Assembling the Tree of Life
Total Page:16
File Type:pdf, Size:1020Kb

Load more
Recommended publications
-
Bibliography Database of Living/Fossil Sharks, Rays and Chimaeras (Chondrichthyes: Elasmobranchii, Holocephali) Papers of the Year 2016
www.shark-references.com Version 13.01.2017 Bibliography database of living/fossil sharks, rays and chimaeras (Chondrichthyes: Elasmobranchii, Holocephali) Papers of the year 2016 published by Jürgen Pollerspöck, Benediktinerring 34, 94569 Stephansposching, Germany and Nicolas Straube, Munich, Germany ISSN: 2195-6499 copyright by the authors 1 please inform us about missing papers: [email protected] www.shark-references.com Version 13.01.2017 Abstract: This paper contains a collection of 803 citations (no conference abstracts) on topics related to extant and extinct Chondrichthyes (sharks, rays, and chimaeras) as well as a list of Chondrichthyan species and hosted parasites newly described in 2016. The list is the result of regular queries in numerous journals, books and online publications. It provides a complete list of publication citations as well as a database report containing rearranged subsets of the list sorted by the keyword statistics, extant and extinct genera and species descriptions from the years 2000 to 2016, list of descriptions of extinct and extant species from 2016, parasitology, reproduction, distribution, diet, conservation, and taxonomy. The paper is intended to be consulted for information. In addition, we provide information on the geographic and depth distribution of newly described species, i.e. the type specimens from the year 1990- 2016 in a hot spot analysis. Please note that the content of this paper has been compiled to the best of our abilities based on current knowledge and practice, however, -
Phylogeny Classification Additional Readings Clupeomorpha and Ostariophysi
Teleostei - AccessScience from McGraw-Hill Education http://www.accessscience.com/content/teleostei/680400 (http://www.accessscience.com/) Article by: Boschung, Herbert Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama. Gardiner, Brian Linnean Society of London, Burlington House, Piccadilly, London, United Kingdom. Publication year: 2014 DOI: http://dx.doi.org/10.1036/1097-8542.680400 (http://dx.doi.org/10.1036/1097-8542.680400) Content Morphology Euteleostei Bibliography Phylogeny Classification Additional Readings Clupeomorpha and Ostariophysi The most recent group of actinopterygians (rayfin fishes), first appearing in the Upper Triassic (Fig. 1). About 26,840 species are contained within the Teleostei, accounting for more than half of all living vertebrates and over 96% of all living fishes. Teleosts comprise 517 families, of which 69 are extinct, leaving 448 extant families; of these, about 43% have no fossil record. See also: Actinopterygii (/content/actinopterygii/009100); Osteichthyes (/content/osteichthyes/478500) Fig. 1 Cladogram showing the relationships of the extant teleosts with the other extant actinopterygians. (J. S. Nelson, Fishes of the World, 4th ed., Wiley, New York, 2006) 1 of 9 10/7/2015 1:07 PM Teleostei - AccessScience from McGraw-Hill Education http://www.accessscience.com/content/teleostei/680400 Morphology Much of the evidence for teleost monophyly (evolving from a common ancestral form) and relationships comes from the caudal skeleton and concomitant acquisition of a homocercal tail (upper and lower lobes of the caudal fin are symmetrical). This type of tail primitively results from an ontogenetic fusion of centra (bodies of vertebrae) and the possession of paired bracing bones located bilaterally along the dorsal region of the caudal skeleton, derived ontogenetically from the neural arches (uroneurals) of the ural (tail) centra. -
Sturgeons of the Caspian Sea and Ural River
