Ghost Nipper (Trypaea Australiensis)
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Evolutionary History of Inversions in the Direction of Architecture-Driven
bioRxiv preprint doi: https://doi.org/10.1101/2020.05.09.085712; this version posted May 10, 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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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-NC 4.0 International license. Evolutionary history of inversions in the direction of architecture- driven mutational pressures in crustacean mitochondrial genomes Dong Zhang1,2, Hong Zou1, Jin Zhang3, Gui-Tang Wang1,2*, Ivan Jakovlić3* 1 Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China. 2 University of Chinese Academy of Sciences, Beijing 100049, China 3 Bio-Transduction Lab, Wuhan 430075, China * Corresponding authors Short title: Evolutionary history of ORI events in crustaceans Abbreviations: CR: control region, RO: replication of origin, ROI: inversion of the replication of origin, D-I skew: double-inverted skew, LBA: long-branch attraction bioRxiv preprint doi: https://doi.org/10.1101/2020.05.09.085712; this version posted May 10, 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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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-NC 4.0 International license. Abstract Inversions of the origin of replication (ORI) of mitochondrial genomes produce asymmetrical mutational pressures that can cause artefactual clustering in phylogenetic analyses. It is therefore an absolute prerequisite for all molecular evolution studies that use mitochondrial data to account for ORI events in the evolutionary history of their dataset. -
Systematics, Phylogeny, and Taphonomy of Ghost Shrimps (Decapoda): a Perspective from the Fossil Record
73 (3): 401 – 437 23.12.2015 © Senckenberg Gesellschaft für Naturforschung, 2015. Systematics, phylogeny, and taphonomy of ghost shrimps (Decapoda): a perspective from the fossil record Matúš Hyžný *, 1, 2 & Adiël A. Klompmaker 3 1 Geological-Paleontological Department, Natural History Museum Vienna, Burgring 7, 1010 Vienna, Austria; Matúš Hyžný [hyzny.matus@ gmail.com] — 2 Department of Geology and Paleontology, Faculty of Natural Sciences, Comenius University, Mlynská dolina, Ilkovičova 6, SVK-842 15 Bratislava, Slovakia — 3 Florida Museum of Natural History, University of Florida, 1659 Museum Road, PO Box 117800, Gaines- ville, FL 32611, USA; Adiël A. Klompmaker [[email protected]] — * Correspond ing author Accepted 06.viii.2015. Published online at www.senckenberg.de/arthropod-systematics on 14.xii.2015. Editor in charge: Stefan Richter. Abstract Ghost shrimps of Callianassidae and Ctenochelidae are soft-bodied, usually heterochelous decapods representing major bioturbators of muddy and sandy (sub)marine substrates. Ghost shrimps have a robust fossil record spanning from the Early Cretaceous (~ 133 Ma) to the Holocene and their remains are present in most assemblages of Cenozoic decapod crustaceans. Their taxonomic interpretation is in flux, mainly because the generic assignment is hindered by their insufficient preservation and disagreement in the biological classification. Fur- thermore, numerous taxa are incorrectly classified within the catch-all taxonCallianassa . To show the historical patterns in describing fos- sil ghost shrimps and to evaluate taphonomic aspects influencing the attribution of ghost shrimp remains to higher level taxa, a database of all fossil species treated at some time as belonging to the group has been compiled: 250 / 274 species are considered valid ghost shrimp taxa herein. -
Synopsis of the Family Callianassidae, with Keys to Subfamilies, Genera and Species, and the Description of New Taxa (Crustacea: Decapoda: Thalassinidea)
