Clam Polymesoda Erosa Harvested from the Wild
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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 -
(Polymesoda Expansa) in the Panikel Village, Segara Anakan, Cilacap
E3S Web of Conferences 147, 02018 (2020) https://doi.org/10.1051/e3sconf/202014702018 3rd ISMFR The Population of Mangrove Clam (Polymesoda expansa) in The Panikel Village, Segara Anakan, Cilacap Widianingsih Widianingsih* , Ria Azizah Tri Nuraini, Ita Riniatsih, Retno Hartati, Sri Redjeki, Hadi Endrawati, Elsa Lusia Agus, and Robertus Triaji Mahendrajaya Department of Marine Sciences, Faculty Fisheries and Marine Sciences, Diponegoro University, Jl. Prof. Sudharto, Tembalang, Semarang, Central Java, Indonesia Abstract. Mangrove clam Polymesoda expansa belonged to the family Corbiculidae. The clam itself is a semi-infauna that lives partially below the soft sediment around the roots of mangrove trees. The purpose of this research is to study the population P. expansa in Panikel Area, Segara Anakan, Cilacap. The size of the sampling site for this research was 10x10 m. Mangrove clam P. expansa was taken by handpicking. Sampling was conducted in April and June 2019. The water quality parameters were taken in-situ. According to the research result, the highest population of P. expansa in Panikel occurred in June amounting to 85 individuals. In the Panikel area, P. expansa has a positive correlation between the total weight and shell length not only in April but also in June. It can be concluded that the mangrove area in Panikel Village is suitable for supporting P. expamsa population. 1 Introduction Segara Anakan is one of the largest estuaries on Java Island. It is a mangrove shallow coastal lagoon located in South Central Java (108°46’ E–109°03’ E, 8°35’ S–8°48’ S (Fig 1). It is separated from the Indian Ocean by the rocky mountainous Island of Nusakambangan [1]. -
Paleocene Freshwater, Brackish-Water and Marine Molluscs from Al-Khodh, Oman
Late Cretaceous to ?Paleocene freshwater, brackish-water and marine molluscs from Al-Khodh, Oman Simon Schneider, heinz A. KollmAnn & mArtin PicKford Bivalvia and Gastropoda from the late Campanian to Maastrichtian deltaic Al-Khodh Formation and from the overlying ?Paleocene shallow marine Jafnayn Limestone Formation of northeastern Oman are described. Freshwater bivalves include three species of Unionidae, left in open nomenclature, due to limited preservation. These are the first pre-Pleistocene unionids recorded from the Arabian Peninsula, where large freshwater bivalves are absent today. Brackish-water bivalves are represented by two species of Cyrenidae. Geloina amithoscutana sp. nov. extends the range of Geloina to the Mesozoic and to ancient Africa. Muscatella biszczukae gen. et sp. nov. has a unique combination of characters not shared with other genera in the Cyrenidae. Brackish-water gastropods comprise Stephaniphera coronata gen. et sp. nov. in the Hemisinidae; Subtemenia morgani in the new genus Subtemenia (Pseudomelaniidae); Cosinia sp. (Thiaridae); Pyrazus sp. (Batillariidae); and Ringiculidae sp. indet. From the Jafnayn Limestone Formation, several marginal marine mollusc taxa are also reported. The fossils are assigned to four mollusc communities and associations, which are indicative of different salinity regimes. • Key words: Unionidae, Cyrenidae, Pseudomelaniidae, Hemisinidae, taxonomy, palaeobiogeography. SCHNEIDER, S., KOLLMANN, H.A. & PICKFORD, M. 2020. Late Cretaceous to ?Paleocene freshwater, brackish-water and marine molluscs from Al-Khodh, Oman. Bulletin of Geosciences 95(2), 179–204 (10 figures, 5 tables). Czech Geo- l ogical Survey, Prague. ISSN 1214-1119. Manuscript received August 12, 2019; accepted in revised form March 30, 2020; published online May 30, 2020; issued May 30, 2020. -
Discovery of the Carolina Marsh Clam, Polymesoda Caroliniana (Bosc), a Supposed Florida Disjunct Species, in Everglades National Park, Florida
