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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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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. -
Coral Injuries Caused by Spirobranchus Opercula with and Without Epibiotic Turf Algae at Curaçao
Marine Biology (2019) 166:60 https://doi.org/10.1007/s00227-019-3504-6 SHORT NOTE Coral injuries caused by Spirobranchus opercula with and without epibiotic turf algae at Curaçao Bert W. Hoeksema1,2 · Dagmar Wels1 · Roeland J. van der Schoot1 · Harry A. ten Hove1 Received: 11 January 2019 / Accepted: 26 March 2019 © The Author(s) 2019 Abstract Reef-dwelling Christmas tree worms (Spirobranchus spp.) are common coral associates. Their calcareous tubes are usually embedded in the coral skeleton and can be closed by an operculum. Tubes not overgrown by coral tissue either remain bare or become covered by algae. Despite their widespread distribution, high abundance and striking appearance, little is known about the impact of these worms on their hosts. We quantifed visible coral damage caused by Spirobranchus in Curaçao (Southern Caribbean) and found that 62.6% of worm opercula (n = 1323) caused abrasions and tissue loss in their hosts. Filamentous turf algae, known to be potentially harmful to corals, covered 76.9% of the opercula. Examination of the six most frequently inhabited host species showed a variation in the damage percentages, although this was independent of the presence of epibiotic algae on 78.4% of all opercula. Since injured corals are more susceptible to diseases, the overall nega- tive impact of Spirobranchus worms on their hosts may be more severe than previously assumed. Introduction and Nishihira 1996), even if the host becomes overgrown by sponges and octocorals, which in turn can act as replacement Coral-dwelling tubeworms of the genus Spirobranchus hosts (Hoeksema et al. 2015, 2016; García-Hernández and (Polychaeta: Serpulidae), known popularly as Christmas Hoeksema 2017). -
Hotspots, Extinction Risk and Conservation Priorities of Greater Caribbean and Gulf of Mexico Marine Bony Shorefishes
Old Dominion University ODU Digital Commons Biological Sciences Theses & Dissertations Biological Sciences Summer 2016 Hotspots, Extinction Risk and Conservation Priorities of Greater Caribbean and Gulf of Mexico Marine Bony Shorefishes Christi Linardich Old Dominion University, [email protected] Follow this and additional works at: https://digitalcommons.odu.edu/biology_etds Part of the Biodiversity Commons, Biology Commons, Environmental Health and Protection Commons, and the Marine Biology Commons Recommended Citation Linardich, Christi. "Hotspots, Extinction Risk and Conservation Priorities of Greater Caribbean and Gulf of Mexico Marine Bony Shorefishes" (2016). Master of Science (MS), Thesis, Biological Sciences, Old Dominion University, DOI: 10.25777/hydh-jp82 https://digitalcommons.odu.edu/biology_etds/13 This Thesis is brought to you for free and open access by the Biological Sciences at ODU Digital Commons. It has been accepted for inclusion in Biological Sciences Theses & Dissertations by an authorized administrator of ODU Digital Commons. For more information, please contact [email protected]. HOTSPOTS, EXTINCTION RISK AND CONSERVATION PRIORITIES OF GREATER CARIBBEAN AND GULF OF MEXICO MARINE BONY SHOREFISHES by Christi Linardich B.A. December 2006, Florida Gulf Coast University A Thesis Submitted to the Faculty of Old Dominion University in Partial Fulfillment of the Requirements for the Degree of MASTER OF SCIENCE BIOLOGY OLD DOMINION UNIVERSITY August 2016 Approved by: Kent E. Carpenter (Advisor) Beth Polidoro (Member) Holly Gaff (Member) ABSTRACT HOTSPOTS, EXTINCTION RISK AND CONSERVATION PRIORITIES OF GREATER CARIBBEAN AND GULF OF MEXICO MARINE BONY SHOREFISHES Christi Linardich Old Dominion University, 2016 Advisor: Dr. Kent E. Carpenter Understanding the status of species is important for allocation of resources to redress biodiversity loss. -
Concentración Y Tiempo Máximo De Exposición De Juveniles De Pargo
