13. Kneriidae = 13. Kneriidae
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Constraints on the Timescale of Animal Evolutionary History
Palaeontologia Electronica palaeo-electronica.org Constraints on the timescale of animal evolutionary history Michael J. Benton, Philip C.J. Donoghue, Robert J. Asher, Matt Friedman, Thomas J. Near, and Jakob Vinther ABSTRACT Dating the tree of life is a core endeavor in evolutionary biology. Rates of evolution are fundamental to nearly every evolutionary model and process. Rates need dates. There is much debate on the most appropriate and reasonable ways in which to date the tree of life, and recent work has highlighted some confusions and complexities that can be avoided. Whether phylogenetic trees are dated after they have been estab- lished, or as part of the process of tree finding, practitioners need to know which cali- brations to use. We emphasize the importance of identifying crown (not stem) fossils, levels of confidence in their attribution to the crown, current chronostratigraphic preci- sion, the primacy of the host geological formation and asymmetric confidence intervals. Here we present calibrations for 88 key nodes across the phylogeny of animals, rang- ing from the root of Metazoa to the last common ancestor of Homo sapiens. Close attention to detail is constantly required: for example, the classic bird-mammal date (base of crown Amniota) has often been given as 310-315 Ma; the 2014 international time scale indicates a minimum age of 318 Ma. Michael J. Benton. School of Earth Sciences, University of Bristol, Bristol, BS8 1RJ, U.K. [email protected] Philip C.J. Donoghue. School of Earth Sciences, University of Bristol, Bristol, BS8 1RJ, U.K. [email protected] Robert J. -
Testing the Potential of Environmental DNA Methods for Surveying Lake Tanganyika's Highly Diverse Fish Communities Christopher J
Testing the potential of environmental DNA methods for surveying Lake Tanganyika's highly diverse fish communities Christopher James Doble A thesis submitted for the degree of Doctor of Philosophy Department of Genetics, Evolution and Environment University College London April 2020 1 Declaration I, Christopher James Doble, confirm the work presented in this thesis is my own. Where information has been derived from other sources, I confirm this has been indicated in the thesis. Christopher James Doble Date: 27/04/2020 2 Statement of authorship I planned and undertook fieldwork to the Kigoma region of Lake Tanganyika, Tanzania in 2016 and 2017. This included obtaining research permits, collecting environmental DNA samples and undertaking fish community visual survey data used in Chapters three and four. For Chapter two, cichlid reference database sequences were sequenced by Walter Salzburger’s research group at the University of Basel. I extracted required regions from mitochondrial genome alignments during a visit to Walter’s research group. Other reference sequences were obtained by Sanger sequencing. I undertook the DNA extractions and PCR amplifications for all samples, with the clean-up and sequencing undertaken by the UCL Sequencing facility. I undertook the method development, DNA extractions, PCR amplifications and library preparations for each of the next generation sequencing runs in Chapters three and four at the NERC Biomolecular Analysis Facility Sheffield. Following training by Helen Hipperson at the NERC Biomolecular Analysis Facility in Sheffield, I undertook the bioinformatic analysis of sequence data in Chapters three and four. I also carried out all the data analysis within each chapter. Chapters two, three and parts of four have formed a manuscript recently published in Environmental DNA (Doble et al. -
The Covert World of Fish Biofluorescence: a Phylogenetically Widespread and Phenotypically Variable Phenomenon
