Evolutionary History of the Butterflyfishes (F: Chaetodontidae
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Phylogenetic Models Linking Speciation and Extinction to Chromosome and Mating System Evolution
Phylogenetic Models Linking Speciation and Extinction to Chromosome and Mating System Evolution by William Allen Freyman A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Integrative Biology and the Designated Emphasis in Computational and Genomic Biology in the Graduate Division of the University of California, Berkeley Committee in charge: Dr. Bruce G. Baldwin, Chair Dr. John P. Huelsenbeck Dr. Brent D. Mishler Dr. Kipling W. Will Fall 2017 Phylogenetic Models Linking Speciation and Extinction to Chromosome and Mating System Evolution Copyright 2017 by William Allen Freyman Abstract Phylogenetic Models Linking Speciation and Extinction to Chromosome and Mating System Evolution by William Allen Freyman Doctor of Philosophy in Integrative Biology and the Designated Emphasis in Computational and Genomic Biology University of California, Berkeley Dr. Bruce G. Baldwin, Chair Key evolutionary transitions have shaped the tree of life by driving the processes of spe- ciation and extinction. This dissertation aims to advance statistical and computational ap- proaches that model the timing and nature of these transitions over evolutionary trees. These methodological developments in phylogenetic comparative biology enable formal, model- based, statistical examinations of the macroevolutionary consequences of trait evolution. Chapter 1 presents computational tools for data mining the large-scale molecular sequence datasets needed for comparative phylogenetic analyses. I describe a novel metric, the miss- ing sequence decisiveness score (MSDS), which assesses the phylogenetic decisiveness of a matrix given the pattern of missing sequence data. In Chapter 2, I introduce a class of phylogenetic models of chromosome number evolution that accommodate both anagenetic and cladogenetic change. -
Reef Fish Biodiversity in the Florida Keys National Marine Sanctuary Megan E
University of South Florida Scholar Commons Graduate Theses and Dissertations Graduate School November 2017 Reef Fish Biodiversity in the Florida Keys National Marine Sanctuary Megan E. Hepner University of South Florida, [email protected] Follow this and additional works at: https://scholarcommons.usf.edu/etd Part of the Biology Commons, Ecology and Evolutionary Biology Commons, and the Other Oceanography and Atmospheric Sciences and Meteorology Commons Scholar Commons Citation Hepner, Megan E., "Reef Fish Biodiversity in the Florida Keys National Marine Sanctuary" (2017). Graduate Theses and Dissertations. https://scholarcommons.usf.edu/etd/7408 This Thesis is brought to you for free and open access by the Graduate School at Scholar Commons. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Scholar Commons. For more information, please contact [email protected]. Reef Fish Biodiversity in the Florida Keys National Marine Sanctuary by Megan E. Hepner A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science Marine Science with a concentration in Marine Resource Assessment College of Marine Science University of South Florida Major Professor: Frank Muller-Karger, Ph.D. Christopher Stallings, Ph.D. Steve Gittings, Ph.D. Date of Approval: October 31st, 2017 Keywords: Species richness, biodiversity, functional diversity, species traits Copyright © 2017, Megan E. Hepner ACKNOWLEDGMENTS I am indebted to my major advisor, Dr. Frank Muller-Karger, who provided opportunities for me to strengthen my skills as a researcher on research cruises, dive surveys, and in the laboratory, and as a communicator through oral and presentations at conferences, and for encouraging my participation as a full team member in various meetings of the Marine Biodiversity Observation Network (MBON) and other science meetings. -
Pacific Plate Biogeography, with Special Reference to Shorefishes
Pacific Plate Biogeography, with Special Reference to Shorefishes VICTOR G. SPRINGER m SMITHSONIAN CONTRIBUTIONS TO ZOOLOGY • NUMBER 367 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 Astrophysics Smithsonian Contributions to Botany Smithsonian Contributions to the Earth Sciences Smithsonian Contributions to the Marine Sciences Smithsonian Contributions to Paleobiology Smithsonian Contributions to Zoo/ogy 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 cf 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. -