ZV-326 (pp 03-152) 02-01-2007 14:37 Pagina 3 Synopsis of the family Callianassidae, with keys to subfamilies, genera and species, and the description of new taxa (Crustacea: Decapoda: Thalassinidea) K. Sakai Sakai, K. Synopsis of the family Callianassidae, with keys to subfamilies, genera and species, and the description of new taxa (Crustacea: Decapoda: Thalassinidea). Zool. Verh. Leiden 326, 30.vii.1999: 1-152, figs 1-33.— ISSN 0024-1652/ISBN 90-73239-72-9. K. Sakai, Shikoku University, 771-1192 Tokushima, Japan, e-mail: [email protected]. Key words: Crustacea; Decapoda; Thalassinidae; Callianassidae; synopsis. A synopsis of the family Callianassidae is presented. Defenitions are given of the subfamilies and genera. Keys to the sufamilies, genera, as well as seperate keys to the species occurring in certain bio- geographical areas are provided. At least the synonymy, type-locality, and distribution of the species are listed. The following new taxa are described: Calliapaguropinae subfamily nov., Podocallichirus genus nov., Callianassa whitei spec. nov., Callianassa gruneri spec. nov., Callianassa ngochoae spec. nov., Neocallichirus kempi spec. nov. and Calliax doerjesti spec. nov. Contents Introduction ............................................................................................................................. 3 Systematics .............................................................................................................................. 7 Subfamily Calliapaguropinae nov. ..................................................................................... -
Nonbreeding Eastern Curlews Numenius Madagascariensis Do
Division of Comparative Physiology and Biochemistry, Society for Integrative and Comparative Biology Nonbreeding Eastern Curlews Numenius madagascariensis Do Not Increase the Rate of Intake or Digestive Efficiency before Long‐Distance Migration because of an Apparent Digestive Constraint Author(s): Yuri Zharikov and Gregory A. Skilleter Source: Physiological and Biochemical Zoology, Vol. 76, No. 5 (September/October 2003), pp. 704-715 Published by: The University of Chicago Press. Sponsored by the Division of Comparative Physiology and Biochemistry, Society for Integrative and Comparative Biology Stable URL: http://www.jstor.org/stable/10.1086/376427 . Accessed: 04/11/2015 23:25 Your use of the JSTOR archive indicates your acceptance of the Terms & Conditions of Use, available at . http://www.jstor.org/page/info/about/policies/terms.jsp . JSTOR is a not-for-profit service that helps scholars, researchers, and students discover, use, and build upon a wide range of content in a trusted digital archive. We use information technology and tools to increase productivity and facilitate new forms of scholarship. For more information about JSTOR, please contact [email protected]. The University of Chicago Press and Division of Comparative Physiology and Biochemistry, Society for Integrative and Comparative Biology are collaborating with JSTOR to digitize, preserve and extend access to Physiological and Biochemical Zoology. http://www.jstor.org This content downloaded from 23.235.32.0 on Wed, 4 Nov 2015 23:25:52 PM All use subject to JSTOR Terms and Conditions 704 Nonbreeding Eastern Curlews Numenius madagascariensis Do Not Increase the Rate of Intake or Digestive Efficiency before Long- Distance Migration because of an Apparent Digestive Constraint Yuri Zharikov1,* Introduction Gregory A. -
Methods Collecting Axiidea and Gebiidea (Decapoda): a Review 5-21 Ann
ZOBODAT - www.zobodat.at Zoologisch-Botanische Datenbank/Zoological-Botanical Database Digitale Literatur/Digital Literature Zeitschrift/Journal: Annalen des Naturhistorischen Museums in Wien Jahr/Year: 2015 Band/Volume: 117B Autor(en)/Author(s): Dworschak Peter C. Artikel/Article: Methods collecting Axiidea and Gebiidea (Decapoda): a review 5-21 Ann. Naturhist. Mus. Wien, B 117 5–21 Wien, Jänner 2015 Methods collecting Axiidea and Gebiidea (Decapoda): a review P.C. Dworschak* Abstract Axiidea and Gebiidae (formerly treated together as Thalassinidea) have a crypic lifestyle. Collecting these shrimp therefore requires special field methods. The present paper reviews these methods according to habitats and provides recommendations as well as data on their efficiency. In addition, information on the preservation of these animals is presented. Key words: Thalassinidea, Axiidea, Gebiidea, method, collecting, preservation Zusammenfassung Maulwurfskrebse aus den zwei Unterordungen der zehnfüßigen Krebes Axiidea und Gebiidea (früher zusammengefaßt als Thalassinidea) kommen in temperaten, subtropischen und tropischen Meeren vor und zeichnen sich durch ein Leben im Verborgenen aus. Viele Arten legen tiefe und ausgedehnte Bauten an. Diese Lebensweise erfordert eigene Methoden, um die Krebse zu fangen. Die verschiedenen Fangmethoden werden hier vorgestellt und Angaben zur Effizienz gemacht. Zusätzlich werden Angaben zur Fixierung und Konservierung der Krebse präsentiert. Introduction Formerly treated together as the thalassinideans, the infraorders Gebiidea DE SAINT LAURENT, 1979 and Axiidea DE SAINT LAURENT, 1979 represent two distinctly separate groups of decapods (ROBLES et al. 2009; BRACKEN et al. 2009; DWORSCHAK et al. 2012, POORE et al., 2014). They are commonly called mud shrimp or ghost shrimp, although they are only distantly related to true (dendrobranchiate or caridean) shrimp. -
