The First Scallop
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Probabilistic Models of Species Discovery and Biodiversity
Probabilistic models of species discovery and biodiversity comparisons Stewart M. Ediea,1, Peter D. Smitsb, and David Jablonskia,b,1 aDepartment of the Geophysical Sciences, University of Chicago, Chicago, IL 60637; and bCommittee on Evolutionary Biology, University of Chicago, Chicago, IL 60637 Contributed by David Jablonski, February 16, 2017 (sent for review October 3, 2016; reviewed by Gene Hunt, Mark McPeek, and Andy Purvis) Inferring large-scale processes that drive biodiversity hinges on tion. We use this model to assess the stability of observed differ- understanding the phylogenetic and spatial pattern of species rich- ences in regional and among-clade diversity for a major animal ness. However, clades and geographic regions are accumulating group that has accrued newly described species at an unabated newly described species at an uneven rate, potentially affecting rate for the past 165 years: the marine bivalves. the stability of currently observed diversity patterns. Here, we In our Bayesian time series model [available from Zenodo present a probabilistic model of species discovery to assess the (doi.org/10.5281/zenodo.159033)], the number of species de- uncertainty in diversity levels among clades and regions. We use scribed in a given year is a function of the long- and short-term a Bayesian time series regression to estimate the long-term trend trends in description rate. We first model the trajectory of in the rate of species description for marine bivalves and find a dis- species accumulation using only the history of currently valid tinct spatial bias in the accumulation of new species. Despite these species description beginning with Linnaeus (14), the start- biases, probabilistic estimates of future species richness show con- ing point of formal taxonomy. -
Pectinoidea (Bivalvia: Propeamussiidae, Entoliidae and Pectinidae) from the Tarava Seamounts, Society Islands and the Tuamotu Archipelago (French Polynesia)
Pectinoidea (Bivalvia: Propeamussiidae, Entoliidae and Pectinidae) from the Tarava Seamounts, Society Islands and the Tuamotu Archipelago (French Polynesia) Henk H. DIJKSTRA Naturalis Biodiversity Center, Department of Marine Zoology, P.O. Box 9517, 2300 RA Leiden (The Netherlands) [email protected] Philippe MAESTRATI Muséum national d’Histoire naturelle, Département Systématique et Évolution, UMR 7138, case postale 51, 57, rue Cuvier, F-75231 Paris cedex 05 (France) [email protected] Dijkstra H. H. & Maestrati P. 2013. — Pectinoidea (Bivalvia: Propeamussiidae, Entoliidae and Pectinidae) from the Tarava Seamounts, Society Islands and the Tuamotu Archipelago (French Polynesia). Zoosystema 35 (3): 361-375. http://dx.doi.org/10.5252/z2013n3a2 ABSTRACT Eighteen species of Pectinoidea (six Propeamussiidae Abbott, 1954, one KEY WORDS Bivalvia, Entoliidae Teppner, 1922, eleven Pectinidae Rafinesque, 1815) are listed from French Polynesia, the Tarava Seamounts, Society Islands and Tuamotu Archipelago, French littoral, Polynesia. Four Propeamussiidae species (Parvamussium lamellatum n. sp., bathyal, new species, Parvamussium scutulatum n. sp., Parvamussium vesiculosum n. sp., Cyclopecten new records. comptulus n. sp.) are new to science. RÉSUMÉ Pectinoidea (Bivalvia: Propeamussiidae, Entoliidae and Pectinidae) des Monts sous- marins Tarava, des Îles de la Société et de l’Archipel des Tuamotu (Polynésie française). Dix-huit espèces de Pectinoidea (six Propeamussiidae Abbott, 1954, un Ento- MOTS CLÉS Bivalvia, liidae Teppner, 1922, onze Pectinidae Rafinesque, 1815) ont été récoltées des Polynésie française, Monts sous-marins Tarava, des Îles de la Société, et de l’Archipel des Tuamotu, littoral, Polynésie française. Quatre espèces de Propeamussiidae (Parvamussium lamel- bathyal, espèces nouvelles, latum n. sp., Parvamussium scutulatum n. sp., Parvamussium vesiculosum n. sp., nouvelles occurences. -
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 -
From the Indonesian Archipelago