State of research of the Osteichthyes fish related to coral reefs in the Honduran Caribbean with catalogued records Estado del conocimiento de los peces osteíctios asociados a los arrecifes de coral en el Caribe de Honduras, con registros catalogados Anarda Isabel Salgado Ordoñez1, Julio Enrique Mérida Colindres1* & Gustavo Adolfo Cruz1 ABSTRACT Research on Honduran coral reef fish has been isolated and scattered. A list of fish species related to coral reefs was consolidated to establish a compiled database with updated taxonomy. The study was conducted between October 2017 and December 2018. Using primary and secondary sources, all potential species in the Western Atlantic were considered, and their actual presence was confirmed using catalogued records published in peer-reviewed journals that included Honduras. In addition, the specimens kept in the Museum of Natural History of Universidad Nacional Autónoma de Honduras were added. Once the list was consolidated, the taxonomic status of each species was updated based on recent literature. A total of 159 species and 76 genera were registered in 32 families. The family with the most species was Labrisomidae with 27 species (17%). Five families had more than five 5 genera registered, while four 4 were represented by more than 16 species, which is equivalent to 42% genera and 51% species. Gobiidae was represented by 10 genera (13%) and 21 species (13%), of which two 2 were endemic: Tigrigobius rubrigenis and Elacatinus lobeli. In turn, Grammatidae was represented by one endemic species Lipogramma idabeli (1.8%). The species Diodon holocanthus and Sphoeroides testudineus represent the first catalogued records for Honduras. -
Baseline Ecological Inventory for Three Bays National Park, Haiti OCTOBER 2016
Baseline Ecological Inventory for Three Bays National Park, Haiti OCTOBER 2016 Report for the Inter-American Development Bank (IDB) 1 To cite this report: Kramer, P, M Atis, S Schill, SM Williams, E Freid, G Moore, JC Martinez-Sanchez, F Benjamin, LS Cyprien, JR Alexis, R Grizzle, K Ward, K Marks, D Grenda (2016) Baseline Ecological Inventory for Three Bays National Park, Haiti. The Nature Conservancy: Report to the Inter-American Development Bank. Pp.1-180 Editors: Rumya Sundaram and Stacey Williams Cooperating Partners: Campus Roi Henri Christophe de Limonade Contributing Authors: Philip Kramer – Senior Scientist (Maxene Atis, Steve Schill) The Nature Conservancy Stacey Williams – Marine Invertebrates and Fish Institute for Socio-Ecological Research, Inc. Ken Marks – Marine Fish Atlantic and Gulf Rapid Reef Assessment (AGRRA) Dave Grenda – Marine Fish Tampa Bay Aquarium Ethan Freid – Terrestrial Vegetation Leon Levy Native Plant Preserve-Bahamas National Trust Gregg Moore – Mangroves and Wetlands University of New Hampshire Raymond Grizzle – Freshwater Fish and Invertebrates (Krystin Ward) University of New Hampshire Juan Carlos Martinez-Sanchez – Terrestrial Mammals, Birds, Reptiles and Amphibians (Françoise Benjamin, Landy Sabrina Cyprien, Jean Roudy Alexis) Vermont Center for Ecostudies 2 Acknowledgements This project was conducted in northeast Haiti, at Three Bays National Park, specifically in the coastal zones of three communes, Fort Liberté, Caracol, and Limonade, including Lagon aux Boeufs. Some government departments, agencies, local organizations and communities, and individuals contributed to the project through financial, intellectual, and logistical support. On behalf of TNC, we would like to express our sincere thanks to all of them. First, we would like to extend our gratitude to the Government of Haiti through the National Protected Areas Agency (ANAP) of the Ministry of Environment, and particularly Minister Dominique Pierre, Ministre Dieuseul Simon Desras, Mr. -
Cayman Islands Based on These Data and Survey Data from the Reef Environmental Education Foundation Database