Photo and image credits: Front Cover: Top left, beluga sturgeon (Huso huso); Top Right: Russian sturgeon (Acipenser gueldenstaedtii); Bottom: stellate sturgeon (Acipenser stellatus); Todd Stailey, Tennessee Aquarium. Back Cover: “FISH IS OUR TREASURE”, Phaedra Doukakis, Ph. D. IOCS; Page 1: Shannon Crownover, The Nature Conservancy; Page 6, 9, 10, 11: Phaedra Doukakis, Ph. D., IOCS; Page 4, 5, 7 designed by Grace Lewis. Brochure content was developed by Alison Ormsby, Ph.D. and Phaedra Doukakis, Ph. D. with editorial review by Yael Wyner, Ph. D. Layout was designed by Grace Lewis. The brochure was developed under a generous grant from Agip KCO. Agip KCO Tel.: international line: 1, K. Smagulov Street +39 02 9138 3300 Atyrau, 06002 Tel: local lines: Republic of Kazakhstan (+7) 7122 92 3300 Fax: (+7) 7122 92 3310 Designed and printed in Kazakhstan www.agipkco.com Sturgeons of the Caspian Sea and Ural River www.oceanconservationscience.org A Unique and Precious Resource What are Sturgeon? River, other rivers off the Caspian Sea are used by sturgeons for With bony plates called scutes on their bodies and ancestors that reproduction, including the Volga River in Russia and the Kura date to the time of dinosaurs, sturgeons are unusual fish. Unlike River in Azerbaijan. However, dams on the Volga and Kura have other types of fish, sturgeons have scutes instead of scales. blocked sturgeons from being able to migrate upriver, and have changed the quality of the rivers so they are no longer able to support sturgeon reproduction. Reproduction: For sturgeon, the process of mixing female eggs and male sperm to create a fertilized egg that hatches into a baby sturgeon. -
CHECKLIST and BIOGEOGRAPHY of FISHES from GUADALUPE ISLAND, WESTERN MEXICO Héctor Reyes-Bonilla, Arturo Ayala-Bocos, Luis E
ReyeS-BONIllA eT Al: CheCklIST AND BIOgeOgRAphy Of fISheS fROm gUADAlUpe ISlAND CalCOfI Rep., Vol. 51, 2010 CHECKLIST AND BIOGEOGRAPHY OF FISHES FROM GUADALUPE ISLAND, WESTERN MEXICO Héctor REyES-BONILLA, Arturo AyALA-BOCOS, LUIS E. Calderon-AGUILERA SAúL GONzáLEz-Romero, ISRAEL SáNCHEz-ALCántara Centro de Investigación Científica y de Educación Superior de Ensenada AND MARIANA Walther MENDOzA Carretera Tijuana - Ensenada # 3918, zona Playitas, C.P. 22860 Universidad Autónoma de Baja California Sur Ensenada, B.C., México Departamento de Biología Marina Tel: +52 646 1750500, ext. 25257; Fax: +52 646 Apartado postal 19-B, CP 23080 [email protected] La Paz, B.C.S., México. Tel: (612) 123-8800, ext. 4160; Fax: (612) 123-8819 NADIA C. Olivares-BAñUELOS [email protected] Reserva de la Biosfera Isla Guadalupe Comisión Nacional de áreas Naturales Protegidas yULIANA R. BEDOLLA-GUzMáN AND Avenida del Puerto 375, local 30 Arturo RAMíREz-VALDEz Fraccionamiento Playas de Ensenada, C.P. 22880 Universidad Autónoma de Baja California Ensenada, B.C., México Facultad de Ciencias Marinas, Instituto de Investigaciones Oceanológicas Universidad Autónoma de Baja California, Carr. Tijuana-Ensenada km. 107, Apartado postal 453, C.P. 22890 Ensenada, B.C., México ABSTRACT recognized the biological and ecological significance of Guadalupe Island, off Baja California, México, is Guadalupe Island, and declared it a Biosphere Reserve an important fishing area which also harbors high (SEMARNAT 2005). marine biodiversity. Based on field data, literature Guadalupe Island is isolated, far away from the main- reviews, and scientific collection records, we pres- land and has limited logistic facilities to conduct scien- ent a comprehensive checklist of the local fish fauna, tific studies. -
Chondrichthyan Fishes (Sharks, Skates, Rays) Announcements
Chondrichthyan Fishes (sharks, skates, rays) Announcements 1. Please review the syllabus for reading and lab information! 2. Please do the readings: for this week posted now. 3. Lab sections: 4. i) Dylan Wainwright, Thursday 2 - 4/5 pm ii) Kelsey Lucas, Friday 2 - 4/5 pm iii) Labs are in the Northwest Building basement (room B141) 4. Lab sections done: first lab this week on Thursday! 5. First lab reading: Agassiz fish story; lab will be a bit shorter 6. Office hours: we’ll set these later this week Please use the course web site: note the various modules Outline Lecture outline: -- Intro. to chondrichthyan phylogeny -- 6 key chondrichthyan defining traits (synapomorphies) -- 3 chondrichthyan behaviors -- Focus on several major groups and selected especially interesting ones 1) Holocephalans (chimaeras or ratfishes) 2) Elasmobranchii (sharks, skates, rays) 3) Batoids (skates, rays, and sawfish) 4) Sharks – several interesting groups Not remotely possible to discuss today all the interesting groups! Vertebrate tree – key ―fish‖ groups Today Chondrichthyan Fishes sharks Overview: 1. Mostly marine 2. ~ 1,200 species 518 species of sharks 650 species of rays 38 species of chimaeras Skates and rays 3. ~ 3 % of all ―fishes‖ 4. Internal skeleton made of cartilage 5. Three major groups 6. Tremendous diversity of behavior and structure and function Chimaeras Chondrichthyan Fishes: 6 key traits Synapomorphy 1: dentition; tooth replacement pattern • Teeth are not fused to jaws • New rows move up to replace old/lost teeth • Chondrichthyan teeth are -
ESS 345 Ichthyology
ESS 345 Ichthyology Evolutionary history of fishes 12 Feb 2019 (Who’s birthday?) Quote of the Day: We must, however, acknowledge, as it seems to me, that man with all his noble qualities... still bears in his bodily frame the indelible stamp of his lowly origin._______, (1809-1882) Evolution/radiation of fishes over time Era Cenozoic Fig 13.1 Fishes are the most primitive vertebrate and last common ancestor to all vertebrates They start the branch from all other living things with vertebrae and a cranium Chordata Notochord Dorsal hollow nerve cord Pharyngeal gill slits Postanal tail Urochordata Cephalochordata Craniates (mostly Vertebrata) Phylum Chordata sister is… Echinodermata Synapomorphy – They are deuterostomes Fish Evolutionary Tree – evolutionary innovations in vertebrate history Sarcopterygii Chondrichthyes Actinopterygii (fish) For extant fishes Osteichthyes Gnathostomata Handout Vertebrata Craniata Figure only from Berkeley.edu Hypothesis of fish (vert) origins Background 570 MYA – first large radiation of multicellular life – Fossils of the Burgess Shale – Called the Cambrian explosion Garstang Hypothesis 1928 Neoteny of sessile invertebrates Mistake that was “good” Mudpuppy First Vertebrates Vertebrates appear shortly after Cambrian explosion, 530 MYA – Conodonts Notochord replaced by segmented or partially segmented vertebrate and brain is enclosed in cranium Phylogenetic tree Echinoderms, et al. Other “inverts” Vertebrate phyla X Protostomes Deuterostomes Nephrozoa – bilateral animals First fishes were jawless appearing -
THE CASE AGAINST Marine Mammals in Captivity Authors: Naomi A
s l a m m a y t T i M S N v I i A e G t A n i p E S r a A C a C E H n T M i THE CASE AGAINST Marine Mammals in Captivity The Humane Society of the United State s/ World Society for the Protection of Animals 2009 1 1 1 2 0 A M , n o t s o g B r o . 1 a 0 s 2 u - e a t i p s u S w , t e e r t S h t u o S 9 8 THE CASE AGAINST Marine Mammals in Captivity Authors: Naomi A. Rose, E.C.M. Parsons, and Richard Farinato, 4th edition Editors: Naomi A. Rose and Debra Firmani, 4th edition ©2009 The Humane Society of the United States and the World Society for the Protection of Animals. All rights reserved. ©2008 The HSUS. All rights reserved. Printed on recycled paper, acid free and elemental chlorine free, with soy-based ink. Cover: ©iStockphoto.com/Ying Ying Wong Overview n the debate over marine mammals in captivity, the of the natural environment. The truth is that marine mammals have evolved physically and behaviorally to survive these rigors. public display industry maintains that marine mammal For example, nearly every kind of marine mammal, from sea lion Iexhibits serve a valuable conservation function, people to dolphin, travels large distances daily in a search for food. In learn important information from seeing live animals, and captivity, natural feeding and foraging patterns are completely lost. -
First Record of Swimming Speed of the Pacific Sleeper Shark Somniosus
Journal of the Marine First record of swimming speed of the Pacific Biological Association of the United Kingdom sleeper shark Somniosus pacificus using a baited camera array cambridge.org/mbi Yoshihiro Fujiwara , Yasuyuki Matsumoto, Takumi Sato, Masaru Kawato and Shinji Tsuchida Original Article Research Institute for Global Change (RIGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Yokosuka, Kanagawa 237-0061, Japan Cite this article: Fujiwara Y, Matsumoto Y, Sato T, Kawato M, Tsuchida S (2021). First record of swimming speed of the Pacific Abstract sleeper shark Somniosus pacificus using a baited camera array. Journal of the Marine The Pacific sleeper shark Somniosus pacificus is one of the largest predators in deep Suruga Biological Association of the United Kingdom Bay, Japan. A single individual of the sleeper shark (female, ∼300 cm in total length) was 101, 457–464. https://doi.org/10.1017/ observed with two baited camera systems deployed simultaneously on the deep seafloor in S0025315421000321 the bay. The first arrival was recorded 43 min after the deployment of camera #1 on 21 July 2016 at a depth of 609 m. The shark had several remarkable features, including the Received: 26 July 2020 Revised: 14 April 2021 snout tangled in a broken fishing line, two torn anteriormost left-gill septums, and a parasitic Accepted: 14 April 2021 copepod attached to each eye. The same individual appeared at camera #2, which was First published online: 18 May 2021 deployed at a depth of 603 m, ∼37 min after it disappeared from camera #1 view. Finally, the same shark returned to camera #1 ∼31 min after leaving camera #2. -
Updated Checklist of Marine Fishes (Chordata: Craniata) from Portugal and the Proposed Extension of the Portuguese Continental Shelf
European Journal of Taxonomy 73: 1-73 ISSN 2118-9773 http://dx.doi.org/10.5852/ejt.2014.73 www.europeanjournaloftaxonomy.eu 2014 · Carneiro M. et al. This work is licensed under a Creative Commons Attribution 3.0 License. Monograph urn:lsid:zoobank.org:pub:9A5F217D-8E7B-448A-9CAB-2CCC9CC6F857 Updated checklist of marine fishes (Chordata: Craniata) from Portugal and the proposed extension of the Portuguese continental shelf Miguel CARNEIRO1,5, Rogélia MARTINS2,6, Monica LANDI*,3,7 & Filipe O. COSTA4,8 1,2 DIV-RP (Modelling and Management Fishery Resources Division), Instituto Português do Mar e da Atmosfera, Av. Brasilia 1449-006 Lisboa, Portugal. E-mail: [email protected], [email protected] 3,4 CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal. E-mail: [email protected], [email protected] * corresponding author: [email protected] 5 urn:lsid:zoobank.org:author:90A98A50-327E-4648-9DCE-75709C7A2472 6 urn:lsid:zoobank.org:author:1EB6DE00-9E91-407C-B7C4-34F31F29FD88 7 urn:lsid:zoobank.org:author:6D3AC760-77F2-4CFA-B5C7-665CB07F4CEB 8 urn:lsid:zoobank.org:author:48E53CF3-71C8-403C-BECD-10B20B3C15B4 Abstract. The study of the Portuguese marine ichthyofauna has a long historical tradition, rooted back in the 18th Century. Here we present an annotated checklist of the marine fishes from Portuguese waters, including the area encompassed by the proposed extension of the Portuguese continental shelf and the Economic Exclusive Zone (EEZ). The list is based on historical literature records and taxon occurrence data obtained from natural history collections, together with new revisions and occurrences. -