New Gene Order Rearrangements and Distinct Patterns of Codons Usage In
Manuscript to be reviewed Digging deeper: New gene order rearrangements and distinct patterns of codons usage in mitochondrial genomes among shrimps from the Axiidea, Gebiidea and Caridea (Crustacea: Decapoda) Mun Hua Tan 1, 2 , Han Ming Gan Corresp., 1, 2 , Yin Peng Lee 1, 2 , Gary C. B. Poore 3 , Christopher M Austin 1, 2, 4 1 School of Science, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia 2 Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia 3 Museum of Victoria, Melbourne, Victoria, Australia 4 School of Life and Environmental Sciences, Deakin University, Burwood, Australia Corresponding Author: Han Ming Gan Email address: [email protected] Background. Whole mitochondrial DNA is being increasingly utilized for comparative genomic and phylogenetic studies at deep and shallow evolutionary levels for a range of taxonomic groups. Although mitogenome sequences are deposited at an increasing rate into public databases, their taxonomic representation is unequal across major taxonomic groups. In the case of decapod crustaceans, several infraorders, including Axiidea (ghost shrimps, sponge shrimps, mud lobsters) and Caridea (true shrimps), are still under-represented, limiting comprehensive phylogenetic studies that utilize mitogenomic information. Methods. Sequence reads from partial genome scans were generated using the Illumina MiSeq platform and mitogenome sequences were assembled from these low coverage reads. In addition to examine phylogenetic relationships within the three infraorders, Axiidea, Gebiidea and Caridea, we also investigated the diversity and frequency of codon usage bias and mitogenome gene order rearrangements. Results. We present new mitogenome sequences for five shrimp species from Australia that includes two ghost shrimps, Callianassa ceramica and Trypaea australiensis, along with three caridean shrimps, Macrobrachium bullatum, Alpheus lobidens and Caridina cf. -
440 FELDER.P65
DIVERSITY AND ECOLOGICAL SIGNIFICANCE OF DEEP-BURROWING MACROCRUSTACEANS IN COASTAL TROPICAL WATERS OF THE AMERICAS (DECAPODA: THALASSINIDEA) DARRYL L. FELDER cology of thalassin- row construction by the laomediid idean shrimp in in- INFRAORDER: THALASSINIDEA Latreille, 1831 Axianassa australis Rodrigues and tertidal and subtidal Shimizu in Brazil (Dworschak and marine and estuarine habitats has Superfamily - Thalassinoidea Dana, 1852 Rodrigues, 1997) and recruitment and gained growing attention in literature Family - Thalassinidae Dana, 1852 growth of the callianassid Lepidoph- of the last decade. Most recent eco- thalmus sinuensis Lemaitre and Rodri- logical focus has been accorded to a Superfamily - Callianassoidea Dana, 1852 gues on the Caribbean coast of Co- limited set of genera assignable to * Family - Callianassidae Dana, 1852 lombia (Nates and Felder, 1999). Eco- several of the eleven families com- Callianassa sensu stricto, Biffarius, logical studies at the community and prising this infraorder (see * in box). Neotrypaea, Trypaea, Lepidophthalmus, ecosystems level form a larger body In accord with Tudge et al. (2000), Callichirus, Sergio, Nihonotrypaea, Glypturus, of recent work, which calls attention the preferred nomenclature does not Corallianassa, Eucalliax, Neocallichirus, to varied roles of thalassinidean popu- conform to that proposed by Sakai “C.” tyrrhena, “C.” candida, “C.” filholi, lations in determining assemblage (1999). Also, as used here, the abbre- “C.” truncata,“C.” kraussi, “C.” laurae structure and their involvement -
An Introduced Asian Parasite Threatens Northeastern Pacific