City University of New York (CUNY) CUNY Academic Works Publications and Research Baruch College 2014 The Covert World of Fish Biofluorescence: A Phylogenetically Widespread and Phenotypically Variable Phenomenon John S. Sparks American Museum of Natural History Robert C. Schelly American Museum of Natural History W. Leo Smith University of Kansas Matthew P. Davis University of Kansas Dan Tchernov University of Haifa See next page for additional authors How does access to this work benefit ou?y Let us know! More information about this work at: https://academicworks.cuny.edu/bb_pubs/29 Discover additional works at: https://academicworks.cuny.edu This work is made publicly available by the City University of New York (CUNY). Contact: [email protected] Authors John S. Sparks, Robert C. Schelly, W. Leo Smith, Matthew P. Davis, Dan Tchernov, Vincent A. Pieribone, and David F. Gruber This article is available at CUNY Academic Works: https://academicworks.cuny.edu/bb_pubs/29 The Covert World of Fish Biofluorescence: A Phylogenetically Widespread and Phenotypically Variable Phenomenon John S. Sparks1,2*., Robert C. Schelly1,2, W. Leo Smith3, Matthew P. Davis3, Dan Tchernov4, Vincent A. Pieribone1,5, David F. Gruber2,6*. 1 Department of Ichthyology, American Museum of Natural History, Division of Vertebrate Zoology, New York, New York United States of America, 2 Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America, 3 Biodiversity Institute, University of Kansas, Lawrence, Kansas, United States of America, 4 Marine Biology Department, The Leon H. Charney School of Marine Sciences, University of Haifa, Mount Carmel, Haifa, Israel, 5 Department of Cellular and Molecular Physiology, The John B. -
Teleostei: Gonorynchiformes)
Mesozoic Fishes 5 – Global Diversity and Evolution, G. Arratia, H.-P. Schultze & M. V. H. Wilson (eds.): pp. 325-362, 21 figs., 2 tabs., 2 apps. © 2013 by Verlag Dr. Friedrich Pfeil, München, Germany – ISBN 978-3-89937-159-8 The fi rst fossil shellear and its implications for the evolution and divergence of the Kneriidae (Teleostei: Gonorynchiformes) Matthew P. DAVIS, Gloria ARRATIA and Thomas M. KAISER Abstract A new genus and species of shellear (Gonorynchiformes: Kneriidae), †Mahengichthys singidaensis, is described from the Eocene Mahenge deposits in Tanzania, Africa. This work represents the first record of a fossil kneriid gonorynchiform fish. Previously, all gonorynchiform fossils have been attributed to either the families Chanidae or Gonorynchidae, with some taxa incertae sedis. We explore the phylogenetic position of †Mahengichthys singidaensis within the gonorynchiforms, utilizing parsimony and maximum likelihood methodologies that incorporate both morphological and molecular data. Our results indicate that †Mahengichthys singidaensis is a kneriid gonorynchiform within the tribe Kneriini, which includes the extant genera Kneria and Parakneria. This phylogenetic work provides a framework for estimating the divergence times of the Kneriidae for the first time using Bayesian methodology with calibrations that include information regarding extinct kneriids. We infer that the exclusively freshwater family Kneriidae most likely diverged and diversified during the Cretaceous to Paleogene in Sub-Saharan Africa, following the continent’s separation from South America. Introduction The order Gonorynchiformes includes seven extant and approximately seventeen extinct genera of fishes that exhibit incredible morphological diversity, with the clade dating back to the Early Cretaceous (FARA et al. 2010, POYATO-ARIZA et al. -
The Tree of Life and a New Classification of Bony Fishes
The Tree of Life and a New Classification of Bony Fishes April 18, 2013 · Tree of Life Ricardo Betancur-R.1, Richard E. Broughton2, Edward O. Wiley3, Kent Carpenter4, J. Andrés López5, Chenhong Li 6, Nancy I. Holcroft7, Dahiana Arcila1, Millicent Sanciangco4, James C Cureton II2, Feifei Zhang2, Thaddaeus Buser, Matthew A. Campbell5, Jesus A Ballesteros1, Adela Roa-Varon8, Stuart Willis9, W. Calvin Borden10, Thaine Rowley11, Paulette C. Reneau12, Daniel J. Hough2, Guoqing Lu13, Terry Grande10, Gloria Arratia3, Guillermo Ortí1 1 The George Washington University, 2 University of Oklahoma, 3 University of Kansas, 4 Old Dominion University, 5 University of Alaska Fairbanks, 6 Shanghai Ocean University, 7 Johnson County Community College, 8 George Washington University, 9 University of Nebraska-Lincoln, 10 Loyola University Chicago, 11 University of Nebraska- Omaha, 12 Florida A&M University, 13 University of Nebraska at Omaha Betancur-R. R, Broughton RE, Wiley EO, Carpenter K, López JA, Li C, Holcroft NI, Arcila D, Sanciangco M, Cureton II JC, Zhang F, Buser T, Campbell MA, Ballesteros JA, Roa-Varon A, Willis S, Borden WC, Rowley T, Reneau PC, Hough DJ, Lu G, Grande T, Arratia G, Ortí G. The Tree of Life and a New Classification of Bony Fishes. PLOS Currents Tree of Life. 2013 Apr 18 [last modified: 2013 Apr 23]. Edition 1. doi: 10.1371/currents.tol.53ba26640df0ccaee75bb165c8c26288. Abstract The tree of life of fishes is in a state of flux because we still lack a comprehensive phylogeny that includes all major groups. The situation is most critical for a large clade of spiny-finned fishes, traditionally referred to as percomorphs, whose uncertain relationships have plagued ichthyologists for over a century. -