A contribution to the knowledge of the pectinacean Mollusca (Bivalvia: Propeamussiidae, Entoliidae, Pectinidae) from the Indonesian Archipelago H.H. Dijkstra Dijkstra, H.H. A contribution to the knowledge of the pectinacean Mollusca (Bivalvia: Propea- mussiidae, Entoliidae, Pectinidae) from the Indonesian Archipelago. Zool. Verh. Leiden 271, 24.xii.l991: l-57, figs. 1-94, 1 table. — ISSN 0024-1652. Key words: Mollusca; Bivalvia; Propeamussiidae; Entoliidae; Pectinidae; taxonomy; Indonesia. Abstract: During the Indonesian-Dutch SNELLIUS -II Expedition (1984-1985) to the Indonesian Archipelago 46 pectinacean species were collected from the Flores Sea and Banda Sea (5°52'-9°57'S, 118°12'-123°58'E) at littoral to bathyal depth (835 m). One new pectinid genus, viz. Glorichlamys gen. nov., six new propeamussiids, viz. Parvamussium araneum spec. nov., Parvamussium carbaseum spec. nov., Parvamussium cassium spec. nov., Parvamussium undosum spec. nov., Parvamussium virgatum spec. nov., Cyclopecten cancellus spec. nov., and one new entoliid, viz. Pectinella aequoris spec. nov. are described. Twelve new records of Pectinacea for this region are mentioned. For Ostrea squamosa Gmelin, 1791 a lectotype is designated. In addition Pectinidae of the SNELLIUS-Expedition (1929- 1930) to the eastern region of Indonesia, and material collected by Dr B.W. Hoeksema near Sulawesi (1985, 1986) are reported upon. H.H. Dijkstra, Zoological Museum Amsterdam, P.O. Box 4766, 1009 AT Amsterdam, The Netherlands. Contents Introduction 3 Acknowledgements and abbreviations 5 Systematic part 6 Propeamussiidae 6 Entoliidae 23 Pectinidae 25 References 50 Index 55 Introduction For several centuries already Pectinidae are known from the Indonesian Archi• pelago. These were brought to Europe by explorers and commercial travellers. -
The Shell Matrix of the European Thorny Oyster, Spondylus Gaederopus: Microstructural and Molecular Characterization
The shell matrix of the european thorny oyster, Spondylus gaederopus: microstructural and molecular characterization. Jorune Sakalauskaite, Laurent Plasseraud, Jérôme Thomas, Marie Alberic, Mathieu Thoury, Jonathan Perrin, Frédéric Jamme, Cédric Broussard, Beatrice Demarchi, Frédéric Marin To cite this version: Jorune Sakalauskaite, Laurent Plasseraud, Jérôme Thomas, Marie Alberic, Mathieu Thoury, et al.. The shell matrix of the european thorny oyster, Spondylus gaederopus: microstructural and molecular characterization.. Journal of Structural Biology, Elsevier, 2020, 211 (1), pp.107497. 10.1016/j.jsb.2020.107497. hal-02906399 HAL Id: hal-02906399 https://hal.archives-ouvertes.fr/hal-02906399 Submitted on 17 Nov 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. The shell matrix of the European thorny oyster, Spondylus gaederopus: microstructural and molecular characterization List of authors: Jorune Sakalauskaite1,2, Laurent Plasseraud3, Jérôme Thomas2, Marie Albéric4, Mathieu Thoury5, Jonathan Perrin6, Frédéric Jamme6, Cédric Broussard7, Beatrice Demarchi1, Frédéric Marin2 Affiliations 1. Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123 Turin, Italy; 2. Biogeosciences, UMR CNRS 6282, University of Burgundy-Franche-Comté, 6 Boulevard Gabriel, 21000 Dijon, France. 3. Institute of Molecular Chemistry, ICMUB UMR CNRS 6302, University of Burgundy- Franche-Comté, 9 Avenue Alain Savary, 21000 Dijon, France. -
Methods and Materials for Aquaculture Production of Sea Scallops (Placopecten Magellanicus)
Methods and Materials for Aquaculture Production of Sea Scallops (Placopecten magellanicus) Dana L. Morse • Hugh S. Cowperthwaite • Nathaniel Perry • Melissa Britsch Contents Rationale and background. .1 Scallop biology . 1 Spat collection . 2 Nursery culture. 3 Growout. .4 Bottom cages . 4 Pearl nets. 5 Lantern nets. 5 Suspension cages . 6 Ear hanging. 6 Husbandry and fouling control. 7 Longline design and materials . 7 Moorings and mooring lines. 7 Longline (or backline) . 7 Tension buoys . 7 Marker buoys . 7 Compensation buoys . 8 Longline weights. 8 Site selection . 8 Economic considerations & recordkeeping . 8 Scallop products, biotoxins & public health . 8 Literature Cited. 9 Additional Reading. 