Biol Invasions DOI 10.1007/s10530-011-0151-3 ORIGINAL PAPER An introduced Asian parasite threatens northeastern Pacific estuarine ecosystems John W. Chapman • Brett R. Dumbauld • Gyo Itani • John C. Markham Received: 25 November 2010 / Accepted: 30 November 2011 Ó Springer Science+Business Media B.V. (outside the USA) 2011 Abstract The introduced Asian parasitic bopyrid its impacts have remained in doubt. Six criteria reveal isopod, Orthione griffenis, was first discovered on the that Orthione is introduced to North America: its Pacific coast of North America in Washington in 1988 conspecificity with disjunct Asian populations, its and next in California in 1992. The range of Orthione earliest (1950s) collections in Asia, its late discovery presently extends from British Columbia to Baja among symbiotic species associated with Upogebia, California, where it infests at least two species of the its historical absence, and its appearance in North native estuary mud shrimp, Upogebia. Intense Orthi- America coincident with extensive new ballast water one infestations are associated with the apparent traffic from Asia. Orthione is the first recognized demise of many local populations of Upogebia bopyrid isopod invasion globally. Coexistence of U. pugettensis yet nonindigenous origins of Orthione in pugettensis, which are ecosystem engineers, with its North America and thus the ecological significance of newly acquired parasite cannot be assumed. Orthione threatens eastern Pacific estuary ecosystems where Upogebia were previously abundant. Electronic supplementary material The online version of this article (doi:10.1007/s10530-011-0151-3) contains Keywords Isopod Á Parasite Á Estuary Á Extinction Á supplementary material, which is available to authorized users. -
And Nutrients: Consequences for Benthic Community Structure and Ecosystem Functioning
Interactions between ecosystem engineering by burrowing sandprawns (Callichirus kraussi) and nutrients: consequences for benthic community structure and ecosystem functioning Welly Qwabe Dissertation Submitted for the degree of Doctor of PhilosophyTown in the Department of Biological Sciences University of Cape Town Cape Supervisor: of Dr Deena Pillay University University of Cape Town, Faculty of Science Department of Biological Sciences Rondebosch, 7701 Cape Town South Africa The copyright of this thesis vests inTown the author. No quotation from it or information derived from it is to be published without full acknowledgement of the source. The thesis is to be used for private study or non- commercial research purposes Capeonly. of Published by the University of Cape Town (UCT) in terms of the non-exclusive license granted to UCT by the author. University TABLE OF CONTENT Page Plagiarism declaration………………………………………………………………………………………….…. 1 Acknowledgments………………………………………………………………………………………………….. 2 Abstracts…………………………………………………………………………………………………………………. 4 CHAPTER 1: INTRODUCTION AND LITERATURE REVIEW……………………………….………. 8 1.1 The ecosystem engineering concept……………………………………………………………….… 9 1.2 Development and controversies regarding the concept of ecosystem engineering……………………………………............................................................................ 10 1.3 Ecosystem engineering in intertidal soft-sediment habitats…………………………….… 12 1.4 The burrowing sandprawn Callichirus kraussi: organism of this study………........... 1 6 1.5 Ecosystem engineering -
CALL Call CALL
click for previous page 239 2.3.3 FAMILY CALLIANASSIDAE Dana, 1852 CALL Callianassidae Dana, 1852 Proceedinqs Academv Natural Sciences, Philadelphia, 6:l2, 14. Name placed on the Official List of Family Names in Zoology, in Opinion 434 (published in 1956). Recent studies of the family do not agree on the number of genera to be recognized. De Saint Laurent (1973, 1979) divided the family into 9 genera, while Poore & Griffin (1979) only recognized three, as several of their species of Callianassa S.I. could not be assigned with confidence to any of De Saint Laurent’s genera. Poore & Griffin therefore only recognized the genera Callianassa Leach, 1814, Ctenocheles Kishinouye, 1926, and Gourretia De Saint Laurent, 1973, and placed all the other genera recognized by De Saint Laurent in the synonymy of Callianassa. Recently, Manning & Felder (1986:437-443) redefined the genus Callichirus Stimpson, 1866, placing in it 4 species formerly assigned to Callianassa; they convincingly showed Callichirus to be distinct from Callianassa s.l. None of the four species at present