Conserved Keratin Gene Clusters in Ancient Fish: an Evolutionary Seed for Terrestrial Adaptation
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Vertebrates (Vertebrata) S. Blair Hedges Vertebrates are treated here as a separate phylum Department of Biology, 208 Mueller Laboratory, Pennsylvania State rather than a subphylum of Chordata. 7 e morpho- University, University Park, PA 16802-5301, USA ([email protected]) logical disparity among the chordates (urochordates, cepahalochordates, and vertebrates), and their deep time of separation based on molecular clocks (5) is as great Abstract as that among other groups of related animal phyla (e.g., The vertebrates (~58,000 sp.) comprise a phylum of mostly arthropods, tardigrades, and onycophorans). 7 e phyl- mobile, predatory animals. The evolution of jaws and ogeny of the lineages covered here is uncontroversial, for limbs were key traits that led to subsequent diversifi cation. the most part. Evidence from nuclear genes and morph- Atmospheric oxygen change appears to have played a major ology (1, 2, 6, 7) agree in the backbone phylogeny of ver- role, with an initial rise in the late Precambrian (~580–542 tebrates represented by these nested groups: Tetrapoda million years ago, Ma) permitting larger body size, followed (Lissamphibia, Amniota), Sarcopterygii (Actinistia, by two Paleozoic pulses affecting prey. The First Pulse Dipnoi, Tetrapoda), Osteichthyes (Actinopterygii, (~430–390 Ma) brought fi shes to brackish and freshwater Sarcopterygii), and Gnathostomata (Chondrichthyes, environments where they diversifi ed, with one lineage giv- Osteichthyes). ing rise to tetrapods. The Second Pulse (~340–250 Ma) led to Cyclostomata wa s or ig i na l ly considered a ba sa l, mono- a Permo-Carboniferous explosion of tetrapods, adapting to phyletic group based on morphology (8), but later mor- diverse terrestrial niches. -
A Review of Hearing by Sturgeon and Lamprey
A Review of Hearing by Sturgeon and Lamprey Arthur N. Popper Environmental BioAcoustics, LLC Rockville, MD 20853 Submitted to the U.S. Army Corps of Engineers, Portland District August 12, 2005 ms-coe Sturgeon & Lamprey Page 1 of 23 Contents 1. Introduction............................................................................................................................... 3 2. Hearing Capabilities, Detection, and Sound Production ...................................................... 3 a. Sensory cells of the ear ....................................................................................................... 4 b. The Lateral Line.................................................................................................................. 4 c. The Inner Ear ........................................................................................................................ 6 d. Hearing ................................................................................................................................. 7 e. Why Do Fish Hear ................................................................................................................ 9 f. Sound Production .................................................................................................................... 9 3. Underwater Acoustics – A brief overview ............................................................................ 10 4. Bioacoustics of sturgeon and lamprey.................................................................................. -
Caecilia Guntheri Dunn, 1942 (Gymnophiona, Caeciliidae) in Central America
17 2 NOTES ON GEOGRAPHIC DISTRIBUTION Check List 17 (2): 649–653 https://doi.org/10.15560/17.2.649 First record of Caecilia guntheri Dunn, 1942 (Gymnophiona, Caeciliidae) in Central America Luis C. Elizondo-Lara Programa de Maestría en Ciencias Biológicas, Vicerrectoría de Investigación y Postgrado, Universidad de Panamá, Panama City, Panama • luis. [email protected]; [email protected] https://orcid.org/0000-0002-8647-6717 Departamento de Fisiología y Comportamiento Animal, Facultad de Ciencias Naturales Exactas y Tecnología, Universidad de Panamá, Panama City, Panama Red Mesoamericana y del Caribe para la Conservación de Anfibios y Reptiles Abstract I report the first encounter in Central America of an individual of