Fish (Spinibarbus Hollandi) Dynamics in Relation to Changing Hydrological Conditions: Physical Modelling, Individual-Based Numerical Modelling, and Case Study
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Molecular phylogeny ofthe Puntius (Hamilton, 1822) based on nuclear gene RAG2 Faezeh Yazdani Moghaddam1, *, Mansour Aliabadian1, *, Siti Khalijah Daud2, Mahvash Seifali3 1Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran. 2Biology Department, Faculty of Science, Universiti Putra Malaysia, 43400UPM Serdang, Selangor, Malaysia. 3Department of Biology, Faculty of Science, University Alzahra, Tehran, Iran. Received: 11September 2012, 2012; Accepted: 24 November 2012 Abstract The tropical Asian cyprinid genus Puntius is a major part of the ichthyofauna in Southeast Asia. Systematic status of the genus Puntius among Cyprinidae, the most prominent freshwater fish all over the world, remain to be substantiated. The molecular phylogenetic analyses derived from Recombination activating genesequences (RAG2) for 35 representative samples of Malaysian Puntius and their allies, indicated paraphyly of the genus Puntius among common cyprinid groups of Southeast Asia. At a larger scale, while the monophyly of Cyprinidae and the subfamily Cyprininae were confirmed, the monophyly of the tribe Barbinini, Cyprinini, or Puntius (Systomus) were not supported. Keywords: Cyprinidae, Puntius, Systomus, recombination activating gene 2, phylogeny. Introduction which contains some 220 nominal species (about 120 of these considered valid), has seen a Family Cyprinidae with more than 3,268 species significant accretion of new species in recent and 321 genera is one of the largest freshwater years. Many species are traded internationally as fish families in the world, in which, phylogenetic ornamentals (Collins et al., 2012). Carrying the relationships among Malaysian cyprinids remain generic name, Puntius, was made familiar by largely unresolved (Cunha et al., 2002; Liu and Hamilton in 1822, but later researchers have used Chen, 2003). -
BMC Evolutionary Biology Biomed Central
BMC Evolutionary Biology BioMed Central Research article Open Access Evolution of miniaturization and the phylogenetic position of Paedocypris, comprising the world's smallest vertebrate Lukas Rüber*1, Maurice Kottelat2, Heok Hui Tan3, Peter KL Ng3 and Ralf Britz1 Address: 1Department of Zoology, The Natural History Museum, Cromwell Road, London SW7 5BD, UK, 2Route de la Baroche 12, Case postale 57, CH-2952 Cornol, Switzerland (permanent address) and Raffles Museum of Biodiversity Research, National University of Singapore, Kent Ridge, Singapore 119260 and 3Department of Biological Sciences, National University of Singapore, Kent Ridge, Singapore 119260 Email: Lukas Rüber* - [email protected]; Maurice Kottelat - [email protected]; Heok Hui Tan - [email protected]; Peter KL Ng - [email protected]; Ralf Britz - [email protected] * Corresponding author Published: 13 March 2007 Received: 23 October 2006 Accepted: 13 March 2007 BMC Evolutionary Biology 2007, 7:38 doi:10.1186/1471-2148-7-38 This article is available from: http://www.biomedcentral.com/1471-2148/7/38 © 2007 Rüber et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Paedocypris, a highly developmentally truncated fish from peat swamp forests in Southeast Asia, comprises the world's smallest vertebrate. Although clearly a cyprinid fish, a hypothesis about its phylogenetic position among the subfamilies of this largest teleost family, with over 2400 species, does not exist. -
Fish Fauna in Gianh River Basin, Quang Binh Province, North Centre Vietnam
STUDIA UNIVERSITATIS MOLDAVIAE, 2015, nr.1(81) Seria “{tiin\e reale [i ale naturii” ISSN 1814-3237 ISSN online 1857-498X p.138-147 FISH FAUNA IN GIANH RIVER BASIN, QUANG BINH PROVINCE, NORTH CENTRE VIETNAM Ho Anh TUAN, Ngo Xuan QUANG*, Laurenţia UNGUREANU**, Dumitru BULAT** Vinh University, Moldova State University *Institute of Tropical Biology – Ho Chi Minh city – Vietnam ** Institute of Zoology (Academy of Sciences of Moldova) We carried out 12 field surveys in 2003 - 2011 at 36 study sites and collected 5699 specimens. Over time of analysis, we have identified 181 fish species belong to 139 genera, 64 families of 16 orders of the ichthyofauna in Gianh River, 5 rare species recorded in the Red Book of Vietnam (2007), 84 species having economic value, 68 species in upstream, 64 species distributed in the middle, 61 