STATUS OF CORAL REEFS OF LITTLE CAYMAN AND GRAND CAYMAN, BRITISH WEST INDIES, IN 1999 (PART 2: FISHES) BY CHRISTY V. PATTENGILL-SEMMENS,1 and BRICE X. SEMMENS2 ABSTRACT The fish assemblages at 33 sites around the islands of Grand Cayman and Little Cayman were assessed in June 1999 for the Atlantic and Gulf Rapid Reef Assessment initiative using belt transects and Roving Diver Technique surveys. A comprehensive species list, with 58 new records, was compiled for the Cayman Islands based on these data and survey data from the Reef Environmental Education Foundation database. In general, the reefs on Little Cayman appeared to support larger and more individual fishes than those of Grand Cayman. A multidimensional scaling ordination plot showed no clear island pattern but did reveal that the windward or leeward location of each site was an important factor affecting fish community composition. All but two sites followed a pattern of distinct windward and leeward clusters, and these clusters also correlated to macroalgal abundance. The relationship between macroalgal abundance and herbivore density was analyzed and significant correlations were found with surgeonfishes (Acanthuridae) and parrotfishes (Scaridae) using multiple regression. INTRODUCTION Fishes have the potential to provide sensitive indices of reef health. Certain predatory fish species dominate the top of coral reef food webs, hence their density reflects a vast number of human and natural disturbances from habitat alteration to direct exploitation (Ferreira et al., 1998). Similarly, the presence and abundance of herbivorous fishes affect algal composition and cover (Ogden and Lobel, 1978). In response to concerns about the widespread deterioration of reef condition in the Caribbean basin, the Atlantic and Gulf Rapid Reef Assessment (AGRRA) initiative was designed to provide a regional perspective using a standardized methodology. -
Habitat Selection of the Coral-Dwelling Spinyhead Blenny, Acanthemblemaria Spinosa, at Curaçao, Dutch Caribbean
Mar Biodiv DOI 10.1007/s12526-016-0543-9 CARIBBEAN CORAL REEFS Habitat selection of the coral-dwelling spinyhead blenny, Acanthemblemaria spinosa, at Curaçao, Dutch Caribbean Thijs Böhm1 & Bert W. Hoeksema1,2 Received: 5 May 2016 /Revised: 24 June 2016 /Accepted: 28 June 2016 # The Author(s) 2016. This article is published with open access at Springerlink.com Abstract The distribution, abundance, and habitat preferences Introduction of the spinyhead blenny, Acanthemblemaria spinosa (Perciformes, Blennioidei, Chaenopsidae), were studied on cor- Cryptobenthic fishes are usually the most diverse and abundant al reefs along the leeward side of Curaçao, southern Caribbean. component of reef fish fauna, but they are easily overlooked The blennies inhabited small holes inside coral, which predom- because of their small sizes and hidden lifestyles (Munday and inantly consisted of calcareous tubes constructed by coral- Jones 1998; Ahmadia et al. 2012a). Their high abundance sug- associated serpulid worms of the species Spirobranchus gests that they play an important role in the food webs on coral giganteus. About 50 % of the fish inhabited holes in dead coral, reefs (Wilson 2001;DepczunskiandBellwood2003). and the rest had their holes in live corals of eight species. The Distribution patterns of such small reef fishes depend on various fishes showed a clustered distribution pattern and their abun- environmental factors, such as the availability of food and shelter, dance was higher at shallow depths (5 and 10 m) than at 15 m. and depth preferences (Williams 1991; Zikova et al. 2011; Although males generally had a larger body size than females Ahmadia et al. 2012a, b; Dalben and Floeter 2012; Harborne and needed larger holes for shelter and guarding eggs, no sexual et al. -
Acanthemblemaria Spinosa (Spinyhead Blenny)