Mantas, Dolphins & Coral Reefs – a Maldives Cruise
Mantas, Dolphins & Coral Reefs – A Maldives Cruise Naturetrek Tour Report 8 – 17 February 2019 Hawksbill Turtle Manta Ray Short-finned Pilot Whale Black-footed Anemone Fish Report & images compiled by Sara Frost Naturetrek Mingledown Barn Wolf's Lane Chawton Alton Hampshire GU34 3HJ UK T: +44 (0)1962 733051 E: [email protected] W: www.naturetrek.co.uk Tour Report Mantas, Dolphins & Coral Reefs – A Maldives Cruise Tour participants: Sara Frost and Chas Anderson (tour leaders) with 15 Naturetrek clients Summary Our time spent cruising around the beautiful Maldivian islands and atolls resulted in some superb marine wildlife encounters, and lovely warm evenings anchored off remote tropical islands, a dazzling variety of colourful fish, numerous turtles and dolphins and a daily visual feast of innumerable shades of turquoise! The highlight was the group’s encounter with a group of 6 Manta Rays while snorkelling. We enjoyed a morning’s excitement as the Mantas appeared and disappeared alongside us, their huge mouths wide open as they fed on the plankton, with all of the group getting fantastic close-up views! Every morning and evening, the group enjoyed a pre-breakfast and pre-dinner snorkel on coral reefs, where the colour and variety of fish was wonderful! Regal Angelfish, parrotfish, sea cucumbers, many different types of butterflyfish and wrasses, Maldive Anemonefish, reef squid, triggerfish, Moorish Idols, both White- and Black- tipped Reef Sharks and Hawksbill Turtles were just a few of the highlights! Back on board, while cruising between atolls, islands and reefs, seven confirmed species of cetacean were seen: several groups of Spinner Dolphins (including one huge group of at least 500), Pan-tropical Spotted Dolphins, both Common and Indo- Pacific Bottlenose Dolphins, plus Fraser’s Dolphins, plus Risso’s Dolphins and two groups of Pilot Whales – the first being very inquisitive and spending an hour with us spy hopping alongside the boat! All in all, it was a wonderful trip that will never be forgotten. -
Relative Gut Lengths of Coral Reef Butterflyfishes (Pisces
Relative gut lengths of coral reef butterflyfishes (Pisces: Chaetodontidae) ML Berumen1, 2 *, MS Pratchett3, BA Goodman4 1. Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, 23955, Kingdom of Saudi Arabia 2. Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA 3. ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia 4. Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309 * Corresponding author: Email: [email protected] Phone: +966 544700019 Keywords: Chaetodontidae; corallivory; Papua New Guinea; relative gut length Abstract Variation in gut length of closely related animals is known to generally be a good predictor of dietary habits. We examined gut length in 28 species of butterflyfishes (Chaetodontidae), which encompass a wide range of dietary types (planktivores, omnivores, corallivores). We found general dietary patterns to be a good predictor of relative gut length, although we found high variation among groups and covariance with body size. The longest gut lengths are found in species that exclusively feed on the living tissue of corals, while the shortest gut length is found in a planktivorous species. Although we tried to control for phylogeny, corallivory has arisen multiple times in this family, confounding our analyses. The butterflyfishes, a speciose family with a wide range of dietary habits, may nonetheless provide an ideal system for future work studying gut physiology associated with specialisation and foraging behaviours. Introduction Relative gut lengths of vertebrates have long been studied and compared within and among species (e.g., Al-Hussaini 1949). The most common explanations for relatively longer guts in herbivores focus on the chemical defences of plants (e.g., Levin 1976; Hay and Fenical 1988), the indigestibility of plant fibre (e.g., Stevens 1989; Karasov and Martinez del Rio 2007), or the poor nutritional quality of plants as food. -