Gulf and Caribbean Research Volume 3 Issue 2 January 1971 Discovery of the Carolina Marsh Clam, Polymesoda caroliniana (Bosc), A Supposed Florida Disjunct Species, in Everglades National Park, Florida D.C. Tabb D.R. Moore Follow this and additional works at: https://aquila.usm.edu/gcr Part of the Marine Biology Commons Recommended Citation Tabb, D. and D. Moore. 1971. Discovery of the Carolina Marsh Clam, Polymesoda caroliniana (Bosc), A Supposed Florida Disjunct Species, in Everglades National Park, Florida. Gulf Research Reports 3 (2): 265-281. Retrieved from https://aquila.usm.edu/gcr/vol3/iss2/8 DOI: https://doi.org/10.18785/grr.0302.08 This Article is brought to you for free and open access by The Aquila Digital Community. It has been accepted for inclusion in Gulf and Caribbean Research by an authorized editor of The Aquila Digital Community. For more information, please contact [email protected]. DISCOVERY OF THE CAROLINA MARSH CLAM, POLYMESODA CAROIJINIANA (BOSC) ,A SUPPOSED FLORIDA DISJUNCT SPECIES, IN EVERGLADES NATIONAL PARK, FLORIDA' by D. C. Tabb and D. R. Moore INTRODUCTION The presence of disjunct species of animals on either side of the Florida peninsula has been reported by a number of authors. The littorinid mollusk, Littorina irrorata Say, which has a range from Massachusetts to the Rio Grande of Texas, except for south Florida, is one such species (Bequaert 1943). The marsh crab, Sesarma cinemum (Bosc) , is another example of an animal with a distribution from Virginia to the western Gulf of Campeche except for a break in southern Florida (Rathbun, 1918). -
Clam (Polymesoda Sp.) Density at Various Habitats of Mangrove Forest in Kendari Bay Southeast Sulawesi
Clam (Polymesoda sp.) Density at Various Habitats of Mangrove Forest in Kendari bay Southeast Sulawesi Bahtiar Faculty of Fisheries and Marine Sciences University of Halu Oleo *Corresponding author: [email protected] Abstract Clams are bivalves that have been associated with mangrove forest in Kendari Bay for decades. These clams have experienced ecological pressures as their exploitation is increasingand degradation of mangrove forest occurred extensively. This research was conducted from November 2013 to October 2014 in mangrove area of Kendari Bay to determine its density in various habitat conditions of the mangrove forest. Three sampling stations were chosen based upon the mangrove density, namely station I was a thick density of mangrove, station II was located in areas with low density of mangrove, and station III was a medium density of mangrove with intensive clam exploitation. The clam and substrate sampling as well as measurement of mangrove density were done using quadratic transects that were taken perpendicular to the sea during low tide. The clam density was analyzed using standard formula, whereas the suitability of clam habitat was analyzed using principal component analysis and cluster analysis on multivariate statistical packages program. The result showed that the clam density was found higher at station I (13.65±3.74 ind.m-2) than station II and III that was 6.62 ± 2.46 ind.m-2and 5.72±1.53ind.m-2, respectively. The high density of clam at station I is characterized by the high mangrove density of each category of seedlings (3,200 ind.ha-1), saplings (2,960 ind.ha-1) and trees (180 ind.ha-1).At station I, there was higher silt fraction (3.454) and soil organic matter content compared to other sampling stations, suggesting that those factors contributed to the high density of clams. -
Noaa 13648 DS1.Pdf