species in downstream and 100 species in the estuary. Keywords: Cypriniformes, Perciformes, Fish fauna, Phong Nha – Ke Bang, classification, Vietnam, Gianh river, Quang Binh. IHTIOFAUNA DIN BAZINUL RÂULUI GIANH, PROVINCIA QUANG BINH, VIETNAMUL CENTRAL DE NORD În perioada anilor 2003-2011 au fost efectuate 12 cercetări de teren la 36 de situri şi au fost colectate 5699 de exemplare. În urma analizelor îndelungate am identificat 181 de specii de peşti din cadrul a 139 genuri, 64 de familii cuprinse în 16 ordine ale ihtiofaunei din bazinul râului Gianh. Dintre acestea, 5 specii rare sunt înregistrate în Cartea Roşie a Vietnamului (2007), iar 84 de specii au valoare economică. 68 de specii au fost colectate în amonte, 64 de specii distribuite în cursul mijlociu al râului, 61 de specii în aval şi 100 de specii din estuar. -
Minnows and Molecules: Resolving the Broad and Fine-Scale Evolutionary Patterns of Cypriniformes
Minnows and molecules: resolving the broad and fine-scale evolutionary patterns of Cypriniformes by Carla Cristina Stout A dissertation submitted to the Graduate Faculty of Auburn University in partial fulfillment of the requirements for the Degree of Doctor of Philosophy Auburn, Alabama May 7, 2017 Keywords: fish, phylogenomics, population genetics, Leuciscidae, sequence capture Approved by Jonathan W. Armbruster, Chair, Professor of Biological Sciences and Curator of Fishes Jason E. Bond, Professor and Department Chair of Biological Sciences Scott R. Santos, Professor of Biological Sciences Eric Peatman, Associate Professor of Fisheries, Aquaculture, and Aquatic Sciences Abstract Cypriniformes (minnows, carps, loaches, and suckers) is the largest group of freshwater fishes in the world. Despite much attention, previous attempts to elucidate relationships using molecular and morphological characters have been incongruent. The goal of this dissertation is to provide robust support for relationships at various taxonomic levels within Cypriniformes. For the entire order, an anchored hybrid enrichment approach was used to resolve relationships. This resulted in a phylogeny that is largely congruent with previous multilocus phylogenies, but has much stronger support. For members of Leuciscidae, the relationships established using anchored hybrid enrichment were used to estimate divergence times in an attempt to make inferences about their biogeographic history. The predominant lineage of the leuciscids in North America were determined to have entered North America through Beringia ~37 million years ago while the ancestor of the Golden Shiner (Notemigonus crysoleucas) entered ~20–6 million years ago, likely from Europe. Within Leuciscidae, the shiner clade represents genera with much historical taxonomic turbidity. Targeted sequence capture was used to establish relationships in order to inform taxonomic revisions for the clade. -
Three New Diplozoidae Mitogenomes Expose Unusual Compositional
Zhang et al. BMC Evolutionary Biology (2018) 18:133 https://doi.org/10.1186/s12862-018-1249-3 RESEARCH ARTICLE Open Access Three new Diplozoidae mitogenomes expose unusual compositional biases within the Monogenea class: implications for phylogenetic studies Dong Zhang1,2 , Hong Zou1, Shan G. Wu1, Ming Li1, Ivan Jakovlić3, Jin Zhang3, Rong Chen3, Wen X. Li1 and Gui T. Wang1* Abstract Background: As the topologies produced by previous molecular and morphological studies were contradictory and unstable (polytomy), evolutionary relationships within the Diplozoidae family and the Monogenea class (controversial relationships among the Discocotylinea, Microcotylinea and Gastrocotylinea suborders) remain unresolved. Complete mitogenomes carry a relatively large amount of information, sufficient to provide a much higher phylogenetic resolution than traditionally used morphological traits and/or single molecular markers. However, their implementation is hampered by the scarcity of available monogenean mitogenomes. Therefore, we sequenced and characterized mitogenomes belonging to three Diplozoidae family species, and conducted comparative genomic and phylogenomic analyses for the entire Monogenea class. Results: Taxonomic identification was inconclusive, so two of the species were identified merely to the genus level. The complete mitogenomes of Sindiplozoon sp. and Eudiplozoon sp. are 14,334 bp and 15,239 bp in size, respectively. Paradiplozoon opsariichthydis (15,385 bp) is incomplete: an approximately 2000 bp-long gap within a non-coding region could not be sequenced. Each genome contains the standard 36 genes (atp8 is missing). G + T content and the degree of GC- and AT-skews of these three mitogenome (and their individual elements) were higher than in other monogeneans. nad2, atp6 and nad6 were the most variable PCGs, whereas cox1, nad1 and cytb were the most conserved. -