Genetic Change and Rates of Cladogenesis
GENETIC CHANGE AND RATES OF CLADOGENESIS JOHN C. AVISE* AND FRANCISCO J. AYALA Depariment of Genetics, University of Californiu, Davis, California 95616 Manuscript received May 12, 1975 Revised copy received July 28, 1975 ABSTRACT Models are introduced which predict ratios of mean levels of genetic divergence in species-rich versus species-poor phylads under two competing assumptions: (1) genetic differentiation is a function of time, unrelated to the number of cladogenetic events and (2) genetic differentiation is proportional to the number of speciation events in the group. The models are simple, general, and biologically real, but not precise. They lead to qualitatively distinct predic- tions about levels of genetic divergence depending upon the relationship between rates of speciation and amount of genetic change. When genetic dis- tance between species is a function of time, mean genetic distances in speciose and depauperate phylads of equal evolutionary age are very similar. On the contrary, when genetic distance is a function of the number of speciations in the history of a phylad, the ratio of mean genetic distances separating species in speciose versus depauperate phylads is greater than one, and increases rapidly as the frequency of speciations in one group relative to the other increases. The models may be tested with data from natural populations to assess (1) possible correlations between rates of anagenesis and cladogenesis and (2) the amount of genetic differentiation accompanying the speciation process. The data collected in electrophoretic surveys and other kinds of studies can be used to test the predictions of the models. For this purpose genetic distances need to be measured in speciose and depauperate phylads of equal evolutionary age. -
Chelmon Rostratus (Linnaeus, 1758) Coradion Altivelis Mcculloch, 1916
click for previous page 3258 Bony Fishes Chelmon rostratus (Linnaeus, 1758) En - Copperbanded butterflyfish. Maximum total length about 20 cm. Inhabits coral reefs at depths of 3 to 20 m. Feeds on crabs, worms, and other invertebrates; usually in pairs. Frequently exported through the aquarium trade. Distributed from the Andaman Sea eastward throughout the Indo-Malayan region, northward to southern Japan and the Great Barrier Reef. Coradion altivelis McCulloch, 1916 En - Highfin coralfish; Fr - Coradion à grande voile. Maximum total length about 15 cm. Inhabits outer reef slopes and drop-offs at depths of 3 to 15 m. Omnivorous; usually in pairs. Rarely exported through the aquarium trade. Distributed from the Andaman Sea eastward throughout the Indo-Malayan region, northward to southern Japan and the Great Barrier Reef. Perciformes: Percoidei: Chaetodontidae 3259 Coradion chrysozonus (Kuhl and van Hasselt in Cuvier, 1831) En - Orangebanded coralfish. Maximum total length about 15 cm. Inhabits outer reef slopes and drop-offs at depths of 3 to 15 m. Omnivorous; usually in pairs. Rarely exported through the aquarium trade. Distributed from the Andaman Sea eastward throughout the Indo-Malayan region, northward to southern Japan and the Great Barrier Reef. Coradion melanopus (Cuvier, 1831) En - Two-eyed coralfish. Maximum total length about 13 cm. Inhabits lagoons and coral reefs at depths of 3 to 15 m. Omnivorous; usually in pairs. Rarely exported through the aquarium trade. Distributed throughout the Indo-Malayan region eastward to Papua New Guinea. 3260 Bony Fishes Forcipiger flavissimus Jordan and McGregor, 1898 En - Forcepsfish; Fr - Chelmon à long bec. Maximum total length about 15 cm. -
Lineages, Splits and Divergence Challenge Whether the Terms Anagenesis and Cladogenesis Are Necessary