UWI The Online Guide to the Animals of Trinidad and Tobago Diversity Acanthemblemaria spinosa (Spinyhead Blenny) Family: Chaenopsidae (Tube Blennies) Order: Perciformes (Perch and Allied Fish) Class: Actinopterygii (Ray-finned Fish) Fig. 1. Spinyhead blenny, Acanthemblemaria spinosa. [http://www.fishbase.org/Photos/PicturesSummary.php?StartRow=1&ID=16486&what=species&TotRec=4, downloaded 2 November 2016] TRAITS. Small, tube-dwelling blennies (Skaphandrus, 2016), with an elongated body (Wikipedia, 2016) (Fig. 1). The maximum length is 3.1cm (Fishbase, 2016) with an average of 20-25mm long (Clark et al., 2005). There is minor sexual diphorphism between the sexes with males being larger and outnumbering their female counterparts 2:1. Body with 20-22 dorsal spines; 2 anal spines; 21-25 anal soft rays; and 13-16 dorsal soft rays (IUCN, 2016). Colour ranges from pale grey to yellow (Synder and Burgess, 2016) to green and brown (Greenfield and Johnson, 1981). Body characteristic of brown blotches and white spots (Skaphandrus, 2016). Head is rounded with numerous branched and unbranched cirri; fleshy stalks and spikes (Synder and Burgess, 2016). DISTRIBUTION. Widespread over the western Atlantic (Fig. 2) on coral reefs. Spans from Florida to Bahamas and throughout the Caribbean islands (Clarke et al., 2005). UWI The Online Guide to the Animals of Trinidad and Tobago Diversity HABITAT AND ECOLOGY. Inhabits shallow marine waters less than 15m in depth. They are found mainly on elkorn corals (Buchheim and Hixon, 1992) and Acropora palmata corals (Greenfield and Johnson, 1981). Spinyheand blennies live and spend most of their life confined in calcareous worm holes (holes created by invertebrates in corals - Fig. -
Coral Reef Ecosystems of Reserva Natural De La Parguera (Puerto
Coral reef ecosystems of Reserva Natural de La Parguera (Puerto Rico): Spatial and temporal patterns in fish and benthic communities (2001-2007) A cooperative investigation between NOAA and the University of Puerto Rico April 2010 SImon J. Pittman Sarah D. Hile Christopher F.G. Jeffrey Randy Clark Kimberly Woody Brook Herlach Chris Caldow Mark Monaco Richard Appeldoorn NOAA Technical Memorandum NOS NCCOS 107 Mention of trade names or commercial products does not constitute endorsement or recommendation for their use by the United States government. ACKNOWLEDGEMENTS: This report was made possible through the participation of the individuals recognized above. Their efforts with data collection, field support, and report production are highly appreciated. Specific recognition goes to Sarah Hile and Jamie Higgins for report layout and production, to Matt Kendall and Richard Appeldoorn for critically reviewing the report, to Alicia Clarke for copy editing the document, and to Michelle Sharer for the Spanish translation of the Executive Summary. Very special gratitude goes to our dedicated boat captain Angel “Capitan” Nazario and his assistant Joel “Joeito” Rivera. Additional logistic support during field missions came from Victor La Santa and Roxanna Noriega (West Divers), Milton Carlo (University of Puerto Rico, Isla Magueyes), and our friends at Hotel Villa Parguera. Citation for the entire document: Pittman, S.J., S.D. Hile, C.F.G. Jeffrey, R. Clark, K. Woody, B.D. Herlach, C. Caldow, M.E. Monaco, R. Appeldoorn. 2010. Coral reef ecosystems of Reserva Natural La Parguera (Puerto Rico): Spatial and temporal patterns in fish and benthic communities (2001-2007). NOAA Technical Memorandum NOS NCCOS 107. -
Jobos Bay Estuarine Profile a NATIONAL ESTUARINE RESEARCH RESERVE
Jobos Bay Estuarine Profile A NATIONAL ESTUARINE RESEARCH RESERVE Revised June 2008 by Angel Dieppa, Research Coordinator Ralph Field Editor Eddie N. Laboy Jorge Capellla Pedro O.Robles Carmen M. González Authors Photo credits: Cover: Cayos Caribe: Copyright by Luis Encarnación Egrets: Copyright by Pedro Oscar Robles Gumbo-limbo tree: Copyright by Eddie N. Laboy Chapter 3 photos: Copyright by Eddie Laboy JOBOS BAY ESTUARINE PROFILE: A NATIONAL ESTUARINE RESEARCH RESERVE (2002) For additional information, please contact: Jobos Bay NERR PO Box 159 Aguirre, PR 00704 ii ACKNOWLEDGEMENTS The Jobos Bay National Estuarine Research Reserve is part of the National Estuarine Research Reserve System, established by Section 315 of the Coastal Zone Management Act, as amended. Additional information about this system can be obtained from the Estuarine Reserve Division, Office of Ocean and Coastal Resource Management, National Oceanic and Atmospheric Administration, US Department of Commerce, 1305 East-West Highway, Silver Spring, Maryland 20910. This profile was prepared under Grants NA77OR0457 and