annelida: Polychaeta) based on 18S rDNA sequence data, and implications for opercular evolution Janina Lehrkea,Ã, Harry A. ten Hoveb, Tara A. Macdonaldc, Thomas Bartolomaeusa, Christoph Bleidorna,1 aInstitute for Zoology, Animal Systematics and Evolution, Freie Universitaet Berlin, Koenigin-Luise-Street 1-3, 14195 Berlin, Germany bZoological Museum, University of Amsterdam, P.O. Box 94766, 1090 GT Amsterdam, The Netherlands cBamfield Marine Sciences Centre, Bamfield, British Columbia, Canada, V0R 1B0 Received 19 December 2005; accepted 2 June 2006 Abstract Phylogenetic relationships of (19) serpulid taxa (including Spirorbinae) were reconstructed based on 18S rRNA gene sequence data. Maximum likelihood, Bayesian inference, and maximum parsimony methods were used in phylogenetic reconstruction. Regardless of the method used, monophyly of Serpulidae is confirmed and four monophyletic, well- supported major clades are recovered: the Spirorbinae and three groups hitherto referred to as the Protula-, Serpula-, and Pomatoceros-group. Contrary to the taxonomic literature and the hypothesis of opercular evolution, the Protula- clade contains non-operculate (Protula, Salmacina) and operculate taxa both with pinnulate and non-pinnulate peduncle (Filograna vs. Vermiliopsis), and most likely is the sister group to Spirorbinae. Operculate Serpulinae and poorly or non-operculate Filograninae are paraphyletic. It is likely that lack of opercula in some serpulid genera is not a plesiomorphic character state, but reflects a special adaptation. r 2007 Gesellschaft fu¨r Biologische Systematik. Published by Elsevier GmbH. All rights reserved. Keywords: Serpulidae; Phylogeny; Operculum; 18S rRNA gene; Annelida; Polychaeta Introduction distinctive calcareous tubes and bilobed tentacular crowns, each with numerous radioles that bear shorter Serpulids are common members of marine hard- secondary branches (pinnules) on the inner side. -
Effects of Sediment and Suspended Solids on Freshwater Mussels
Effects of Sediment and Suspended Solids on Freshwater Mussels Jim Stoeckel School of Fisheries, Aquaculture, and Aquatic Sciences Auburn University Why is sediment a problem? Mussels are adapted to live in sediments Not all sediments are the same • Firm, stable sediment = GOOD • Unstable or Flocculent sediment = BAD Dislodgement Mussels sink into sediment Sediments taken in or during filtering Sediments are easily suspended activities Potential Impacts • Clearance rates tend to decrease • Pseudofeces production tends to increase • Feeding • Spawning How do Bivalves Sort Particles? Pseudofeces Sorted by: 1) inorganic vs. organic 2) Nitrogen vs Carbon rich 3) Algal species ? Site: 1) Gills – maybe 2) Palps – Yes! Feces: Passed Pseudofeces: Rejected particles bound in mucus through 1) “non-food” digestive 2) Excess food system Ingestion: Particles pass into stomach Selection Efficiency Varies Among Species and Habitat Good Poor What about unionid mussels? Payne et al. 1995 High TSS LOW TSS Palp area : Gill area = 3.78 +/- 0.95 Palp area : Gill area = 11.5 +/- 1.3 Two General Causes of High Suspended Solids Poor land use practices Eutrophication Inorganic: Organic: sand, silt, phytoplankton clay bacteria Eutrophication experiments in a semi-natural setting • Created eutrophication gradient • 6, 0.1 ha ponds South Auburn • 2 – no fertilization Fisheries • 2 – moderate fertilization Research • 2 – high fertilization Station • Monitored weekly – Secchi – Total suspended solids (TSS) • Organic and Inorganic Experimental mussel • Ligumia subrostrata -
Biomineralization of Polychaete Annelids in the Fossil Record
minerals Review Biomineralization of Polychaete Annelids in the Fossil Record Olev Vinn Department of Geology, University of Tartu, Ravila 14A, 50411 Tartu, Estonia; [email protected]; Tel.: +372-5067728 Received: 31 August 2020; Accepted: 25 September 2020; Published: 29 September 2020 Abstract: Ten distinct microstructures occur in fossil serpulids and serpulid tubes can contain several layers with different microstructures. Diversity and complexity of serpulid skeletal structures has greatly increased throughout their evolution. In general, Cenozoic serpulid skeletal structures are better preserved than Mesozoic ones. The first complex serpulid microstructures comparable to those of complex structures of molluscs appeared in the Eocene. The evolution of serpulid tube microstructures can be explained by the importance of calcareous tubes for serpulids as protection against predators and environmental disturbances. Both fossil cirratulids and sabellids are single layered and have only spherulitic prismatic tube microstructures. Microstructures of sabellids and cirratulids have not evolved since the appearance of calcareous species in the