9 Appendix I . 9 Example of an annual cash flow statement. 9 Acknowledgements . 9 Authors’ contact information Dana L. Morse Nathaniel Perry Maine Sea Grant and University of Maine Pine Point Oyster Company Cooperative Extension 10 Pine Ridge Road, Cape Elizabeth, ME 04107 193 Clark’s Cove Road, Walpole, ME 04573 [email protected] [email protected] Melissa Britsch Hugh S. Cowperthwaite University of Maine, Darling Marine Center Coastal Enterprises, Inc. 193 Clark’s Cove Road, Walpole, ME 04573 30 Federal Street, Brunswick, ME 04011 [email protected] [email protected] The University of Maine is an EEO/AA employer and does not discriminate on the grounds of race, color, religion, sex, sexual orientation, transgender status, gender expression, national origin, citizenship status, age, disability, genetic information or veteran’s status in employment, education, and all other programs and activities. The following person has been designated to handle inquiries regarding non-discrimination policies: Director of Equal Opportunity, 101 North Stevens Hall, University of Maine, Orono, ME 04469-5754, 207.581.1226, TTY 711 (Maine Relay System). -
New Report and Taxonomic Comparison of Anadara and Tegillarca Species of Arcidae (Bivalvia: Arcoidea) from Southern Coast of India
International Journal of Science and Research (IJSR) ISSN (Online): 2319-7064 Index Copernicus Value (2013): 6.14 | Impact Factor (2013): 4.438 New Report and Taxonomic Comparison of Anadara and Tegillarca Species of Arcidae (Bivalvia: Arcoidea) from Southern Coast of India Souji.S1, Tresa Radhakrishnan2 Department of Aquatic Biology and Fisheries, University of Kerala, Thiruvananthapuram-695 581, Kariyavattom, Kerala, India Abstract: Arcacea family is economically important group of animals. Most of the species in this family are misplaced into invalid subgenera and Indian arcids are wanted a revision in systematic positon. In the case of Arcidae family; all of the species are treated under Anadara as main genera, however, some authors considered that the Tegillarca genus is only a sub genus of Arcidae family. Anadara is the commercially important genus of bivalves of Arcidae family. These two genera are confused by many taxonomists and some considered that the morphometric changes of Tegillarca are only the habitual adaptation. But the collected samples from the same habitat from the southern part of India is clearly demarked the distinction between Anadara species and Tegillarca species. In this paper the differences between these two genera are illustrated with the help of specimens from the same habitat and with the help of taxonomic literature of these genera. Species level classification was done based on the morphometric characters like peculiarities of (i) periostracum, (ii) cardinal area, (iii) umbo, (iv) adductor muscle scar and (v) pallial line. The specimens were collected from Neendakara, Vizhinjam and Kovalam along with the south west coast and Thiruchendur in Tamil Nadu, south east coast of India. -
Early Ontogeny of Jurassic Bakevelliids and Their Bearing on Bivalve Evolution
Early ontogeny of Jurassic bakevelliids and their bearing on bivalve evolution NIKOLAUS MALCHUS Malchus, N. 2004. Early ontogeny of Jurassic bakevelliids and their bearing on bivalve evolution. Acta Palaeontologica Polonica 49 (1): 85–110. Larval and earliest postlarval shells of Jurassic Bakevelliidae are described for the first time and some complementary data are given concerning larval shells of oysters and pinnids. Two new larval shell characters, a posterodorsal outlet and shell septum are described. The outlet is homologous to the posterodorsal notch of oysters and posterodorsal ridge of arcoids. It probably reflects the presence of the soft anatomical character post−anal tuft, which, among Pteriomorphia, was only known from oysters. A shell septum was so far only known from Cassianellidae, Lithiotidae, and the bakevelliid Kobayashites. A review of early ontogenetic shell characters strongly suggests a basal dichotomy within the Pterio− morphia separating taxa with opisthogyrate larval shells, such as most (or all?) Praecardioida, Pinnoida, Pterioida (Bakevelliidae, Cassianellidae, all living Pterioidea), and Ostreoida from all other groups. The Pinnidae appear to be closely related to the Pterioida, and the Bakevelliidae belong to the stem line of the Cassianellidae, Lithiotidae, Pterioidea, and Ostreoidea. The latter two superfamilies comprise a well constrained clade. These interpretations are con− sistent with recent phylogenetic hypotheses based on palaeontological and genetic (18S and 28S mtDNA) data. A more detailed phylogeny is hampered by the fact that many larval shell characters are rather ancient plesiomorphies. Key words: Bivalvia, Pteriomorphia, Bakevelliidae, larval shell, ontogeny, phylogeny. Nikolaus Malchus [[email protected]], Departamento de Geologia/Unitat Paleontologia, Universitat Autòno− ma Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Spain. -
Abstract Volume
ABSTRACT VOLUME August 11-16, 2019 1 2 Table of Contents Pages Acknowledgements……………………………………………………………………………………………...1 Abstracts Symposia and Contributed talks……………………….……………………………………………3-225 Poster Presentations…………………………………………………………………………………226-291 3 Venom Evolution of West African Cone Snails (Gastropoda: Conidae) Samuel Abalde*1, Manuel J. Tenorio2, Carlos M. L. Afonso3, and Rafael Zardoya1 1Museo Nacional de Ciencias Naturales (MNCN-CSIC), Departamento de Biodiversidad y Biologia Evolutiva 2Universidad de Cadiz, Departamento CMIM y Química Inorgánica – Instituto de Biomoléculas (INBIO) 3Universidade do Algarve, Centre of Marine Sciences (CCMAR) Cone snails form one of the most diverse families of marine animals, including more than 900 species classified into almost ninety different (sub)genera. Conids are well known for being active predators on worms, fishes, and even other snails. Cones are venomous gastropods, meaning that they use a sophisticated cocktail of hundreds of toxins, named conotoxins, to subdue their prey. Although this venom has been studied for decades, most of the effort has been focused on Indo-Pacific species. Thus far, Atlantic species have received little attention despite recent radiations have led to a hotspot of diversity in West Africa, with high levels of endemic species. In fact, the Atlantic Chelyconus ermineus is thought to represent an adaptation to piscivory independent from the Indo-Pacific species and is, therefore, key to understanding the basis of this diet specialization. We studied the transcriptomes of the venom gland of three individuals of C. ermineus. The venom repertoire of this species included more than 300 conotoxin precursors, which could be ascribed to 33 known and 22 new (unassigned) protein superfamilies, respectively. Most abundant superfamilies were T, W, O1, M, O2, and Z, accounting for 57% of all detected diversity. -
TREATISE ONLINE Number 48
TREATISE ONLINE Number 48 Part N, Revised, Volume 1, Chapter 31: Illustrated Glossary of the Bivalvia Joseph G. Carter, Peter J. Harries, Nikolaus Malchus, André F. Sartori, Laurie C. Anderson, Rüdiger Bieler, Arthur E. Bogan, Eugene V. Coan, John C. W. Cope, Simon M. Cragg, José R. García-March, Jørgen Hylleberg, Patricia Kelley, Karl Kleemann, Jiří Kříž, Christopher McRoberts, Paula M. Mikkelsen, John Pojeta, Jr., Peter W. Skelton, Ilya Tëmkin, Thomas Yancey, and Alexandra Zieritz 2012 Lawrence, Kansas, USA ISSN 2153-4012 (online) paleo.ku.edu/treatiseonline PART N, REVISED, VOLUME 1, CHAPTER 31: ILLUSTRATED GLOSSARY OF THE BIVALVIA JOSEPH G. CARTER,1 PETER J. HARRIES,2 NIKOLAUS MALCHUS,3 ANDRÉ F. SARTORI,4 LAURIE C. ANDERSON,5 RÜDIGER BIELER,6 ARTHUR E. BOGAN,7 EUGENE V. COAN,8 JOHN C. W. COPE,9 SIMON M. CRAgg,10 JOSÉ R. GARCÍA-MARCH,11 JØRGEN HYLLEBERG,12 PATRICIA KELLEY,13 KARL KLEEMAnn,14 JIřÍ KřÍž,15 CHRISTOPHER MCROBERTS,16 PAULA M. MIKKELSEN,17 JOHN POJETA, JR.,18 PETER W. SKELTON,19 ILYA TËMKIN,20 THOMAS YAncEY,21 and ALEXANDRA ZIERITZ22 [1University of North Carolina, Chapel Hill, USA, [email protected]; 2University of South Florida, Tampa, USA, [email protected], [email protected]; 3Institut Català de Paleontologia (ICP), Catalunya, Spain, [email protected], [email protected]; 4Field Museum of Natural History, Chicago, USA, [email protected]; 5South Dakota School of Mines and Technology, Rapid City, [email protected]; 6Field Museum of Natural History, Chicago, USA, [email protected]; 7North -