Biological Journal of the Linnean Society, 2015, , – . With 2 figures. Lineages, splits and divergence challenge whether the terms anagenesis and cladogenesis are necessary FELIX VAUX*, STEVEN A. TREWICK and MARY MORGAN-RICHARDS Ecology Group, Institute of Agriculture and Environment, Massey University, Palmerston North, New Zealand Received 3 June 2015; revised 22 July 2015; accepted for publication 22 July 2015 Using the framework of evolutionary lineages to separate the process of evolution and classification of species, we observe that ‘anagenesis’ and ‘cladogenesis’ are unnecessary terms. The terms have changed significantly in meaning over time, and current usage is inconsistent and vague across many different disciplines. The most popular definition of cladogenesis is the splitting of evolutionary lineages (cessation of gene flow), whereas anagenesis is evolutionary change between splits. Cladogenesis (and lineage-splitting) is also regularly made synonymous with speciation. This definition is misleading as lineage-splitting is prolific during evolution and because palaeontological studies provide no direct estimate of gene flow. The terms also fail to incorporate speciation without being arbitrary or relative, and the focus upon lineage-splitting ignores the importance of divergence, hybridization, extinction and informative value (i.e. what is helpful to describe as a taxon) for species classification. We conclude and demonstrate that evolution and species diversity can be considered with greater clarity using simpler, more transparent terms than anagenesis and cladogenesis. Describing evolution and taxonomic classification can be straightforward, and there is no need to ‘make words mean so many different things’. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 00, 000–000. -
Fishes of Terengganu East Coast of Malay Peninsula, Malaysia Ii Iii
i Fishes of Terengganu East coast of Malay Peninsula, Malaysia ii iii Edited by Mizuki Matsunuma, Hiroyuki Motomura, Keiichi Matsuura, Noor Azhar M. Shazili and Mohd Azmi Ambak Photographed by Masatoshi Meguro and Mizuki Matsunuma iv Copy Right © 2011 by the National Museum of Nature and Science, Universiti Malaysia Terengganu and Kagoshima University Museum All rights reserved. No part of this publication may be reproduced or transmitted in any form or by any means without prior written permission from the publisher. Copyrights of the specimen photographs are held by the Kagoshima Uni- versity Museum. For bibliographic purposes this book should be cited as follows: Matsunuma, M., H. Motomura, K. Matsuura, N. A. M. Shazili and M. A. Ambak (eds.). 2011 (Nov.). Fishes of Terengganu – east coast of Malay Peninsula, Malaysia. National Museum of Nature and Science, Universiti Malaysia Terengganu and Kagoshima University Museum, ix + 251 pages. ISBN 978-4-87803-036-9 Corresponding editor: Hiroyuki Motomura (e-mail: [email protected]) v Preface Tropical seas in Southeast Asian countries are well known for their rich fish diversity found in various environments such as beautiful coral reefs, mud flats, sandy beaches, mangroves, and estuaries around river mouths. The South China Sea is a major water body containing a large and diverse fish fauna. However, many areas of the South China Sea, particularly in Malaysia and Vietnam, have been poorly studied in terms of fish taxonomy and diversity. Local fish scientists and students have frequently faced difficulty when try- ing to identify fishes in their home countries. During the International Training Program of the Japan Society for Promotion of Science (ITP of JSPS), two graduate students of Kagoshima University, Mr. -
Paleobiology & Paleontology
Geos 315W Course Syllabus Paleobiology & Lectures: MWF 9:15 AM –10:15 AM 233 Reichardt Paleontology Labs: M 2:15-5:15 PM M 6:00-9:00 PM 4 Credits 229 Reichardt Prerequisites: Geos 112 or Biol 103 or Biol 115 Engl 111 and Engl 211 or Engl 213 Professor: Sarah J. Fowell TA: Alec Rizzo E-mail: [email protected] E-mail: [email protected] Office: 326 Reichardt Office: 305 Reichardt Phone: 474-7810 Hours: By appointment Hours: T 11:00–12:30 W 1:00-2:30 Required Items: • i >clicker: i>clickers will be checked out to students for a $30 deposit (cash only). You will get your deposit back when you return the clicker at the end of the semester. If you lose your clicker or fail to return it, the department will retain your deposit and put it toward the purchase of a replacement. Go to the Geology Department office (308 Reichardt) check out your clicker. Scored clicking will begin on Wednesday, September 11. Recommended Textbook: • Benton & Harper, 2009. Introduction to Paleobiology and the Fossil Record. Wiley-Blackwell, ISBN: 978-1405141574. Go to amazon.com to purchase, rent, or download the Kindle Edition of this textbook. P aleontological investigations seek to describe temporal and spatial changes in Earth's flora and fauna within the context of geological processes, stratigraphy, and evolution. Consequently, the study of paleontology requires a working knowledge of more than one discipline. One of the principal goals of this course is to demonstrate the interdependence of scientific disciplines in any investigation of large- scale patterns and events in the natural world. -