Jurassic and Oligocene, respectively. The lack of evolution in sabellids and cirratulids may result from the unimportance of biomineralization for these groups as only few species of sabellids and cirratulids have ever built calcareous tubes. Keywords: biominerals; calcite; aragonite; skeletal structures; serpulids; sabellids; cirratulids; evolution 1. Introduction Among polychaete annelids, calcareous tubes are known in serpulids, cirratulids and sabellids [1–3]. The earliest serpulids and sabellids are known from the Permian [4], and cirratulids from the Oligocene [5]. Only serpulids dwell exclusively within calcareous tubes. Polychaete annelids build their tubes from calcite, aragonite or a mixture of both polymorphs. Calcareous polychaete tubes possess a variety of ultrastructural fabrics, from simple to complex, some being unique to annelids [1]. -
Freshwater Mussels of the Pacific Northwest
Freshwater Mussels of the Pacifi c Northwest Ethan Nedeau, Allan K. Smith, and Jen Stone Freshwater Mussels of the Pacifi c Northwest CONTENTS Part One: Introduction to Mussels..................1 What Are Freshwater Mussels?...................2 Life History..............................................3 Habitat..................................................5 Role in Ecosystems....................................6 Diversity and Distribution............................9 Conservation and Management................11 Searching for Mussels.............................13 Part Two: Field Guide................................15 Key Terms.............................................16 Identifi cation Key....................................17 Floaters: Genus Anodonta.......................19 California Floater...................................24 Winged Floater.....................................26 Oregon Floater......................................28 Western Floater.....................................30 Yukon Floater........................................32 Western Pearlshell.................................34 Western Ridged Mussel..........................38 Introduced Bivalves................................41 Selected Readings.................................43 www.watertenders.org AUTHORS Ethan Nedeau, biodrawversity, www.biodrawversity.com Allan K. Smith, Pacifi c Northwest Native Freshwater Mussel Workgroup Jen Stone, U.S. Fish and Wildlife Service, Columbia River Fisheries Program Offi ce, Vancouver, WA ACKNOWLEDGEMENTS Illustrations, -
Copyrighted Material
319 Index a oral cavity 195 guanocytes 228, 231, 233 accessory sex glands 125, 316 parasites 210–11 heart 235 acidophils 209, 254 pharynx 195, 197 hemocytes 236 acinar glands 304 podocytes 203–4 hemolymph 234–5, 236 acontia 68 pseudohearts 206, 208 immune system 236 air sacs 305 reproductive system 186, 214–17 life expectancy 222 alimentary canal see digestive setae 191–2 Malpighian tubules 232, 233 system taxonomy 185 musculoskeletal system amoebocytes testis 214 226–9 Cnidaria 70, 77 typhlosole 203 nephrocytes 233 Porifera 28 antennae nervous system 237–8 ampullae 10 Decapoda 278 ocelli 240 Annelida 185–218 Insecta 301, 315 oral cavity 230 blood vessels 206–8 Myriapoda 264, 275 ovary 238 body wall 189–94 aphodus 38 pedipalps 222–3 calciferous glands 197–200 apodemes 285 pharynx 230 ciliated funnel 204–5 apophallation 87–8 reproductive system 238–40 circulatory system 205–8 apopylar cell 26 respiratory system 236–7 clitellum 192–4 apopyle 38 silk glands 226, 242–3 coelomocytes 208–10 aquiferous system 21–2, 33–8 stercoral sac 231 crop 200–1 Arachnida 221–43 sucking stomach 230 cuticle 189 biomedical applications 222 taxonomy 221 diet 186–7 body wall 226–9 testis 239–40 digestive system 194–203 book lungs 236–7 tracheal tube system 237 dissection 187–9 brain 237 traded species 222 epidermis 189–91 chelicera 222, 229 venom gland 241–2 esophagus 197–200 circulatory system 234–6 walking legs 223 excretory system 203–5 COPYRIGHTEDconnective tissue 228–9 MATERIALzoonosis 222 ganglia 211–13 coxal glands 232, 233–4 archaeocytes 28–9 giant nerve -
Ponderous Ark Aquaculture in Florida