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. -
Default Word Template
SC-04-19 4th Meeting of the Southern Indian Ocean Fisheries Agreement (SIOFA) Scientific Committee 25–29 March 2019, Yokohama, Japan Draft manuscript for an ecological risk assessment for the effects of bottom fishing gears on deepwater chondrichthyans in high seas areas of the Southern Indian and South Pacific oceans Relates to agenda item: 7 Working paper Info paper Delegation of Australia Abstract This paper provides a draft manuscript for an ecological risk assessment for the effects of bottom fishing gears on deepwater chondrichthyans in high seas areas of the Southern Indian and South Pacific Oceans. 1 Recommendations It is recommended that the SC: • Note that this PSA and SAFE analysis has identified a number of species of deepwater chondrichthyans at high or extreme relative vulnerability to fishing using demersal trawl, midwater trawl, demersal longline and demersal gillnet gears; • Note that a number of these species assessed to be at the high or extreme vulnerability are taken in association with commercial deepwater shark fisheries; • Note there is limited catch, effort and biological information for many species of deepwater chondrichthyan; • Note that some species of deepwater chondrichthyans are highly vulnerable to overfishing due to their life history characteristics; and • Recommend to the Meeting of the Parties that stock assessment for species of deepwater chondrichthyans taken in association with commercial deepwater shark fisheries is urgently required to estimate sustainable yields and mitigate the potential for overexploitation that has been seen in similar fisheries globally. 2 Ecological risk assessment for the effects of bottom fishing gears on deepwater chondrichthyans in high seas areas of the Southern Indian and South Pacific oceans L. -
Transposable Elements and Teleost Migratory Behaviour
International Journal of Molecular Sciences Article Transposable Elements and Teleost Migratory Behaviour Elisa Carotti 1,†, Federica Carducci 1,†, Adriana Canapa 1, Marco Barucca 1,* , Samuele Greco 2 , Marco Gerdol 2 and Maria Assunta Biscotti 1 1 Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy; [email protected] (E.C.); [email protected] (F.C.); [email protected] (A.C.); [email protected] (M.A.B.) 2 Department of Life Sciences, University of Trieste, Via L. Giorgieri, 5-34127 Trieste, Italy; [email protected] (S.G.); [email protected] (M.G.) * Correspondence: [email protected] † Equal contribution. Abstract: Transposable elements (TEs) represent a considerable fraction of eukaryotic genomes, thereby contributing to genome size, chromosomal rearrangements, and to the generation of new coding genes or regulatory elements. An increasing number of works have reported a link between the genomic abundance of TEs and the adaptation to specific environmental conditions. Diadromy represents a fascinating feature of fish, protagonists of migratory routes between marine and fresh- water for reproduction. In this work, we investigated the genomes of 24 fish species, including 15 teleosts with a migratory behaviour. The expected higher relative abundance of DNA transposons in ray-finned fish compared with the other fish groups was not confirmed by the analysis of the dataset considered. The relative contribution of different TE types in migratory ray-finned species did not show clear differences between oceanodromous and potamodromous fish. On the contrary, a remarkable relationship between migratory behaviour and the quantitative difference reported for short interspersed nuclear (retro)elements (SINEs) emerged from the comparison between anadro- mous and catadromous species, independently from their phylogenetic position.