The Intermuscular Bones and Ligaments of Teleostean Fishes *
* The Intermuscular Bones and Ligaments of Teleostean Fishes COLIN PATTERSON and G. DAVID JOHNSON m I I SMITHSONIAN CONTRIBUTIONS TO ZOOLOGY • NUMBER 559 SERIES PUBLICATIONS OF THE SMITHSONIAN INSTITUTION Emphasis upon publication as a means of "diffusing knowledge" was expressed by the first Secretary of the Smithsonian. In his formal plan for the institution, Joseph Henry outlined a program that included the following statement: "It is proposed to publish a series of reports, giving an account of the new discoveries in science, and of the changes made from year to year in all branches of knowledge." This theme of basic research has been adhered to through the years by thousands of titles issued in series publications under the Smithsonian imprint, commencing with Smithsonian Contributions to Knowledge in 1848 and continuing with the following active series: Smithsonian Contributions to Anthropology Smithsonian Contributions to Botany Smithsonian Contributions to the Earth Sciences Smithsonian Contributions to the Marine Sciences Smithsonian Contributions to Paleobiology Smithsonian Contributions to Zoology Smithsonian Folklife Studies Smithsonian Studies in Air and Space Smithsonian Studies in History and Technology In these series, the Institution publishes small papers and full-scale monographs that report the research and collections of its various museums and bureaux or of professional colleagues in the world of science and scholarship. The publications are distributed by mailing lists to libraries, universities, and similar institutions throughout the world. Papers or monographs submitted for series publication are received by the Smithsonian Institution Press, subject to its own review for format and style, only through departments of the various Smithsonian museums or bureaux, where the manuscripts are given substantive review. -
HANDBOOK of FISH BIOLOGY and FISHERIES Volume 1 Also Available from Blackwell Publishing: Handbook of Fish Biology and Fisheries Edited by Paul J.B
HANDBOOK OF FISH BIOLOGY AND FISHERIES Volume 1 Also available from Blackwell Publishing: Handbook of Fish Biology and Fisheries Edited by Paul J.B. Hart and John D. Reynolds Volume 2 Fisheries Handbook of Fish Biology and Fisheries VOLUME 1 FISH BIOLOGY EDITED BY Paul J.B. Hart Department of Biology University of Leicester AND John D. Reynolds School of Biological Sciences University of East Anglia © 2002 by Blackwell Science Ltd a Blackwell Publishing company Chapter 8 © British Crown copyright, 1999 BLACKWELL PUBLISHING 350 Main Street, Malden, MA 02148‐5020, USA 108 Cowley Road, Oxford OX4 1JF, UK 550 Swanston Street, Carlton, Victoria 3053, Australia The right of Paul J.B. Hart and John D. Reynolds to be identified as the Authors of the Editorial Material in this Work has been asserted in accordance with the UK Copyright, Designs, and Patents Act 1988. All rights reserved. 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 or otherwise, except as permitted by the UK Copyright, Designs, and Patents Act 1988, without the prior permission of the publisher. First published 2002 Reprinted 2004 Library of Congress Cataloging‐in‐Publication Data has been applied for. Volume 1 ISBN 0‐632‐05412‐3 (hbk) Volume 2 ISBN 0‐632‐06482‐X (hbk) 2‐volume set ISBN 0‐632‐06483‐8 A catalogue record for this title is available from the British Library. Set in 9/11.5 pt Trump Mediaeval by SNP Best‐set Typesetter Ltd, Hong Kong Printed and bound in the United Kingdom by TJ International Ltd, Padstow, Cornwall. -
Etyfish Gonorynchifo