Fish Species Composition, Distribution and Community Structure in The
www.nature.com/scientificreports OPEN Fish species composition, distribution and community structure in the lower reaches of Received: 16 October 2018 Accepted: 7 June 2019 Ganjiang River, Jiangxi, China Published: xx xx xxxx Maolin Hu 1,2,3, Chaoyang Wang1, Yizhen Liu1,2, Xiangyu Zhang1 & Shaoqing Jian1,3 The Ganjiang River (length: 823 km; drainage area: 82,809 km2) is the largest river that fows into Poyang Lake and an important tributary of the Yangtze River. In this study, fsh fauna were collected from 10 stations in the lower reaches of the river (YC: Yichun, XY: Xinyu, SG: Shanggao, GA: Ganan, ZS: Zhangshu, FC: Fengcheng, NC: Nanchang, QS: Qiaoshe, NX: Nanxin, CC: Chucha) from March 2017 to February 2018. The species composition and distribution as well as spatio-temporal variation in biodiversity and abundance were then examined. Overall, 12,680 samples comprising15 families and 84 species were collected, the majority of which belonged to the Order Cypriniformes (69.05% of the total species collected) and Cyprinidae (64.29%). Moreover, of these 84 species, 36 (42.86%) were endemic to China. Dominant species were Cyprinus carpio (index of relative importance (IRI): 17.19%), Pseudobrama simoni (IRI: 10.81%) and Xenocypris argentea (IRI: 10.20%). Subsequent cluster analysis divided the samples into three signifcantly diferent groups by sample site. Meanwhile, Margalef species richness and Shannon−Wiener diversity indices were both low, and along with analyses of abundance-biomass curves suggested moderate disturbance. Current threats to the conservation of fsh biodiversity in the lower reaches were also reviewed and management solutions suggested. The results will help form the basis for reasonable exploitation and protection of freshwater fsh in the lower reaches of the Ganjiang River. -
Fishes of the World
Fishes of the World Fishes of the World Fifth Edition Joseph S. Nelson Terry C. Grande Mark V. H. Wilson Cover image: Mark V. H. Wilson Cover design: Wiley This book is printed on acid-free paper. Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved. Published by John Wiley & Sons, Inc., Hoboken, New Jersey. Published simultaneously in Canada. No part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, recording, scanning, or otherwise, except as permitted under Section 107 or 108 of the 1976 United States Copyright Act, without either the prior written permission of the Publisher, or authorization through payment of the appropriate per-copy fee to the Copyright Clearance Center, 222 Rosewood Drive, Danvers, MA 01923, (978) 750-8400, fax (978) 646-8600, or on the web at www.copyright.com. Requests to the Publisher for permission should be addressed to the Permissions Department, John Wiley & Sons, Inc., 111 River Street, Hoboken, NJ 07030, (201) 748-6011, fax (201) 748-6008, or online at www.wiley.com/go/permissions. Limit of Liability/Disclaimer of Warranty: While the publisher and author have used their best efforts in preparing this book, they make no representations or warranties with the respect to the accuracy or completeness of the contents of this book and specifically disclaim any implied warranties of merchantability or fitness for a particular purpose. No warranty may be createdor extended by sales representatives or written sales materials. The advice and strategies contained herein may not be suitable for your situation. -
Complete Mitochondrial Genome of the Freshwater Fish Onychostoma Lepturum (Teleostei, Cyprinidae): Genome Characterization and Phylogenetic Analysis