r LOAI<CO Qpy N Guide to Gammon Tidal IVlarsh Invertebrates of the Northeastern Gulf of IVlexico by Richard W. Heard UniversityofSouth Alabama, Mobile, AL 36688 and CiulfCoast Research Laboratory, Ocean Springs, MS39564" Illustrations by rimed:tul""'"' ' "=tel' ""'Oo' OR" Iindu B. I utz URt,i',"::.:l'.'.;,',-'-.,":,':::.';..-'",r;»:.",'> i;."<l'IPUS Is,i<'<i":-' "l;~:», li I lb~'ab2 Thisv,ork isa resultofreseaich sponsored inpart by the U.S. Department ofCommerce, NOAA, Office ofSea Grant, underGrani Nos. 04 8 Mol 92,NA79AA D 00049,and NA81AA D 00050, bythe Mississippi Alabama SeaGrant Consortium, byche University ofSouth Alabama, bythe Gulf Coast Research Laboratory, andby the Marine EnvironmentalSciences Consortium. TheU.S. Government isauthorized toproduce anddistribute reprints forgovern- inentalpurposes notwithstanding anycopyright notation that may appear hereon. *Preseitt address. This Handbook is dedicated to WILL HOLMES friend and gentleman Copyright! 1982by Mississippi hlabama SeaGrant Consortium and R. W. Heard All rightsreserved. No part of thisbook may be reproduced in any manner without permissionfrom the author. Printed by Reinbold Lithographing& PrintingCo., BooneviBe,MS 38829. CONTENTS 27 PREFACE FamilyMysidae OrderTanaidacea Tanaids!,....... 28 INTRODUCTION FamilyParatanaidae........, .. 29 30 SALTMARSH INVERTEBRATES ., FamilyApseudidae,......,... Order Cumacea 30 PhylumCnidaria =Coelenterata!......, . FamilyNannasticidae......,... 31 32 Class Anthozoa OrderIsopoda Isopods! 32 Fainily Edwardsiidae. FamilyAnthuridae -
A Supplementary Nutritional Source to the Mangrove Clam-Polymesoda Erosa
Chemoautotrophy at the Expense of Thiosulphate: A Supplementary Nutritional Source to the Mangrove Clam-Polymesoda Erosa TresaRemya A Thomas CSIR-National Institute of Oceanography Tanya Singh 2CSIR-National Institute of Oceanography Tamil S Kalaimani 2CSIR-National Institute of Oceanography Nandakumar H Khadge CSIR-National Institute of Oceanography Mamatha S Shivaramu CSIR-National Institute of Oceanography Maria-Judith B-D Gonsalves CSIR-National Institute of Oceanography LokaBharathi P Adhikesavan ( [email protected] ) National Institute of Oceanography CSIR Research Article Keywords: Chemoautotrophy, 14C uptake, Polymesoda erosa, spawning phases, mangrove ecosystem Posted Date: June 15th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-561495/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/25 Abstract Chemolithoautotrophy is a primordial process, where chemical energy converts inorganic carbon to organic. The prevalence of chemosynthesis was examined in the mangrove clam, Polymesoda erosa, and the ambient sediment at Chorao Island, Mandovi estuary, Goa. The sediment system is reducing, organically rich, high in electron donors, acceptors, and inorganic carbon. This clam thrives by immersing 75-90% of its body in suldic sediments. Hence, it is hypothesized that it could have an adaptive 2- mechanism like microbially mediated utilization of reduced sulfur compound, S2O3 (model compound) coupled to inorganic carbon uptake. During spawning, maximum carbonate uptake rates of 449 and 594 nmole C g dry wt-1 h-1 were recorded in the gill and foot, respectively. Next generation sequencing revealed that Thiothrix and other sulfur oxidizers gathered from ambient sediment were present in gill, mantle and foot in the ratio 1:3:14 and 1:5:6, respectively. -
Keanekaragaman Bivalvia Di Ekosistem Mangrove Kecamatan Syiah Kuala Kota Banda Aceh Sebagai Penunjang Praktikum Ekologi Hewan
KEANEKARAGAMAN BIVALVIA DI EKOSISTEM MANGROVE KECAMATAN SYIAH KUALA KOTA BANDA ACEH SEBAGAI PENUNJANG PRAKTIKUM EKOLOGI HEWAN SKRIPSI Diajukan Oleh: SRI AFRRIYANTI NIM. 281324898 Mahasiswa Fakultas Tarbiyah dan Keguruan Program Studi Pendidikan Biologi FAKULTAS TARBIYAH DAN KEGURUAN UNIVERSITAS ISLAM NEGERI AR-RANIRY DARUSSALAM – BANDA ACEH 2020 M/ 1441 H SRI AFRRIYANTI NIM. 281324898 Mahasiswa Fakultas Tarbiyah dan Keguruan Program Studi Pendidikan Biologi ii iii , iv ABSTRAK Bivalvia meupakan salah satu Kelas dari Filum Moluska. Bivalvia menempati habitat di dasar perairan yang berlumpur atau berpasir, beberapa hidup pada substrat yang lebih keras seperti lempeng kayu atau batu. Keanekaragaman Bivalvia di Ekosistem Mangrove dapat dijadikan referensi pada praktikum Mata Kuliah Ekologi Hewan pada materi fauna terestrial dan fauna perairan. Ekosistem mangrove Kecamatan Syiah Kuala merupakan salah satu habitat dari Bivalvia yang keanekaragamannya belum pernah dilaporkan. Penelitian ini bertujuan untuk mengetahui keanekaragaman Bivalvia dan untuk mengetahui pemanfaatan hasil penelitian keanekaragaman Bivalvia di ekosistem mangrove Kecamatan Syiah Kuala Kota Banda Aceh Sebagai Penunjang Praktikum Mata Kuliah Ekologi Hewan. Metode yang digunakan dalam penelitian ini adalah metode kombinasi transek garis dan transek kuadrat. Teknik pengambilan sampel penelitian dengan teknik purposive sampling. Lokasi pengambilan sampel terbagi dalam 4 stasiun, yaitu ekosistem mangrove Deah raya, ekosistem mangrove Rukoh, ekosistem mangrove Baet dan ekosistem mangrove di Tibang. Berdasarkan hasil penelitian diketahui bahwa terdapat 11 jenis Bivalvia dari 6 Ordo, yaitu Arcoida, Veneroida, Anisomyria, Ostreoida, Venerida dan Cardiida. Keanekaragaman Bivalvia secara keseluruhan tergolong sedang dengan nilai Ĥ yaitu 1.204149758. Pemanfaatan hasil penelitian keanekaragaman Bivalvia di ekosistem mangrove Kecamatan Syiah Kuala sebagai penunjang praktikum Ekologi Hewan yaitu dalam bentuk buku saku. -
Morphometric Variation Among Three Local Mangrove Clam Species of Corbiculidae
Songklanakarin J. Sci. Technol. 37 (1), 15-20, Jan. - Feb. 2015 http://www.sjst.psu.ac.th Original Article Morphometric variation among three local mangrove clam species of Corbiculidae Hadi Hamli*, Azimah Abdul Rahim, Mohd Hanafi Idris, Abu Hena Mustafa Kamal, and Wong Sing King Department of Animal Science and Fishery, Faculty of Agriculture and Food Sciences, Universiti Putra Malaysia, Bintulu Sarawak Campus, P.O. Box 396, Nyabau Road, Bintulu, Sarawak, 97008 Malaysia. Received: 12 March 2014; Accepted: 8 December 2014 Abstract Three common species of Corbiculidae (Polymesda erosa, P. bengalensis and P. expansa) can be found inhabiting the mangrove areas in Southeast Asia. The morphometric variations of three species were examined based on 15 morphometric characters. A total of 16 populations from six localities were analyzed in the present study. Analysis of variance had revealed significant differences (P<0.05) for LCT/SL and VPM/SL for proportion ratio on morphometric variables among species. Cluster analysis for these populations formed two groups at 70% of similarity. Morphometric characteristics, such as LCT and VPM, of Corbiculidae are proposed to differentiate these three species. Keywords: Corbiculidae, morphometric analysis, mangrove clam, Sarawak, wetland 1. Introduction Corbiculidae can be found in the mangrove area because it is a suitable place to support many types of organisms and Corbiculidae is grouped under bivalvia class, a source of plenty of nutrients (Macintosh et al., 2002). heterodonta subclass (Okutani, 2000). One of the important Malaysia has several places with mangrove such as Sarawak characters that are used to differentiate them with other mangrove forest which covers 173,792 ha from the total of bivalve family is the present of heterodon type of tooth at land (Paul, 2011). -
Patterns of Freshwater Bivalve Global Diversity and the State of Phylogenetic Studies on the Unionoida, Sphaeriidae, and Cyrenidae Author(S): Daniel L
Patterns of Freshwater Bivalve Global Diversity and the State of Phylogenetic Studies on the Unionoida, Sphaeriidae, and Cyrenidae Author(s): Daniel L. Graf Source: American Malacological Bulletin, 31(1):135-153. 2013. Published By: American Malacological Society DOI: http://dx.doi.org/10.4003/006.031.0106 URL: http://www.bioone.org/doi/full/10.4003/006.031.0106 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. Amer. Malac. Bull. 31(1): 135–153 (2013) Patterns of freshwater bivalve global diversity and the state of phylogenetic studies on the Unionoida, Sphaeriidae, and Cyrenidae* Daniel L. Graf Department of Biological Sciences, University of Alabama, Tuscaloosa Alabama 35487 U.S.A. Department of Biology, University of Wisconsin-Stevens Point, Stevens Point Wisconsin 54481 U.S.A. (current address) Correspondence, Daniel Graf: [email protected] Abstract. The objective of this paper is to review the current state of our knowledge of freshwater bivalve diversity and evolution in order to identify some of the “Great Unanswered Questions” in the fi eld. -