NA17OR1252. The Jobos Bay Estuarine Profile is the culmination of a collaborative effort by a very special group of people whose knowledge and commitment made this document possible. Our most sincere gratitude is extended to all of those who contributed, directly or indirectly, to this effort. Particular appreciation goes to Dr. Eddie N. Laboy, from the Interamerican University, Dr. Jorge Capella from the Department of Marine Science, University of Puerto Rico, Mr. Ralph M. Field, and Dr. Pedro Robles, former Research Coordinator of the Reserve, for assisting in writing portions of this document. Dr. Ariel Lugo, Vicente Quevedo, Dr. -
Nuclear and Mitochondrial Sequence Data Reveal and Conceal Different Demographic Histories and Population Genetic Processes in Caribbean Reef Fishes
ORIGINALARTICLE doi:10.1111/j.1558-5646.2010.01071.x NUCLEAR AND MITOCHONDRIAL SEQUENCE DATA REVEAL AND CONCEAL DIFFERENT DEMOGRAPHIC HISTORIES AND POPULATION GENETIC PROCESSES IN CARIBBEAN REEF FISHES Ron I. Eytan1,2 and Michael E. Hellberg1 1Department of Biological Sciences, 107 Life Sciences Building, Louisiana State University, Baton Rouge, Louisiana 70803 2E-mail: [email protected] Received March 18, 2010 Accepted June 10, 2010 Mitochondrial and nuclear sequence data should recover historical demographic events at different temporal scales due to dif- ferences in their effective population sizes and substitution rates. This expectation was tested for two closely related coral reef fish, the tube blennies Acanthemblemaria aspera and A. spinosa. These two have similar life histories and dispersal potentials, and co-occur throughout the Caribbean. Sequence data for one mitochondrial and two nuclear markers were collected for 168 individuals across the species’ Caribbean ranges. Although both species shared a similar pattern of genetic subdivision, A. spinosa had 20–25 times greater nucleotide sequence divergence among populations than A. aspera at all three markers. Substitution rates estimated using a relaxed clock approach revealed that mitochondrial COI is evolving at 11.2% pairwise sequence divergence per million years. This rapid mitochondrial rate had obscured the signal of old population expansions for both species, which were only recovered using the more slowly evolving nuclear markers. However, the rapid COI rate allowed the recovery of a recent expansion in A. aspera corresponding to a period of increased habitat availability. Only by combining both nuclear and mitochondrial data were we able to recover the complex demographic history of these fish. -
Phylogeny and Phylogeography of a Shallow Water Fish
UNIVERSITY OF CALIFORNIA, SAN DIEGO Evolution of the suborder Blennioidei: phylogeny and phylogeography of a shallow water fish clade. A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Marine Biology by Hsiu-Chin Lin Committee in charge: Professor Philip A. Hastings, Chair Professor Ron S. Burton Professor Richard H. Rosenblatt Professor Greg W. Rouse Professor Christopher J. Wills 2009 Copyright Hsiu-Chin Lin, 2009 All rights reserved The dissertation of Hsiu-Chin Lin is approved, and it is acceptable in quality and form for publication on microfilm and electronically: _____________________________________________ _____________________________________________ _____________________________________________ _____________________________________________ _____________________________________________ Chair University of California, San Diego 2009 iii DEDICATION This work is dedicated to my family who are not sure why I have to be far away from home but always have faith in me nonetheless. iv TABLE OF CONTENTS Signature Page……………………………………………………………………………iii Dedication Page…………………………………………………………………………..iv Table of Contents………………………………………………………………………….v List of Figures…………………………………………………………………………...viii List of Tables……………………………………………………………………………...x Acknowledgement………………………………………………………………………..xi Vita……………………………………………………………………………………....xiv Abstract………………………………………………………………………………….xvi Introduction………………………………………………………………………………..1 Chapter 1: Phylogeny of the Suborder Blennioidei (Teleostei: