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Article Evolutionary Dynamics of the OR Gene Repertoire in Teleost Fishes
bioRxiv preprint doi: https://doi.org/10.1101/2021.03.09.434524; this version posted March 10, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Article Evolutionary dynamics of the OR gene repertoire in teleost fishes: evidence of an association with changes in olfactory epithelium shape Maxime Policarpo1, Katherine E Bemis2, James C Tyler3, Cushla J Metcalfe4, Patrick Laurenti5, Jean-Christophe Sandoz1, Sylvie Rétaux6 and Didier Casane*,1,7 1 Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198, Gif-sur-Yvette, France. 2 NOAA National Systematics Laboratory, National Museum of Natural History, Smithsonian Institution, Washington, D.C. 20560, U.S.A. 3Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., 20560, U.S.A. 4 Independent Researcher, PO Box 21, Nambour QLD 4560, Australia. 5 Université de Paris, Laboratoire Interdisciplinaire des Energies de Demain, Paris, France 6 Université Paris-Saclay, CNRS, Institut des Neurosciences Paris-Saclay, 91190, Gif-sur- Yvette, France. 7 Université de Paris, UFR Sciences du Vivant, F-75013 Paris, France. * Corresponding author: e-mail: [email protected]. !1 bioRxiv preprint doi: https://doi.org/10.1101/2021.03.09.434524; this version posted March 10, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Teleost fishes perceive their environment through a range of sensory modalities, among which olfaction often plays an important role. -
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. -
Molecular and Morphological Characterisation of The
Institute of Parasitology, Biology Centre CAS Folia Parasitologica 2021, 68: 007 doi: 10.14411/fp.2021.007 http://folia.paru.cas.cz Research Article Molecular and morphological characterisation of the metacercariae of two species of Cardiocephaloides (Digenea: Strigeidae) infecting endemic South African klipfish (Perciformes: Clinidae) Anja Vermaak1, Nico J. Smit1 and Olena Kudlai1,2,3 1 Water Research Group, Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa; 2 Institute of Ecology, Nature Research Centre, Vilnius, Lithuania; 3 Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic Abstract: South African clinids are a major component of the temperate intertidal regions that are also known to participate in life cycles and transmission of several groups of parasites. However, the knowledge of trematode diversity of these fishes is incomplete. In this study, two species of Clinus Cuvier, the super klipfish Clinus superciliosus (Linnaeus) and the bluntnose klipfish Clinus cot- toides Valenciennes, were collected from six localities along the South African coast and examined for the presence of trematodes. Metacercariae of Cardiocephaloides Sudarikov, 1959 were found in the eye vitreous humour and brain of C. superciliosus and in the eye vitreous humour of C. cottoides. Detailed analyses integrating morphological and molecular sequence data (28S rDNA, ITS2 rDNA-region, and COI mtDNA) revealed that these belong to two species, Cardiocephaloides physalis (Lutz, 1926) and an unknown species of Cardiocephaloides. This study provides the first report of clinid fishes serving as intermediate hosts for trematodes, reveals that the diversity of Cardiocephaloides in South Africa is higher than previously recorded, and highlights the need for further research to elucidate the life cycles of these trematode species. -
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. -
Ostracoda an Introduction.Pdf
The Ostracoda (from Wikipedia, 5/5/2009: http://en.wikipedia.org/wiki/Ostracod) Ostracoda is a class of the Crustacea, sometimes known as the seed shrimp because of their appearance. Ostracods are small crustaceans, typically around one mm in size, but varying between 0.2 to 30 mm, laterally compressed and protected by a bivalve-like, chitinous or calcareous valve or "shell". The hinge of the two valves is in the upper, dorsal region of the body. Some 65,000 species (13,000 of which are extant taxa) have been identified, grouped into several orders. This group may not be monophyletic. Ostracod taxa are grouped into a Class based on gross morphology. Ecologically, marine ostracods can be part of the zooplankton or (most commonly) they are part of the benthos, living on or inside the upper layer of the sea floor. Many ostracods, especially the Podocopida, are also found in fresh water and some are known from humid continental forest soils. The body consists of a cephalon (head), separated from the thorax by a slight constriction. The segmentation is unclear. The abdomen is regressed or absent whereas the adult gonads are relatively large. There are 5–8 pairs of appendages. The branchial plates are responsible for oxygenation. The epidermal cells may also secrete calcium carbonate after the chitinous layer is formed, resulting in a chalk layer enveloped by chitin. This calcification is not equally pronounced in all orders. During every instar transition, the old carapace (chitinous and calcified) is rejected and a new, larger is formed and calcified. The outer lamella calcifies completely, while the inner lamella calcifies partially, with the rest remaining chitinous. -
1 Exon Probe Sets and Bioinformatics Pipelines for All Levels of Fish Phylogenomics
bioRxiv preprint doi: https://doi.org/10.1101/2020.02.18.949735; this version posted February 19, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Exon probe sets and bioinformatics pipelines for all levels of fish phylogenomics 2 3 Lily C. Hughes1,2,3,*, Guillermo Ortí1,3, Hadeel Saad1, Chenhong Li4, William T. White5, Carole 4 C. Baldwin3, Keith A. Crandall1,2, Dahiana Arcila3,6,7, and Ricardo Betancur-R.7 5 6 1 Department of Biological Sciences, George Washington University, Washington, D.C., U.S.A. 7 2 Computational Biology Institute, Milken Institute of Public Health, George Washington 8 University, Washington, D.C., U.S.A. 9 3 Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian 10 Institution, Washington, D.C., U.S.A. 11 4 College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China 12 5 CSIRO Australian National Fish Collection, National Research Collections of Australia, 13 Hobart, TAS, Australia 14 6 Sam Noble Oklahoma Museum of Natural History, Norman, O.K., U.S.A. 15 7 Department of Biology, University of Oklahoma, Norman, O.K., U.S.A. 16 17 *Corresponding author: Lily C. Hughes, [email protected]. 18 Current address: Department of Organismal Biology and Anatomy, University of Chicago, 19 Chicago, IL. 20 21 Keywords: Actinopterygii, Protein coding, Systematics, Phylogenetics, Evolution, Target 22 capture 23 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.02.18.949735; this version posted February 19, 2020. -
Belonidae Bonaparte 1832 Needlefishes
ISSN 1545-150X California Academy of Sciences A N N O T A T E D C H E C K L I S T S O F F I S H E S Number 16 September 2003 Family Belonidae Bonaparte 1832 needlefishes By Bruce B. Collette National Marine Fisheries Service Systematics Laboratory National Museum of Natural History, Washington, DC 20560–0153, U.S.A. email: [email protected] Needlefishes are a relatively small family of beloniform fishes (Rosen and Parenti 1981 [ref. 5538], Collette et al. 1984 [ref. 11422]) that differ from other members of the order in having both the upper and the lower jaws extended into long beaks filled with sharp teeth (except in the neotenic Belonion), the third pair of upper pharyngeal bones separate, scales on the body relatively small, and no finlets following the dorsal and anal fins. The nostrils lie in a pit anterior to the eyes. There are no spines in the fins. The dorsal fin, with 11–43 rays, and anal fin, with 12–39 rays, are posterior in position; the pelvic fins, with 6 soft rays, are located in an abdominal position; and the pectoral fins are short, with 5–15 rays. The lateral line runs down from the pectoral fin origin and then along the ventral margin of the body. The scales are small, cycloid, and easily detached. Precaudal vertebrae number 33–65, caudal vertebrae 19–41, and total verte- brae 52–97. Some freshwater needlefishes reach only 6 or 7 cm (2.5 or 2.75 in) in total length while some marine species may attain 2 m (6.5 ft). -
The 17Th International Colloquium on Amphipoda