Caecilia guntheri Dunn, 1942 (Gymnophiona, Caeciliidae). The individual was observed and collected in a primary evergreen submontane forest in Cerro Pirre, Darien Province, Republic of Panama. It was identified mainly by the low counts of secondary and primary folds. The encounter of this individual of C. guntheri highlights the disjunct populations and apparently the results of dispersion of this species from South to Central America by biotic exchange as result of the closure of the Isthmus of Panama. Keywords Amphibians, biotic exchange, Cerro Pirre, Darien, disjunct distribution, Panama Academic editor: Javier Ernesto Cortés Suárez | Received 28 December 2020 | Accepted 28 March 2021 | Published 13 April 2021 Citation: Elizondo-Lara LC (2021) First record of Caecilia guntheri Dunn, 1942 (Gymnophiona, Caeciliidae) in Central America. Check List 17 (2): 649–653. https://doi.org/10.15560/17.2.649 Introduction The genus Caecilia Linnaeus, 1758 was described from Rica (Köhler 2011; Kubicki and Arias 2017). -
Etar a Área De Distribuição Geográfica De Anfíbios Na Amazônia
Universidade Federal do Amapá Pró-Reitoria de Pesquisa e Pós-Graduação Programa de Pós-Graduação em Biodiversidade Tropical Mestrado e Doutorado UNIFAP / EMBRAPA-AP / IEPA / CI-Brasil YURI BRENO DA SILVA E SILVA COMO A EXPANSÃO DE HIDRELÉTRICAS, PERDA FLORESTAL E MUDANÇAS CLIMÁTICAS AMEAÇAM A ÁREA DE DISTRIBUIÇÃO DE ANFÍBIOS NA AMAZÔNIA BRASILEIRA MACAPÁ, AP 2017 YURI BRENO DA SILVA E SILVA COMO A EXPANSÃO DE HIDRE LÉTRICAS, PERDA FLORESTAL E MUDANÇAS CLIMÁTICAS AMEAÇAM A ÁREA DE DISTRIBUIÇÃO DE ANFÍBIOS NA AMAZÔNIA BRASILEIRA Dissertação apresentada ao Programa de Pós-Graduação em Biodiversidade Tropical (PPGBIO) da Universidade Federal do Amapá, como requisito parcial à obtenção do título de Mestre em Biodiversidade Tropical. Orientador: Dra. Fernanda Michalski Co-Orientador: Dr. Rafael Loyola MACAPÁ, AP 2017 YURI BRENO DA SILVA E SILVA COMO A EXPANSÃO DE HIDRELÉTRICAS, PERDA FLORESTAL E MUDANÇAS CLIMÁTICAS AMEAÇAM A ÁREA DE DISTRIBUIÇÃO DE ANFÍBIOS NA AMAZÔNIA BRASILEIRA _________________________________________ Dra. Fernanda Michalski Universidade Federal do Amapá (UNIFAP) _________________________________________ Dr. Rafael Loyola Universidade Federal de Goiás (UFG) ____________________________________________ Alexandro Cezar Florentino Universidade Federal do Amapá (UNIFAP) ____________________________________________ Admilson Moreira Torres Instituto de Pesquisas Científicas e Tecnológicas do Estado do Amapá (IEPA) Aprovada em de de , Macapá, AP, Brasil À minha família, meus amigos, meu amor e ao meu pequeno Sebastião. AGRADECIMENTOS Agradeço a CAPES pela conceção de uma bolsa durante os dois anos de mestrado, ao Programa de Pós-Graduação em Biodiversidade Tropical (PPGBio) pelo apoio logístico durante a pesquisa realizada. Obrigado aos professores do PPGBio por todo o conhecimento compartilhado. Agradeço aos Doutores, membros da banca avaliadora, pelas críticas e contribuições construtivas ao trabalho. -
Fishes Scales & Tails Scale Types 1
Phylum Chordata SUBPHYLUM VERTEBRATA Metameric chordates Linear series of cartilaginous or boney support (vertebrae) surrounding or replacing the notochord Expanded anterior portion of nervous system THE FISHES SCALES & TAILS SCALE TYPES 1. COSMOID (most primitive) First found on ostracaderm agnathans, thick & boney - composed of: Ganoine (enamel outer layer) Cosmine (thick under layer) Spongy bone Lamellar bone Perhaps selected for protection against eurypterids, but decreased flexibility 2. GANOID (primitive, still found on some living fish like gar) 3. PLACOID (old scale type found on the chondrichthyes) Dentine, tooth-like 4. CYCLOID (more recent scale type, found in modern osteichthyes) 5. CTENOID (most modern scale type, found in modern osteichthyes) TAILS HETEROCERCAL (primitive, still found on chondrichthyes) ABBREVIATED HETEROCERCAL (found on some primitive living fish like gar) DIPHYCERCAL (primitive, found on sarcopterygii) HOMOCERCAL (most modern, found on most modern osteichthyes) Agnatha (class) [connect the taxa] Cyclostomata (order) Placodermi Acanthodii (class) (class) Chondrichthyes (class) Osteichthyes (class) Actinopterygii (subclass) Sarcopterygii (subclass) Dipnoi (order) Crossopterygii (order) Ripidistia (suborder) Coelacanthiformes (suborder) Chondrostei (infra class) Holostei (infra class) Teleostei (infra class) CLASS AGNATHA ("without jaws") Most primitive - first fossils in Ordovician Bottom feeders, dorsal/ventral flattened Cosmoid scales (Ostracoderms) Pair of eyes + pineal eye - present in a few living fish and reptiles - regulates circadian rhythms Nine - seven gill pouches No paired appendages, medial nosril ORDER CYCLOSTOMATA (60 spp) Last living representatives - lampreys & hagfish Notochord not replaced by vertebrae Cartilaginous cranium, scaleless body Sea lamprey predaceous - horny teeth in buccal cavity & on tongue - secretes anti-coaggulant Lateral Line System No stomach or spleen 5 - 7 year life span - adults move into freshwater streams, spawn, & die. -
An Alignment-Free Computational Tool for Analyzing and Visualizing DNA Sequences' Interrelationships Rallis Karamichalis the University of Western Ontario
Western University Scholarship@Western Electronic Thesis and Dissertation Repository September 2016 Molecular Distance Maps: An alignment-free computational tool for analyzing and visualizing DNA sequences' interrelationships Rallis Karamichalis The University of Western Ontario Supervisor Prof. Lila Kari The University of Western Ontario Graduate Program in Computer Science A thesis submitted in partial fulfillment of the requirements for the degree in Doctor of Philosophy © Rallis Karamichalis 2016 Follow this and additional works at: https://ir.lib.uwo.ca/etd Part of the Other Computer Sciences Commons Recommended Citation Karamichalis, Rallis, "Molecular Distance Maps: An alignment-free computational tool for analyzing and visualizing DNA sequences' interrelationships" (2016). Electronic Thesis and Dissertation Repository. 4071. https://ir.lib.uwo.ca/etd/4071 This Dissertation/Thesis is brought to you for free and open access by Scholarship@Western. It has been accepted for inclusion in Electronic Thesis and Dissertation Repository by an authorized administrator of Scholarship@Western. For more information, please contact [email protected]. Abstract In an attempt to identify and classify species based on genetic evidence, we propose a novel combination of methods to quantify and visualize the interrelationships between thousand of species. This is possible by using Chaos Game Representation (CGR) of DNA sequences to compute genomic signatures which we then compare by computing pairwise distances. In the last step, the original DNA sequences are embedded in a high dimensional space using Multi- Dimensional Scaling (MDS) before everything is projected on a Euclidean 3D space. To start with, we apply this method to a mitochondrial DNA dataset from NCBI containing over 3,000 species. -
The Sterlet Sturgeon Genome Sequence and the Mechanisms Of
The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization Kang Du, Matthias Stöck, Susanne Kneitz, Christophe Klopp, Joost Woltering, Mateus Contar Adolfi, Romain Feron, Dmitry Prokopov, Alexey Makunin, Ilya Kichigin, et al. To cite this version: Kang Du, Matthias Stöck, Susanne Kneitz, Christophe Klopp, Joost Woltering, et al.. The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization. Nature Ecology & Evolution, Nature, 2020, 4 (6), pp.841-852. 10.1038/s41559-020-1166-x. hal-02640938 HAL Id: hal-02640938 https://hal.inrae.fr/hal-02640938 Submitted on 6 Jan 2021 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. ARTICLES https://doi.org/10.1038/s41559-020-1166-x The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization Kang Du1,2, Matthias Stöck 3 ✉ , Susanne Kneitz1, Christophe Klopp 4,5, Joost M. Woltering6, Mateus Contar Adolfi1, Romain Feron 7, Dmitry Prokopov 8, Alexey Makunin 8, Ilya Kichigin8, Cornelia Schmidt1, Petra Fischer1, Heiner Kuhl3, Sven Wuertz3, Jörn Gessner3, Werner Kloas3, Cédric Cabau4,5, Carole Iampietro9, Hugues Parrinello10, Chad Tomlinson11, Laurent Journot10, John H. Postlethwait12, Ingo Braasch13, Vladimir Trifonov8, Wesley C. Warren14, Axel Meyer 6, Yann Guiguen 15 and Manfred Schartl 2,16,17 ✉ Sturgeons seem to be frozen in time. -
The Divergent Genomes of Teleosts