Studies on Molluscan Shells: Contributions from Microscopic and Analytical Methods
Micron 40 (2009) 669–690 Contents lists available at ScienceDirect Micron journal homepage: www.elsevier.com/locate/micron Review Studies on molluscan shells: Contributions from microscopic and analytical methods Silvia Maria de Paula, Marina Silveira * Instituto de Fı´sica, Universidade de Sa˜o Paulo, 05508-090 Sa˜o Paulo, SP, Brazil ARTICLE INFO ABSTRACT Article history: Molluscan shells have always attracted the interest of researchers, from biologists to physicists, from Received 25 April 2007 paleontologists to materials scientists. Much information is available at present, on the elaborate Received in revised form 7 May 2009 architecture of the shell, regarding the various Mollusc classes. The crystallographic characterization of Accepted 10 May 2009 the different shell layers, as well as their physical and chemical properties have been the subject of several investigations. In addition, many researches have addressed the characterization of the biological Keywords: component of the shell and the role it plays in the hard exoskeleton assembly, that is, the Mollusca biomineralization process. All these topics have seen great advances in the last two or three decades, Shell microstructures expanding our knowledge on the shell properties, in terms of structure, functions and composition. This Electron microscopy Infrared spectroscopy involved the use of a range of specialized and modern techniques, integrating microscopic methods with X-ray diffraction biochemistry, molecular biology procedures and spectroscopy. However, the factors governing synthesis Electron diffraction of a specific crystalline carbonate phase in any particular layer of the shell and the interplay between organic and inorganic components during the biomineral assembly are still not widely known. This present survey deals with microstructural aspects of molluscan shells, as disclosed through use of scanning electron microscopy and related analytical methods (microanalysis, X-ray diffraction, electron diffraction and infrared spectroscopy). -
Appendices (3.601Mb)
University of Plymouth PEARL https://pearl.plymouth.ac.uk 04 University of Plymouth Research Theses 01 Research Theses Main Collection 2015 Palaeoecology of the late Permian mass extinction and subsequent recovery Foster, William J. http://hdl.handle.net/10026.1/5467 Plymouth University All content in PEARL is protected by copyright law. Author manuscripts are made available in accordance with publisher policies. Please cite only the published version using the details provided on the item record or document. In the absence of an open licence (e.g. Creative Commons), permissions for further reuse of content should be sought from the publisher or author. Appendix 2.1: Balaton Highlands and Bükk Mountains Investigated sites. The Permian-Triassic succession of Balaton Highlands comprises part of the ALCAPA megaunit (Kóvacs and Haas, 2010) and is represented by Permian fluvial red sandstones and Triassic shallow marine rocks. The Lower Triassic succession in the Balaton Highlands is divided into four formations: the Kóveskál Dolomite Formation, Arács Marl Formation, Hidegkút Formation and Csopak Marl Formation (Figure A2.1). These formations paraconformably overlay the Permian Baltonfelvidék Formation and are capped by the Middle Triassic Aszòfo Dolomite Formation (Haas et al., 2012). Field visits (June 2012) to the Balaton Highlands (Figure A2.2) recorded 5m of the Kóveskál Formation at Balatonfüred; 15m at Balataonálmadi; and 1m of the Csopak Marl Formation at the Sóly section. Broglio Loriga et al. (1990) studied the biostratigraphy of the entire succession, but their data, were acquired from a trench that is no longer exposed (János Haas, pers. comm.) and their collections were not available for study (Renato Posenato, pers.