Mollusca: Bivalvia
AR-1580 11 MOLLUSCA: BIVALVIA Robert F. McMahon Arthur E. Bogan Department of Biology North Carolina State Museum Box 19498 of Natural Sciences The University of Texas at Arlington Research Laboratory Arlington, TX 76019 4301 Ready Creek Road Raleigh, NC 27607 I. Introduction A. Collecting II. Anatomy and Physiology B. Preparation for Identification A. External Morphology C. Rearing Freshwater Bivalves B. Organ-System Function V. Identification of the Freshwater Bivalves C. Environmental and Comparative of North America Physiology A. Taxonomic Key to the Superfamilies of III. Ecology and Evolution Freshwater Bivalvia A. Diversity and Distribution B. Taxonomic Key to Genera of B. Reproduction and Life History Freshwater Corbiculacea C. Ecological Interactions C. Taxonomic Key to the Genera of D. Evolutionary Relationships Freshwater Unionoidea IV. Collecting, Preparation for Identification, Literature Cited and Rearing I. INTRODUCTION ament uniting the calcareous valves (Fig. 1). The hinge lig- ament is external in all freshwater bivalves. Its elasticity North American (NA) freshwater bivalve molluscs opens the valves while the anterior and posterior shell ad- (class Bivalvia) fall in the subclasses Paleoheterodonta (Su- ductor muscles (Fig. 2) run between the valves and close perfamily Unionoidea) and Heterodonta (Superfamilies them in opposition to the hinge ligament which opens Corbiculoidea and Dreissenoidea). They have enlarged them on adductor muscle relaxation. gills with elongated, ciliated filaments for suspension feed- The mantle lobes and shell completely enclose the ing on plankton, algae, bacteria, and microdetritus. The bivalve body, resulting in cephalic sensory structures be- mantle tissue underlying and secreting the shell forms a coming vestigial or lost. Instead, external sensory struc- pair of lateral, dorsally connected lobes. -
Dense Transcriptome Sampling Drastically Improves the Bivalve Tree of Life
Resolving the relationships of clams and royalsocietypublishing.org/journal/rspb cockles: dense transcriptome sampling drastically improves the bivalve tree of life Sarah Lemer1,2,Ru¨diger Bieler3 and Gonzalo Giribet2 Research 1University of Guam Marine Laboratory, 303 University Drive, UOG Station, Mangilao, GU 96923, USA 2 Cite this article: Lemer S, Bieler R, Giribet G. Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA 2019 Resolving the relationships of clams and 3Integrative Research Center, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, cockles: dense transcriptome sampling IL 60605, USA drastically improves the bivalve tree of life. SL, 0000-0003-0048-7296 Proc. R. Soc. B 286: 20182684. http://dx.doi.org/10.1098/rspb.2018.2684 Bivalvia has been the subject of extensive recent phylogenetic work to attempt resolving either the backbone of the bivalve tree using transcriptomic data, or the tips using morpho-anatomical data and up to five genetic markers. Yet the first approach lacked decisive taxon sampling and the second failed to resolve Received: 27 November 2018 many interfamilial relationships, especially within the diverse clade Impari- Accepted: 11 January 2019 dentia. Here we combine dense taxon sampling with 108 deep-sequenced Illumina-based transcriptomes to provide resolution in nodes that required additional study. We designed specific data matrices to address the poorly resolved relationships within Imparidentia. Our results support the overall backbone of the bivalve tree, the monophyly of Bivalvia and all its main Subject Category: nodes, although the monophyly of Protobranchia remains less clear.