Postprint copy Annu. Rev. Anim. Biosci. 2018. 6:X--X https://doi.org/10.1146/annurev-animal-030117-014821 Copyright © 2018 by Annual Reviews. All rights reserved RAVI ■ VENKATESH DIVERGENT GENOMES OF TELEOSTS THE DIVERGENT GENOMES OF TELEOSTS Vydianathan Ravi and Byrappa Venkatesh Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138673, Singapore; email: [email protected], [email protected] ■ Abstract Boasting nearly 30,000 species, teleosts account for half of all living vertebrates and approximately 98% of all ray-finned fish species (Actinopterygii). Teleosts are also the largest and most diverse group of vertebrates, exhibiting an astonishing level of morphological, physiological, and behavioral diversity. Previous studies had indicated that the teleost lineage has experienced an additional whole-genome duplication event. Recent comparative genomic analyses of teleosts and other bony vertebrates using spotted gar (a nonteleost ray-finned fish) and elephant shark (a cartilaginous fish) as outgroups have revealed several divergent features of teleost genomes. These include an accelerated evolutionary rate of protein-coding and nucleotide sequences, a higher rate of intron turnover, and loss of many potential cis-regulatory elements and shorter conserved syntenic blocks. A combination of these divergent genomic features might have contributed to the evolution of the amazing phenotypic diversity and morphological innovations of teleosts. Keywords whole-genome duplication, evolutionary rate, intron turnover, conserved noncoding elements, conserved syntenic blocks, phenotypic diversity INTRODUCTION With over 68,000 known species (IUCN 2017; http://www.iucnredlist.org), vertebrates are the most dominant and successful group of animals on earth, inhabiting both terrestrial and aquatic habitats. -
Taxonomia Dos Anfíbios Da Ordem Gymnophiona Da Amazônia Brasileira
TAXONOMIA DOS ANFÍBIOS DA ORDEM GYMNOPHIONA DA AMAZÔNIA BRASILEIRA ADRIANO OLIVEIRA MACIEL Belém, Pará 2009 MUSEU PARAENSE EMÍLIO GOELDI UNIVERSIDADE FEDERAL DO PARÁ PROGRAMA DE PÓS-GRADUAÇÃO EM ZOOLOGIA MESTRADO EM ZOOLOGIA Taxonomia Dos Anfíbios Da Ordem Gymnophiona Da Amazônia Brasileira Adriano Oliveira Maciel Dissertação apresentada ao Programa de Pós-graduação em Zoologia, Curso de Mestrado, do Museu Paraense Emílio Goeldi e Universidade Federal do Pará como requisito parcial para obtenção do grau de mestre em Zoologia. Orientador: Marinus Steven Hoogmoed BELÉM-PA 2009 MUSEU PARAENSE EMÍLIO GOELDI UNIVERSIDADE FEDERAL DO PARÁ PROGRAMA DE PÓS-GRADUAÇÃO EM ZOOLOGIA MESTRADO EM ZOOLOGIA TAXONOMIA DOS ANFÍBIOS DA ORDEM GYMNOPHIONA DA AMAZÔNIA BRASILEIRA Adriano Oliveira Maciel Dissertação apresentada ao Programa de Pós-graduação em Zoologia, Curso de Mestrado, do Museu Paraense Emílio Goeldi e Universidade Federal do Pará como requisito parcial para obtenção do grau de mestre em Zoologia. Orientador: Marinus Steven Hoogmoed BELÉM-PA 2009 Com os seres vivos, parece que a natureza se exercita no artificialismo. A vida destila e filtra. Gaston Bachelard “De que o mel é doce é coisa que me nego a afirmar, mas que parece doce eu afirmo plenamente.” Raul Seixas iii À MINHA FAMÍLIA iv AGRADECIMENTOS Primeiramente agradeço aos meus pais, a Teté e outros familiares que sempre apoiaram e de alguma forma contribuíram para minha vinda a Belém para cursar o mestrado. À Marina Ramos, com a qual acreditei e segui os passos da formação acadêmica desde a graduação até quase a conclusão destes tempos de mestrado, pelo amor que foi importante. A todos os amigos da turma de mestrado pelos bons momentos vividos durante o curso. -
A Rapid Biological Assessment of the Upper Palumeu River Watershed (Grensgebergte and Kasikasima) of Southeastern Suriname
Rapid Assessment Program A Rapid Biological Assessment of the Upper Palumeu River Watershed (Grensgebergte and Kasikasima) of Southeastern Suriname Editors: Leeanne E. Alonso and Trond H. Larsen 67 CONSERVATION INTERNATIONAL - SURINAME CONSERVATION INTERNATIONAL GLOBAL WILDLIFE CONSERVATION ANTON DE KOM UNIVERSITY OF SURINAME THE SURINAME FOREST SERVICE (LBB) NATURE CONSERVATION DIVISION (NB) FOUNDATION FOR FOREST MANAGEMENT AND PRODUCTION CONTROL (SBB) SURINAME CONSERVATION FOUNDATION THE HARBERS FAMILY FOUNDATION Rapid Assessment Program A Rapid Biological Assessment of the Upper Palumeu River Watershed RAP (Grensgebergte and Kasikasima) of Southeastern Suriname Bulletin of Biological Assessment 67 Editors: Leeanne E. Alonso and Trond