GONORYNCHIFORMES · 1 The ETYFish Project © Christopher Scharpf and Kenneth J. Lazara COMMENTS: v. 4.0 - 1 May 2019 Subcohort OSTARIOPHYSI ostar, small bone; physa, bladder, referring to Weberian apparatus, a complex of modified vertebrae and ligaments that connect the gas bladder to the inner ear (except for Section Anotophysi) Section ANOTOPHYSA an-, without; oto-, ear; physa, bladder, referring to lack of Weberian apparatus; instead, anotophysans possess a primitive homolog consist- ing of three modified anterior vertebrae associated with cephalic rib bones Order GONORYNCHIFORMES 4 families · 7 genera · 37 species Family CHANIDAE Milkfishes Chanos Lacepède 1803 tautonymous with Mugil chanos (which Lacepède unnecessarily renamed as Chanos arabicus) Chanos chanos (Forsskål 1775) open-mouthed, from an ancient Greek name, possibly referring to how it sometimes feeds at surface with open mouth Family GONORYNCHIDAE Beaked Sandfishes Gonorynchus Scopoli 1777 tautonymous with Cyprinus gonorynchus Gonorynchus abbreviatus Temminck & Schlegel 1846 shortened, presumably referring to shorter head compared to G. gonorynchus Gonorynchus forsteri Ogilby 1911 patronym not identified, possibly in honor of Johann Reinhold Forster (1729-1798), naturalist aboard Captain Cook’s second voyage on HMS Resolution, which first documented the occurrence of Gonorynchus in New Zealand (where this species occurs) in 1769 Gonorynchus gonorynchus (Linnaeus 1766) gonio-, angle; rhynchus, snout, referring to distinctive angular snout used to dig themselves into sand Gonorynchus greyi (Richardson 1845) in honor of Capt. George Grey (1812-1898), Lieutenant-Governor of West Australia, “whose exertions in the cause of Zoology have been productive of several important discoveries,” including this species Gonorynchus moseleyi Jordan & Snyder 1923 in honor of Edwin Lincoln Moseley (1865-1948), professor of biology, State Normal School at Bowling Green, Ohio, USA, who collected type Gonorynchus abbreviatus. -
The Distribution of African Freshwater Fishes Répartition Des Poissons D’Eau Douce Africains
65 Chapitre 4 THE DISTRIBUTION OF AFRICAN FRESHWATER FISHES RÉPARTITION DES POISSONS D’EAU DOUCE AFRICAINS P.H. Skelton The distribution of fishes in the rivers;lakes and other waterbodies of Afiica has always been of great interest to naturalists, scientists, ichthyologists and others involved with the Afiican fauna. By the second half of the 19th Century sufficient knowledge on the distribution of Af?i- cari freshwater fishes was at hand to provoke a few general comments by Günther (1880). Sys- tematic knowledge increased rapidly after this and by the tum of the Century Boulenger (1905) presented the first detailed synthesis of the distribution of Afiican freshwater fishes. This was followed by Pellegrin’s (1912) account before Boulenger’s (1909-l 915) classic Catalogue appea- red and set the stage for the surge of systematic literature on these fishes over the past sixty years or SO.Much of thishterature has dealt with the fauna of particular rivers, lakes or regions SOthat the broad details of’Xiican fish distribution are now known. Pol1 (1973) and Roberts (1975) have summarized and discussed this distribution on a pan Afiican scale. This chapter presents a systematic summary of present knowledge of distribution of fishes in the continenal waters of Afiica. Attention is focussed on families, with noteworthy generic and specific examples being mentioned. No attempt is made to provide a biogeographical analysis as this requires detailed knowledge of both the phyletic relationships of the taxa and the ove- .rall geological and geographical history of the continent (Greenwood, 1983). Furthermore, cur- rent biogeographical analyses demand pattem analysis incorporating different plant and animal groups, information which is not easily available at present. -
The Complete Mitochondrial Genome of the Chinese Hook Snout
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Institute of Hydrobiology, Chinese Academy Of Sciences Gene 399 (2007) 11–19 www.elsevier.com/locate/gene The complete mitochondrial genome of the Chinese hook snout carp Opsariichthys bidens (Actinopterygii: Cypriniformes) and an alternative pattern of mitogenomic evolution in vertebrate ⁎ Xuzhen Wang a, Jun Wang b,c,d, Shunping He a, , Richard L. Mayden e a Laboratory of Fish Phylogenetics and Biogeography, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China b Beijing Institute of Genomics of Chinese Academy of Sciences, Beijing Genomics Institute, Beijing Proteomics Institute, Beijing 101300, China c Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230, Odense M, Denmark d The Institute of Human Genetics, University of Aarhus, DK-8000 Aarhus C, Denmark e Department of Biology, 