known to belong to Callichirus has been reported to be of economic importance. Without taking a definite stand on the generic taxonomy of the Callianassidae, I recognize here, for purely practical reasons, only the genera Callianassa, Callichirus, Ctenocheles and Gourretia. All species reported to be of interest to fisheries belong to the genus Callianassa s.l. as accepted here. Callianassa Leach, 1814 CALL Call Callianassa Leach, 1814, Brewster’s Edinburqh Encyclopaedia, 7:400. Gender feminine. Name placed on the Official List of Generic Names in Zoology by the International Commission on Zoological Nomenclature in their Opinion 434 (published in 1956). -
Influence of Trypaea Australiensis Population Density on Benthic
Journal of Sea Research 61 (2009) 144–152 Contents lists available at ScienceDirect Journal of Sea Research journal homepage: www.elsevier.com/locate/seares Influence of Trypaea australiensis population density on benthic metabolism and nitrogen dynamics in sandy estuarine sediment: A mesocosm simulation Mark A. Jordan a, David T. Welsh a,⁎, Ryan J.K. Dunn b, Peter R. Teasdale a a Australian Rivers Institute and School of Environment, Griffith University Gold Coast campus, Qld 4222, Australia b Griffith School of Engineering, Griffith University Gold Coast campus, Qld 4222, Australia article info abstract Article history: Laboratory mesocosm incubations were undertaken to investigate the influence of natural densities of the Received 31 January 2008 thalassinidean shrimp, Trypaea australiensis (marine yabby) on sediment oxygen demand (SOD), inorganic Received in revised form 3 November 2008 nutrient fluxes, and the N-cycle processes of nitrification, denitrification and dissimilatory nitrate reduction Accepted 24 November 2008 to ammonium (DNRA). Mesocosms (~0.1 m2 ×55 cm deep) of sieved, natural T. australiensis inhabited sands Available online 7 December 2008 were continually flushed with fresh seawater and pre-incubated for two weeks prior to being assigned to one of three treatments; control (no additions), low yabby density (40 T. australiensis m− 2) or high yabby density Keywords: − 2 – fl Bioturbation (80 T. australiensis m ). Thereafter, SOD and sediment water column inorganic nutrient uxes were fi fi Trypaea australiensis determined periodically over a 38 day period. On the nal day rates of denitri cation and dissimilatory 15 Nutrient Dynamics nitrate reduction to ammonium (DNRA) were also determined using the N-isotope pairing technique. -
Population Structure and Fecundity of Upogebia Omissa (Decapoda: Gebiidea: Upogebiidae) in an Estuarine Region in Sergipe, Northeastern Brazil
Pesquisa e Ensino em Ciências ISSN 2526-8236 (online edition) Exatas e da Natureza Pesquisa e Ensino em Ciências 2(2): 95–104 (2018) ARTICLE Research and Teaching in Exatas e da Natureza © 2018 UFCG / CFP / UACEN Exact and Natural Sciences Population structure and fecundity of Upogebia omissa (Decapoda: Gebiidea: Upogebiidae) in an estuarine region in Sergipe, northeastern Brazil Rafael de Carvalho Santos1,2, Luiz Filipe Santos Silva3, Bruna dos Santos3, Juliana Menezes Motta3 & Douglas Fernandes Rodrigues Alves1,4 (1) Universidade Federal de Sergipe, Centro de Ciências Biológicas e da Saúde, Departamento de Biologia, Laboratório de Carcinologia, Rosa Elze, São Cristóvão 49100-000, Sergipe, Brazil. E-mail: [email protected] (2) Universidade Estadual Paulista, Faculdade de Ciências de Bauru, Departamento de Ciências Biológicas, Laboratório de Biologia de Camarões Marinhos e de Água Doce (LABCAM), Bauru 81531-980, São Paulo, Brazil. (3) Universidade Federal de Sergipe, Centro de Ciências Biológicas e da Saúde, Departamento de Biologia, Rosa Elze, São Cristóvão 49100-000, Sergipe, Brazil. (4) Universidade Estadual Paulista, Instituto de Biociências, Departamento de Zoologia, Group of Studies on Crustacean Biology, Ecology and Culture (NEBECC), Botucatu 18618-000, São Paulo, Brazil. E-mail: [email protected] Santos R.C., Silva L.F.S., Santos B., Motta J.M. & Alves D.F.R. (2018) Population structure and fecundity of Upogebia omissa (Decapoda: Gebiidea: Upogebiidae) in an estuarine region in Sergipe, northeastern Brazil. Pesquisa e Ensino em Ciências Exatas e da Natureza, 2(2): 95–104. http://dx.doi.org/10.29215/pecen.v2i2.1064 Academic editor: Mauro de Melo Júnior. Received: 06 April 2018.