H. Larsen CONSERVATION INTERNATIONAL - SURINAME CONSERVATION INTERNATIONAL GLOBAL WILDLIFE CONSERVATION ANTON DE KOM UNIVERSITY OF SURINAME THE SURINAME FOREST SERVICE (LBB) NATURE CONSERVATION DIVISION (NB) FOUNDATION FOR FOREST MANAGEMENT AND PRODUCTION CONTROL (SBB) SURINAME CONSERVATION FOUNDATION THE HARBERS FAMILY FOUNDATION The RAP Bulletin of Biological Assessment is published by: Conservation International 2011 Crystal Drive, Suite 500 Arlington, VA USA 22202 Tel : +1 703-341-2400 www.conservation.org Cover photos: The RAP team surveyed the Grensgebergte Mountains and Upper Palumeu Watershed, as well as the Middle Palumeu River and Kasikasima Mountains visible here. Freshwater resources originating here are vital for all of Suriname. (T. Larsen) Glass frogs (Hyalinobatrachium cf. taylori) lay their -
Copyrighted Material
06_250317 part1-3.qxd 12/13/05 7:32 PM Page 15 Phylum Chordata Chordates are placed in the superphylum Deuterostomia. The possible rela- tionships of the chordates and deuterostomes to other metazoans are dis- cussed in Halanych (2004). He restricts the taxon of deuterostomes to the chordates and their proposed immediate sister group, a taxon comprising the hemichordates, echinoderms, and the wormlike Xenoturbella. The phylum Chordata has been used by most recent workers to encompass members of the subphyla Urochordata (tunicates or sea-squirts), Cephalochordata (lancelets), and Craniata (fishes, amphibians, reptiles, birds, and mammals). The Cephalochordata and Craniata form a mono- phyletic group (e.g., Cameron et al., 2000; Halanych, 2004). Much disagree- ment exists concerning the interrelationships and classification of the Chordata, and the inclusion of the urochordates as sister to the cephalochor- dates and craniates is not as broadly held as the sister-group relationship of cephalochordates and craniates (Halanych, 2004). Many excitingCOPYRIGHTED fossil finds in recent years MATERIAL reveal what the first fishes may have looked like, and these finds push the fossil record of fishes back into the early Cambrian, far further back than previously known. There is still much difference of opinion on the phylogenetic position of these new Cambrian species, and many new discoveries and changes in early fish systematics may be expected over the next decade. As noted by Halanych (2004), D.-G. (D.) Shu and collaborators have discovered fossil ascidians (e.g., Cheungkongella), cephalochordate-like yunnanozoans (Haikouella and Yunnanozoon), and jaw- less craniates (Myllokunmingia, and its junior synonym Haikouichthys) over the 15 06_250317 part1-3.qxd 12/13/05 7:32 PM Page 16 16 Fishes of the World last few years that push the origins of these three major taxa at least into the Lower Cambrian (approximately 530–540 million years ago). -
Jawless Fishes of the World
Jawless Fishes of the World Jawless Fishes of the World: Volume 1 Edited by Alexei Orlov and Richard Beamish Jawless Fishes of the World: Volume 1 Edited by Alexei Orlov and Richard Beamish This book first published 2016 Cambridge Scholars Publishing Lady Stephenson Library, Newcastle upon Tyne, NE6 2PA, UK British Library Cataloguing in Publication Data A catalogue record for this book is available from the British Library Copyright © 2016 by Alexei Orlov, Richard Beamish and contributors All rights for this book reserved. No part of this book may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording or otherwise, without the prior permission of the copyright owner. ISBN (10): 1-4438-8582-7 ISBN (13): 978-1-4438-8582-9 TABLE OF CONTENTS Volume 1 Preface ........................................................................................................ ix M. Docker Part 1: Evolution, Phylogeny, Diversity, and Taxonomy Chapter One ................................................................................................. 2 Molecular Evolution in the Lamprey Genomes and Its Relevance to the Timing of Whole Genome Duplications T. Manousaki, H. Qiu, M. Noro, F. Hildebrand, A. Meyer and S. Kuraku Chapter Two .............................................................................................. 17 Molecular Phylogeny and Speciation of East Asian Lampreys (genus Lethenteron) with reference to their Life-History Diversification Y. Yamazaki and