ZooKeys 1005: 57–72 (2020) A peer-reviewed open-access journal doi: 10.3897/zookeys.1005.57592 RESEARCH ARTICLE https://zookeys.pensoft.net Launched to accelerate biodiversity research Complete mitochondrial genome of the freshwater fish Onychostoma lepturum (Teleostei, Cyprinidae): genome characterization and phylogenetic analysis I-Chen Wang1*, Hung-Du Lin2*, Chih-Ming Liang1, Chi-Chun Huang3, Rong-Da Wang4, Jin-Quan Yang4, Wei-Kuang Wang1 1 Department of Environmental Engineering and Science, Feng Chia University, Taichung 407, Taiwan 2 The Affiliated School of National Tainan First Senior High School, Tainan 701, Taiwan3 Taiwan Endemic Species Research Institute, Nantou 552, Taiwan 4 Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China Corresponding author: Wei-Kuang Wang ([email protected]) Academic editor: M.E. Bichuette | Received 13 August 2020 | Accepted 25 November 2020 | Published 18 December 2020 http://zoobank.org/92DDFB54-0FC4-404D-BF2C-7C0B373E2992 Citation: Wang I-C, Lin H-D, Liang C-M, Huang C-C, Wang R-D, Yang J-Q,Wang W-K (2020) Complete mitochondrial genome of the freshwater fish Onychostoma lepturum (Teleostei, Cyprinidae): genome characterization and phylogenetic analysis. ZooKeys 1005: 57–72. https://doi.org/10.3897/zookeys.1005.57592 Abstract The cyprinid genus Onychostoma Günther, 1896 consists of 24 valid species distributed in Southeast Asia, including Taiwan, Hainan, mainland China and the Indochina region. In the present study, we deter- mined the complete mitochondrial genome of O. lepturum, which is 16,598 bp in length, containing 13 protein-coding genes, two rRNA genes, 22 tRNA genes and a typical control region (D-loop). -
Cytogenetics of Two Onychostoma Species in Taiwan by Ag-NOR And
Zoological Studies 56: 25 (2017) doi:10.6620/ZS.2017.56-25 Cytogenetics of Two Onychostoma Species in Taiwan by Ag-NOR and 18S rDNA Profiles Chiao-Chuan Han1,2, Tsair-Bor Yen3, Nian-Cih Chen4, and Mei-Chen Tseng4,* 1National Museum of Marine Biology and Aquarium, Pingtung 944, Taiwan. E-mail: [email protected] 2Graduate Institute of Marine Biology, National Dong Hwa University, Hualien 974, Taiwan 3Department of Tropical Agriculture and International Cooperation, National Pingtung University of Science and Technology, Pingtung 912, Taiwan. E-mail: [email protected] 4Department of Aquaculture, National Pingtung University of Science and Technology, Pingtung 912, Taiwan (Received 5 June 2017; Accepted 5 September 2017; Published 25 September 2017; Communicated by Hin-Kiu Mok) Chiao-Chuan Han, Tsair-Bor Yen, Nian-Cih Chen, and Mei-Chen Tseng (2017) Both Onychostoma barbatulum and O. alticorpus are primary freshwater fish in Taiwan. The former has been developed as an aquaculture species with high economic value, while the latter is a native endemic species in Taiwan. Understanding the cytogenetic information of these two species is necessary for their selected breeding, recovery, and management. In this study, Giemsa staining, silver-binding nucleolar organizer region (Ag-NOR), C-banding, and fluorescence in situ hybridization (FISH) with 18S ribosomal (r)DNA probes were used to analyze the cytogenetic characteristics. Results of Giemsa staining showed that the two Onychostoma species shared the same number of chromosomes, 2n = 50. Respective karyotype formulas of the female and male were 10 m + 22 sm + 10 st + 8 t and 11 m + 22 sm + 10 st + 7 t in O. -
Cyprinid Phylogeny Based on Bayesian and Maximum Likelihood Analyses of Partitioned Data: Implications for Cyprinidae Systematics
SCIENCE CHINA Life Sciences • RESEARCH PAPER • September 2012 Vol.55 No.9: 761–773 doi: 10.1007/s11427-012-4366-z Cyprinid phylogeny based on Bayesian and maximum likelihood analyses of partitioned data: implications for Cyprinidae systematics WANG XuZhen1, GAN XiaoNi1, LI JunBing1, MAYDEN Richard L.2 & HE ShunPing1* 1Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; 2Department of Biology, Saint Louis University, Saint Louis, Missouri 63103-2010, USA Received April 25, 2012; accepted July 16, 2012 Cyprinidae is the biggest family of freshwater fish, but the phylogenetic relationships among its higher-level taxa are not yet fully resolved. In this study, we used the nuclear recombination activating gene 2 and the mitochondrial 16S ribosomal RNA and cytochrome b genes to reconstruct cyprinid phylogeny. Our aims were to (i) demonstrate the effects of partitioned phylo- genetic analyses on phylogeny reconstruction of cyprinid fishes; (ii) provide new insights into the phylogeny of cyprinids. Our study indicated that unpartitioned strategy was optimal for our analyses; partitioned analyses did not provide better-resolved or -supported estimates of cyprinid phylogeny. Bayesian analyses support the following relationships among the major mono- phyletic groups within Cyprinidae: (Cyprininae, Labeoninae), ((Acheilognathinae, ((Leuciscinae, Tincinae), Gobioninae)), Xenocyprininae). The placement of Danioninae was poorly resolved. Estimates of divergence dates within the family showed that radiation of the major cyprinid groups occurred during the Late Oligocene through the Late Miocene. Our phylogenetic analyses improved our understanding of the evolutionary history of this important fish family. Cyprinidae, phylogeny, molecular dating, partitioned analyses Citation: Wang X Z, Gan X N, Li J B, et al. -