Reef Fishes of the Bird's Head Peninsula, West
Check List 5(3): 587–628, 2009. ISSN: 1809-127X LISTS OF SPECIES Reef fishes of the Bird’s Head Peninsula, West Papua, Indonesia Gerald R. Allen 1 Mark V. Erdmann 2 1 Department of Aquatic Zoology, Western Australian Museum. Locked Bag 49, Welshpool DC, Perth, Western Australia 6986. E-mail: [email protected] 2 Conservation International Indonesia Marine Program. Jl. Dr. Muwardi No. 17, Renon, Denpasar 80235 Indonesia. Abstract A checklist of shallow (to 60 m depth) reef fishes is provided for the Bird’s Head Peninsula region of West Papua, Indonesia. The area, which occupies the extreme western end of New Guinea, contains the world’s most diverse assemblage of coral reef fishes. The current checklist, which includes both historical records and recent survey results, includes 1,511 species in 451 genera and 111 families. Respective species totals for the three main coral reef areas – Raja Ampat Islands, Fakfak-Kaimana coast, and Cenderawasih Bay – are 1320, 995, and 877. In addition to its extraordinary species diversity, the region exhibits a remarkable level of endemism considering its relatively small area. A total of 26 species in 14 families are currently considered to be confined to the region. Introduction and finally a complex geologic past highlighted The region consisting of eastern Indonesia, East by shifting island arcs, oceanic plate collisions, Timor, Sabah, Philippines, Papua New Guinea, and widely fluctuating sea levels (Polhemus and the Solomon Islands is the global centre of 2007). reef fish diversity (Allen 2008). Approximately 2,460 species or 60 percent of the entire reef fish The Bird’s Head Peninsula and surrounding fauna of the Indo-West Pacific inhabits this waters has attracted the attention of naturalists and region, which is commonly referred to as the scientists ever since it was first visited by Coral Triangle (CT). -
Suborder ACANTHUROIDEI EPHIPPIDAE Chaetodipterus Faber
click for previous page Perciformes: Acanthuroidei: Ephippidae 1799 Suborder ACANTHUROIDEI EPHIPPIDAE Spadefishes by W.E. Burgess, Red Bank, New Jersey, USA A single species occurring in the area. Chaetodipterus faber (Broussonet, 1782) HRF Frequent synonyms / misidentifications: None / None. FAO names: En - Atlantic spadefish; Fr - Disque portuguais; Sp - Paguara. Diagnostic characters: Body deep, included 1.2 to 1.5 times in standard length, orbicular, strongly compressed. Mouth small, terminal, jaws provided with bands of brush-like teeth, outer row larger and slightly compressed but pointed at tip. Vomer and palatines toothless. Preopercular margin finely serrate; opercle ends in blunt point. Dorsal fin with 9 spines and 21 to 23 soft rays. Spinous portion of dorsal fin low in adults, distinct from soft-rayed portion; anterior portion of soft dorsal and anal fins prolonged.Juve- niles with third dorsal fin spine prolonged, becoming proportionately smaller with age. Anal fin with 3 spines and 18 or 19 rays. Pectoral fins short, about 1.6 in head, with 17 or 18 soft rays. Caudal fin emarginate. Pelvic fins long, extending to origin of anal fin in adults, beyond that in young. Lateral-line scales 45 to 50. Head and fins scaled. Colour: silvery grey with blackish bars (bars may fade in large individuals) as follows: Eye bar extends from nape through eye to chest; first body bar starts at predorsal area, crosses body behind pectoral fin insertion, and ends on abdomen; second body bar incomplete, extending from anterior dorsal-fin spines vertically toward abdomen but ending just below level of pectoral-fin base;third body bar extends from anterior rays of dorsal fin across body to anterior rays of anal fin;last body bar runs from the middle soft dorsal fin rays to middle soft anal-fin rays; last bar crosses caudal peduncle at caudal-fin base.