Biodiversity Journal, 2017, 8 (2): 391–394 MONOGRAPH The 17th International Colloquium on Amphipoda Sabrina Lo Brutto1,2,*, Eugenia Schimmenti1 & Davide Iaciofano1 1Dept. STEBICEF, Section of Animal Biology, via Archirafi 18, Palermo, University of Palermo, Italy 2Museum of Zoology “Doderlein”, SIMUA, via Archirafi 16, University of Palermo, Italy *Corresponding author, email: [email protected] th th ABSTRACT The 17 International Colloquium on Amphipoda (17 ICA) has been organized by the University of Palermo (Sicily, Italy), and took place in Trapani, 4-7 September 2017. All the contributions have been published in the present monograph and include a wide range of topics. KEY WORDS International Colloquium on Amphipoda; ICA; Amphipoda. Received 30.04.2017; accepted 31.05.2017; printed 30.06.2017 Proceedings of the 17th International Colloquium on Amphipoda (17th ICA), September 4th-7th 2017, Trapani (Italy) The first International Colloquium on Amphi- Poland, Turkey, Norway, Brazil and Canada within poda was held in Verona in 1969, as a simple meet- the Scientific Committee: ing of specialists interested in the Systematics of Sabrina Lo Brutto (Coordinator) - University of Gammarus and Niphargus. Palermo, Italy Now, after 48 years, the Colloquium reached the Elvira De Matthaeis - University La Sapienza, 17th edition, held at the “Polo Territoriale della Italy Provincia di Trapani”, a site of the University of Felicita Scapini - University of Firenze, Italy Palermo, in Italy; and for the second time in Sicily Alberto Ugolini - University of Firenze, Italy (Lo Brutto et al., 2013). Maria Beatrice Scipione - Stazione Zoologica The Organizing and Scientific Committees were Anton Dohrn, Italy composed by people from different countries. -
New Insights from the Neuroanatomy of Parhyale Hawaiensis
bioRxiv preprint doi: https://doi.org/10.1101/610295; this version posted April 18, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. The “amphi”-brains of amphipods: New insights from the neuroanatomy of Parhyale hawaiensis (Dana, 1853) Christin Wittfoth, Steffen Harzsch, Carsten Wolff*, Andy Sombke* Christin Wittfoth, University of Greifswald, Zoological Institute and Museum, Dept. of Cytology and Evolutionary Biology, Soldmannstr. 23, 17487 Greifswald, Germany. https://orcid.org/0000-0001-6764-4941, [email protected] Steffen Harzsch, University of Greifswald, Zoological Institute and Museum, Dept. of Cytology and Evolutionary Biology, Soldmannstr. 23, 17487 Greifswald, Germany. https://orcid.org/0000-0002-8645-3320, sharzsch@uni- greifswald.de Carsten Wolff, Humboldt University Berlin, Dept. of Biology, Comparative Zoology, Philippstr. 13, 10115 Berlin, Germany. http://orcid.org/0000-0002-5926-7338, [email protected] Andy Sombke, University of Vienna, Department of Integrative Zoology, Althanstr. 14, 1090 Vienna, Austria. http://orcid.org/0000-0001-7383-440X, [email protected] *shared last authorship ABSTRACT Background Over the last years, the amphipod crustacean Parhyale hawaiensis has developed into an attractive marine animal model for evolutionary developmental studies that offers several advantages over existing experimental organisms. It is easy to rear in laboratory conditions with embryos available year- round and amenable to numerous kinds of embryological and functional genetic manipulations. However, beyond these developmental and genetic analyses, research on the architecture of its nervous system is fragmentary. -
Proposal for a Revised Classification of the Demospongiae (Porifera) Christine Morrow1 and Paco Cárdenas2,3*
Morrow and Cárdenas Frontiers in Zoology (2015) 12:7 DOI 10.1186/s12983-015-0099-8 DEBATE Open Access Proposal for a revised classification of the Demospongiae (Porifera) Christine Morrow1 and Paco Cárdenas2,3* Abstract Background: Demospongiae is the largest sponge class including 81% of all living sponges with nearly 7,000 species worldwide. Systema Porifera (2002) was the result of a large international collaboration to update the Demospongiae higher taxa classification, essentially based on morphological data. Since then, an increasing number of molecular phylogenetic studies have considerably shaken this taxonomic framework, with numerous polyphyletic groups revealed or confirmed and new clades discovered. And yet, despite a few taxonomical changes, the overall framework of the Systema Porifera classification still stands and is used as it is by the scientific community. This has led to a widening phylogeny/classification gap which creates biases and inconsistencies for the many end-users of this classification and ultimately impedes our understanding of today’s marine ecosystems and evolutionary processes. In an attempt to bridge this phylogeny/classification gap, we propose to officially revise the higher taxa Demospongiae classification. Discussion: We propose a revision of the Demospongiae higher taxa classification, essentially based on molecular data of the last ten years. We recommend the use of three subclasses: Verongimorpha, Keratosa and Heteroscleromorpha. We retain seven (Agelasida, Chondrosiida, Dendroceratida, Dictyoceratida, Haplosclerida, Poecilosclerida, Verongiida) of the 13 orders from Systema Porifera. We recommend the abandonment of five order names (Hadromerida, Halichondrida, Halisarcida, lithistids, Verticillitida) and resurrect or upgrade six order names (Axinellida, Merliida, Spongillida, Sphaerocladina, Suberitida, Tetractinellida). Finally, we create seven new orders (Bubarida, Desmacellida, Polymastiida, Scopalinida, Clionaida, Tethyida, Trachycladida). -
Sharkcam Fishes
SharkCam Fishes A Guide to Nekton at Frying Pan Tower By Erin J. Burge, Christopher E. O’Brien, and jon-newbie 1 Table of Contents Identification Images Species Profiles Additional Info Index Trevor Mendelow, designer of SharkCam, on August 31, 2014, the day of the original SharkCam installation. SharkCam Fishes. A Guide to Nekton at Frying Pan Tower. 5th edition by Erin J. Burge, Christopher E. O’Brien, and jon-newbie is licensed under the Creative Commons Attribution-Noncommercial 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc/4.0/. For questions related to this guide or its usage contact Erin Burge. The suggested citation for this guide is: Burge EJ, CE O’Brien and jon-newbie. 2020. SharkCam Fishes. A Guide to Nekton at Frying Pan Tower. 5th edition. Los Angeles: Explore.org Ocean Frontiers. 201 pp. Available online http://explore.org/live-cams/player/shark-cam. Guide version 5.0. 24 February 2020. 2 Table of Contents Identification Images Species Profiles Additional Info Index TABLE OF CONTENTS SILVERY FISHES (23) ........................... 47 African Pompano ......................................... 48 FOREWORD AND INTRODUCTION .............. 6 Crevalle Jack ................................................. 49 IDENTIFICATION IMAGES ...................... 10 Permit .......................................................... 50 Sharks and Rays ........................................ 10 Almaco Jack ................................................. 51 Illustrations of SharkCam -
Cusk Eels, Brotulas [=Cherublemma Trotter [E
FAMILY Ophidiidae Rafinesque, 1810 - cusk eels SUBFAMILY Ophidiinae Rafinesque, 1810 - cusk eels [=Ofidini, Otophidioidei, Lepophidiinae, Genypterinae] Notes: Ofidini Rafinesque, 1810b:38 [ref. 3595] (ordine) Ophidion [as Ophidium; latinized to Ophididae by Bonaparte 1831:162, 184 [ref. 4978] (family); stem corrected to Ophidi- by Lowe 1843:92 [ref. 2832], confirmed by Günther 1862a:317, 370 [ref. 1969], by Gill 1872:3 [ref. 26254] and by Carus 1893:578 [ref. 17975]; considered valid with this authorship by Gill 1893b:136 [ref. 26255], by Goode & Bean 1896:345 [ref. 1848], by Nolf 1985:64 [ref. 32698], by Patterson 1993:636 [ref. 32940] and by Sheiko 2013:63 [ref. 32944] Article 11.7.2; family name sometimes seen as Ophidionidae] Otophidioidei Garman, 1899:390 [ref. 1540] (no family-group name) Lepophidiinae Robins, 1961:218 [ref. 3785] (subfamily) Lepophidium Genypterinae Lea, 1980 (subfamily) Genypterus [in unpublished dissertation: Systematics and zoogeography of cusk-eels of the family Ophidiidae, subfamily Ophidiinae, from the eastern Pacific Ocean, University of Miami, not available] GENUS Cherublemma Trotter, 1926 - cusk eels, brotulas [=Cherublemma Trotter [E. S.], 1926:119, Brotuloides Robins [C. R.], 1961:214] Notes: [ref. 4466]. Neut. Cherublemma lelepris Trotter, 1926. Type by monotypy. •Valid as Cherublemma Trotter, 1926 -- (Pequeño 1989:48 [ref. 14125], Robins in Nielsen et al. 1999:27, 28 [ref. 24448], Castellanos-Galindo et al. 2006:205 [ref. 28944]). Current status: Valid as Cherublemma Trotter, 1926. Ophidiidae: Ophidiinae. (Brotuloides) [ref. 3785]. Masc. Leptophidium emmelas Gilbert, 1890. Type by original designation (also monotypic). •Synonym of Cherublemma Trotter, 1926 -- (Castro-Aguirre et al. 1993:80 [ref. 21807] based on placement of type species, Robins in Nielsen et al.