3507 Laclede Ave., Saint Louis University, St. Louis, MO 63103, USA Received 31 January 2007; received in revised form 12 April 2007; accepted 18 April 2007 Available online 27 April 2007 Abstract The complete mitochondrial genome sequence of the Chinese hook snout carp, Opsariichthys bidens, was newly determined using the long and accurate polymerase chain reaction method. The 16,611-nucleotide mitogenome contains 13 protein-coding genes, two rRNA genes (12S, 16S), 22 tRNA genes, and a noncoding control region. We use these data and homologous sequence data from multiple other ostariophysan fishes in a phylogenetic evaluation to test hypothesis pertaining to codon usage pattern of O. bidens mitochondrial protein genes as well as to re-examine the ostariophysan phylogeny. -
Freshwater Fishes in Africa - Christian Lévêque and Didier Paugy
ANIMAL RESOURCES AND DIVERSITY IN AFRICA - Freshwater Fishes In Africa - Christian Lévêque and Didier Paugy FRESHWATER FISHES IN AFRICA Christian Lévêque and Didier Paugy IRD, UMR Borea, MNHN, 43 rue Cuvier, 75431 Paris cedex 05, France Keywords: Africa, Inland water, Fish, Biodiversity, Biology, Human utilization Contents 1. The Lakes and Rivers of Africa 2. Advances in African freshwater ichthyology 3. Paleontology 4. Characteristics of the African inland water fish fauna 5. Biogeography 6. Freshwater habitats and fish assemblages 7. Reproductive strategies 8. Life history styles 9. Human utilization 10. Threats to freshwater ecosystems 11. The value of freshwater biodiversity Glossary Bibliography Biographical Sketches Summary The African continent can broadly be divided into two large regions: Low (West and North Africa) and High Africa (South and East Africa). About ten large river basins occupy the continent and most of them flow towards the ocean. However there are also some large endorheic basins such as the Chari and the Okavango. The climate is of utmost importance in determining the distribution of aquatic systems. Altogether, the combined effects of geographic, climatic and topographic factors have given rise to a high diversity of ecosystems, freshwater fishes and assemblages. Currently 3,360 species of fresh and brackish water fish species have been described from Africa. The long period of exondation of most of the African continent, which lasts for UNESCO-EOLSSmore than 600 Myrs ago during the Precambrian, may explain the diversity of the freshwater fish fauna and its unparallel assemblage of so-called archaic families of which mostly areSAMPLE endemic. CHAPTERS Thirteen ichthyological provinces or bioregions, based on their specific fish fauna, have been identified in Africa. -
Origin and Phylogenetic Interrelationships of Teleosts Honoring Gloria Arratia
Origin and Phylogenetic Interrelationships of Teleosts Honoring Gloria Arratia Joseph S. Nelson, Hans-Peter Schultze & Mark V. H. Wilson (editors) TELEOSTEOMORPHA TELEOSTEI TELEOCEPHALA s. str. Leptolepis Pholidophorus † Lepisosteus Amia †? †? † †Varasichthyidae †Ichthyodectiformes Elopidae More advanced teleosts crown- group apomorphy-based group stem-based group Verlag Dr. Friedrich Pfeil • München Contents Preface ................................................................................................................................................................ 7 Acknowledgments ........................................................................................................................................... 9 Gloria Arratia’s contribution to our understanding of lower teleostean phylogeny and classifi cation – Joseph S. Nelson ....................................................................................... 11 The case for pycnodont fi shes as the fossil sister-group of teleosts – J. Ralph Nursall ...................... 37 Phylogeny of teleosts based on mitochondrial genome sequences – Richard E. Broughton ............. 61 Occipito-vertebral fusion in actinopterygians: conjecture, myth and reality. Part 1: Non-teleosts – Ralf Britz and G. David Johnson ................................................................................................................... 77 Occipito-vertebral fusion in actinopterygians: conjecture, myth and reality. Part 2: Teleosts – G. David Johnson and Ralf Britz ..................................................................................................................