The Potential of Blood Ark and Ponderous Ark Aquaculture in Florida Results of Spawning, Larval Rearing, Nursery and Growout Trials Leslie N. Sturmer, Jose M. Nuñez, R. LeRoy Creswell, and Shirley M. Baker TP-169 SEPTEMBER 2009 Cover illustration: Ann Meyers This research was supported by the Cooperative State Research, Education, and Extension Service of the U.S. Department of Agriculture (USDA) under USDA Special Research Grant No. 2002-3445-11946; and by the National Sea Grant College Program of the U.S. Department of Commerce’s National Oceanic and Atmosphere Administration (NOAA) under NOAA Grant No. NA06 OAR-4170014. The views expressed are those of the authors and do not necessarily reflect the views of these organizations. Additional copies are available by contacting: Shellfish Aquaculture Extension Program Florida Sea Grant University of Florida University of Florida PO Box 89 PO Box 110409 Cedar Key, FL 32625-0089 Gainesville, FL 32622-0409 (352)543-5057 (352) 392-2801 www.flseagrant.org TP 169 September 2009 The Potential of Blood Ark (Anadara ovalis) and Ponderous Ark (Noetia ponderosa) Aquaculture in Florida Results of Spawning, Larval Rearing, Nursery, and Growout Trials Leslie N. Sturmer Shellfish Aquaculture Extension Program Cooperative Extension Service Institute of Food and Agricultural Sciences University of Florida Cedar Key Jose M. Nuñez The Whitney Laboratory for Marine Bioscience University of Florida St. Augustine R. LeRoy Creswell Florida Sea Grant College Program Institute of Food and Agricultural Sciences University of Florida Fort Pierce Shirley M. Baker Fisheries and Aquatic Sciences Program School of Forest Resources and Conservation Institute of Food and Agricultural Sciences University of Florida Gainesville September 2009 TP 169 ii Preface In November 1999, a workshop on New Molluscs for Aquaculture was conducted by the University of Florida Cooperative Extension Service, Florida Sea Grant, and the Florida Department of Agriculture and Consumer Services. -
Olympia Oyster (Ostrea Lurida)
COSEWIC Assessment and Status Report on the Olympia Oyster Ostrea lurida in Canada SPECIAL CONCERN 2011 COSEWIC status reports are working documents used in assigning the status of wildlife species suspected of being at risk. This report may be cited as follows: COSEWIC. 2011. COSEWIC assessment and status report on the Olympia Oyster Ostrea lurida in Canada. Committee on the Status of Endangered Wildlife in Canada. Ottawa. xi + 56 pp. (www.sararegistry.gc.ca/status/status_e.cfm). Previous report(s): COSEWIC. 2000. COSEWIC assessment and status report on the Olympia Oyster Ostrea conchaphila in Canada. Committee on the Status of Endangered Wildlife in Canada. Ottawa. vii + 30 pp. (www.sararegistry.gc.ca/status/status_e.cfm) Gillespie, G.E. 2000. COSEWIC status report on the Olympia Oyster Ostrea conchaphila in Canada in COSEWIC assessment and update status report on the Olympia Oyster Ostrea conchaphila in Canada. Committee on the Status of Endangered Wildlife in Canada. Ottawa. 1-30 pp. Production note: COSEWIC acknowledges Graham E. Gillespie for writing the provisional status report on the Olympia Oyster, Ostrea lurida, prepared under contract with Environment Canada and Fisheries and Oceans Canada. The contractor’s involvement with the writing of the status report ended with the acceptance of the provisional report. Any modifications to the status report during the subsequent preparation of the 6-month interim and 2-month interim status reports were overseen by Robert Forsyth and Dr. Gerald Mackie, COSEWIC Molluscs Specialist Subcommittee Co-Chair. For additional copies contact: COSEWIC Secretariat c/o Canadian Wildlife Service Environment Canada Ottawa, ON K1A 0H3 Tel.: 819-953-3215 Fax: 819-994-3684 E-mail: COSEWIC/[email protected] http://www.cosewic.gc.ca Également disponible en français sous le titre Ếvaluation et Rapport de situation du COSEPAC sur l’huître plate du Pacifique (Ostrea lurida) au Canada. -
Quality Molluscan Genomes Jin Sun 1, Runsheng Li 2, Chong Chen 3, Julia D
bioRxiv preprint doi: https://doi.org/10.1101/2020.12.31.424979; this version posted January 2, 2021. 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. Benchmarking Oxford Nanopore read assemblers for high- quality molluscan genomes Jin Sun 1, Runsheng Li 2, Chong Chen 3, Julia D. Sigwart 4,5, Kevin M. Kocot 6* 1 Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China 2 Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong, China 3 X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa Prefecture 237-0061, Japan 4 Senckenberg Museum, Frankfurt, Germany 5 Queen’s University Belfast, Marine Laboratory, Portaferry, N Ireland 6 Department of Biological Sciences and Alabama Museum of Natural History, University of Alabama, Tuscaloosa, Alabama, 35487, USA Keywords: Molluscan genomes, assembly, Oxford Nanopore Technology, scaly-foot snail, Mytilus, phylogeny Summary Choosing the optimum assembly approach is essential to achieving a high-quality genome assembly suitable for comparative and evolutionary genomic investigations. Significant recent progress in long-read sequencing technologies such as PacBio and Oxford Nanopore Technologies (ONT) also brought about a large variety of assemblers. Although these have been extensively tested on model species such as Homo sapiens and Drosophila melanogaster, such benchmarking has not been done in Mollusca which lacks widely adopted model species.