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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 Erosa Harvested from the Wild
ISSN pending (print) PEERS Inc. Multidisciplinary Research Journal (Available at www.peersinc.org) ISSN 2546-0099 (online) Vol. 1, Issue 1, pp. 1-9, January-March, 2017 1 ESTIMATION OF THE EDIBLE WET TISSUE WEIGHT OF THE MANGROVE CLAM POLYMESODA EROSA HARVESTED FROM THE WILD Authors: Biona, Marvin A.; Marte, Clarisse R.; Pasadilla, Aimee Lou G.; Araneta, Bryan Yves G. ABSTRACT A technique on estimating the edible wet tissue weight of the common mangrove clam, Polymesoda erosa captured from the wild was established using Multiple Regression Analysis of five morphometric measurements namely, 1. Shell Length (SL), 2. Shell Width (SW), 3. Shell Height (SH), 4. Shell Volume (SV), and 5. Live Weight (LW). Pearson’s R showed highly significant correlations between the 5 estimating variables and Edible Wet Tissue Weight (WTW) indicating a strong link between them. Multiple Regression Analysis was not directly used to test for the best estimator because of the high correlation between the 5 independent variables. Instead, it was performed to create an estimation formula that will take into consideration all the contributions of the independent variables (SL, SW, SH, SV, and LW) to the estimation of the Edible Wet Tissue Weight. One-Way ANOVA at 0.05 level of significance however showed that there is a significant difference in terms of the contribution of the 5 estimator variables. B-values point to Shell Width and Shell Volume to have a significant contribution to the estimation formula. After considering all five estimators, the Edible Wet Tissue Weight of P. erosa can be estimated as follows: Estimated Wet Tissue Weight= -10.689 (constant) + (0.109 x SL) + (0.122 x SW) + (0.026 x SH) + (0.008 x LW) + (0.045 x SV). -
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 -
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Advances in Oceanography and Limnology, 2018; 9(2): 97-104 ARTICLE DOI: 10.4081/aiol.2018.7857 This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License (CC BY-NC 4.0). Unraveling the complexity of Corbicula clams invasion in Lake Garda (Italy) Joaquín López-Soriano,1* Sergio Quiñonero-Salgado,1 Cristina Cappelletti,2 Filippo Faccenda,2 Francesca Ciutti2 1Associació Catalana de Malacologia-Museu Blau, Plaça Leonardo da Vinci 4-5, Barcelona, Spain; 2Technology Transfer Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy ABSTRACT Lake Garda, the largest Italian lake, is suffering from the introduction of several non-indigenous species during the last decades and can now be considered one of the main European freshwater hotspots of xenodiversity. Among the Bivalvia (Veneroidea, Cyrenidae), Corbicula fluminea and Corbicula fluminalis were first recorded in 2002 and 2008 respectively, and are now widespread in the southern part of the basin. Recent observation of specimens that did not resemble either of these taxa, suggested that the populations of invasive Corbicula of Lake Garda could include some other taxa not previously recorded. With this aim, a thoroughly characterization of Corbicula shells found at Lake Garda was made. By studying morphometric parameters and comparing them with specimens collected in Spain (Ebro and Ter rivers), the presence in Lake Garda of two other related species not previously recorded in Italy, namely C. leana and C. largillierti, has been confirmed. The syntopic presence of at least four species of this genus in a single environment is a singular occurrence both in Italy and Europe. -
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. -
(Bivalvia, Corbiculidae) Na América Do Sul: Histórico De Introdução, Linhagens Androgênicas E Genética Da Invasão
UNIVERSIDADE FEDERAL DO PARANÁ SANDRA LUDWIG CORBICULA SPP. (BIVALVIA, CORBICULIDAE) NA AMÉRICA DO SUL: HISTÓRICO DE INTRODUÇÃO, LINHAGENS ANDROGÊNICAS E GENÉTICA DA INVASÃO CURITIBA 2015 1 SANDRA LUDWIG CORBICULA (BIVALVIA, CORBICULIDAE) SPP. NA AMÉRICA DO SUL: HISTÓRICO DE INTRODUÇÃO, LINHAGENS ANDROGÊNICAS E GENÉTICA DA INVASÃO Tese apresentada ao Programa de Pós- Graduação em Ciências Biológicas – Zoologia, Setor de Ciências Biológicas da Universidade Federal do Paraná, como requisito parcial à obtenção do título de Doutor em Ciências Biológicas área de concentração Zoologia. Orientador: Walter A. P. Boeger, PhD Co-orientador: Dr. Gustavo Darrigran CURITIBA 2015 2 3 AGRADECIMENTOS Ao professor Dr. Walter A. Boeger, por todos os ensinamentos compartilhados, paciência e compreensão. Ao meu co-orientador Professor Dr. Gustavo Darrigran pela difícil tarefa de me co-orientar à distância e por todos os ensinamentos compartilhados durante os quatro anos. À minha querida família, aos meus pais - Francisco e Luzia Ludwig – por terem me apoiado, por sempre estarem com as mãos estendidas a mim. Obrigada por todos os sacrifícios sofridos pela minha vida e minha formação. A minha irmã Luana, pelo exemplo de coragem, determinação, pelo incentivo, pelas sugestões e correções, e acima de tudo, pela amizade incondicional. Agradeço ao meu marido, André Tochetto, pelo companheirismo e pelos esforços em me incentivar desde o começo a nunca desistir de meus sonhos e, batalhar para ser uma profissional dedicada. À minha amiga, Nefertiris por ter me ajudado, apoiado, puxado minha orelha, me consolado e, acima de tudo, pela sua amizade. À minha amiga Patrícia que tem me ajudado com as inúmeras discussões sobre o futuro da área de invasões no Brasil. -
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).