Molecular Variation and Evolution of the Tyrosine Kinase Domains of Insulin Receptor Ira and Irb Genes in Cyprinidae
SCIENCE CHINA Life Sciences • RESEARCH PAPERS • July 2011 Vol.54 No.7: 626–633 doi: 10.1007/s11427-011-4189-3 Molecular variation and evolution of the tyrosine kinase domains of insulin receptor IRa and IRb genes in Cyprinidae KONG XiangHui1,2, WANG XuZhen2 & HE ShunPing2* 1College of Life Science, Henan Normal University, Xinxiang 453007, China; 2Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China Received December 3, 2010; accepted May 30, 2011; published online June 23, 2011 The insulin receptor (IR) gene plays an important role in regulating cell growth, differentiation and development. In the present study, DNA sequences of insulin receptor genes, IRa and IRb, were amplified and sequenced from 37 representative species of the Cyprinidae and from five outgroup species from non-cyprinid Cypriniformes. Based on coding sequences (CDS) of tyro- sine kinase regions of IRa and IRb, molecular evolution and phylogenetic relationships were analyzed to better understand the characteristics of IR gene divergence in the family Cyprinidae. IRa and IRb were clustered into one lineage in the gene tree of the IR gene family, reconstructed using the unweighted pair group method with arithmetic mean (UPGMA). IRa and IRb have evolved into distinct genes after IR gene duplication in Cyprinidae. For each gene, molecular evolution analyses showed that there was no significant difference among different groups in the reconstructed maximum parsimony (MP) tree of Cyprinidae; IRa and IRb have been subjected to similar evolutionary pressure among different lineages. Although the amino acid sequences of IRa and IRb tyrosine kinase regions were highly conserved, our analyses showed that there were clear sequence variations between the tyrosine kinase regions of IRa and IRb proteins. -
Inland Fisheries Resource Enhancement and Conservation in Asia Xi RAP PUBLICATION 2010/22
RAP PUBLICATION 2010/22 Inland fisheries resource enhancement and conservation in Asia xi RAP PUBLICATION 2010/22 INLAND FISHERIES RESOURCE ENHANCEMENT AND CONSERVATION IN ASIA Edited by Miao Weimin Sena De Silva Brian Davy FOOD AND AGRICULTURE ORGANIZATION OF THE UNITED NATIONS REGIONAL OFFICE FOR ASIA AND THE PACIFIC Bangkok, 2010 i The designations employed and the presentation of material in this information product do not imply the expression of any opinion whatsoever on the part of the Food and Agriculture Organization of the United Nations (FAO) concerning the legal or development status of any country, territory, city or area or of its authorities, or concerning the delimitation of its frontiers or boundaries. The mention of specific companies or products of manufacturers, whether or not these have been patented, does not imply that these have been endorsed or recommended by FAO in preference to others of a similar nature that are not mentioned. ISBN 978-92-5-106751-2 All rights reserved. Reproduction and dissemination of material in this information product for educational or other non-commercial purposes are authorized without any prior written permission from the copyright holders provided the source is fully acknowledged. Reproduction of material in this information product for resale or other commercial purposes is prohibited without written permission of the copyright holders. Applications for such permission should be addressed to: Chief Electronic Publishing Policy and Support Branch Communication Division FAO Viale delle Terme di Caracalla, 00153 Rome, Italy or by e-mail to: [email protected] © FAO 2010 For copies please write to: Aquaculture Officer FAO Regional Office for Asia and the Pacific Maliwan Mansion, 39 Phra Athit Road Bangkok 10200 THAILAND Tel: (+66) 2 697 4119 Fax: (+66) 2 697 4445 E-mail: [email protected] For bibliographic purposes, please reference this publication as: Miao W., Silva S.D., Davy B.