Typhoon Damage on a Shallow Mesophotic Reef in Okinawa, Japan
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Molecular Diversity, Phylogeny, and Biogeographic Patterns of Crustacean Copepods Associated with Scleractinian Corals of the Indo-Pacific
Molecular Diversity, Phylogeny, and Biogeographic Patterns of Crustacean Copepods Associated with Scleractinian Corals of the Indo-Pacific Dissertation by Sofya Mudrova In Partial Fulfillment of the Requirements For the Degree of Doctor of Philosophy of Science King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia November, 2018 2 EXAMINATION COMMITTEE PAGE The dissertation of Sofya Mudrova is approved by the examination committee. Committee Chairperson: Dr. Michael Lee Berumen Committee Co-Chair: Dr. Viatcheslav Ivanenko Committee Members: Dr. James Davis Reimer, Dr. Takashi Gojobori, Dr. Manuel Aranda Lastra 3 COPYRIGHT PAGE © November, 2018 Sofya Mudrova All rights reserved 4 ABSTRACT Molecular diversity, phylogeny and biogeographic patterns of crustacean copepods associated with scleractinian corals of the Indo-Pacific Sofya Mudrova Biodiversity of coral reefs is higher than in any other marine ecosystem, and significant research has focused on studying coral taxonomy, physiology, ecology, and coral-associated fauna. Yet little is known about symbiotic copepods, abundant and numerous microscopic crustaceans inhabiting almost every living coral colony. In this thesis, I investigate the genetic diversity of different groups of copepods associated with reef-building corals in distinct parts of the Indo-Pacific; determine species boundaries; and reveal patterns of biogeography, endemism, and host-specificity in these symbiotic systems. A non-destructive method of DNA extraction allowed me to use an integrated approach to conduct a diversity assessment of different groups of copepods and to determine species boundaries using molecular and taxonomical methods. Overall, for this thesis, I processed and analyzed 1850 copepod specimens, representing 269 MOTUs collected from 125 colonies of 43 species of scleractinian corals from 11 locations in the Indo-Pacific. -
5. Putra Shallow Water Hardcorel Revised
Aceh Journal of Animal Science (2019) 4(2): 89-98 DOI: 10.13170/ajas.4.2.14571 Printed ISSN 2502-9568 Electronic ISSN 2622-8734 RESEARCH PAPER Shallow-water hard corals (Hexacorallia: Scleractinia) from Bangka Belitung Islands Waters, Indonesia Singgih Afifa Putra1*, Helmy Akbar2, Indra Ambalika Syari3 1Center for Development, Empowerment of Educators and Education Officer of The Marine and Fisheries Information and Communication Technology, Gowa, Sulawesi Selatan, Indonesia; 2Department of Marine Sciences, Universitas Mulawarman, Samarinda, Kalimantan Timur, Indonesia; 3Department of Marine Sciences, Universitas Bangka Belitung, Bangka, Kep. Bangka Belitung, Indonesia *Corresponding author’s email: [email protected] Received : 07 September 2019 Accepted : 30 October 2019 ABSTRACT Bangka Belitung Islands (Sumatra, Indonesia) has various coastal resources, e.g., coral reefs, seagrass beds, mangrove forests. However, the coral community has been threatened by anthropogenic activities, i.e., tin mining and illegal tin mining. Threatened species assessment is important for mitigation of coral losses and management. The ojective of the present study was to examine the status of Scleractinian corals in Bangka Belitung Islands, Indonesia. A line intercept transect was performed for the coral reef survey. Live and dead coral cover were recorded in the three locations. Corals species were identified following taxonomic revisions. The results showed that there were 142 species of Scleractinian corals recorded from Bangka Belitung Islands. Of these, 22 species are the new report from the areas of the the eastern part of Belitung Island. Family of Merulinidae, Acroporidae, and Poritidae were predominant group in this region. It is concluded that the condition of the coral reef ecosystem in the Belitung Islands is relatively good, but fair in Gaspar Strait and Bangka Island. -
Downloaded from Brill.Com10/11/2021 12:50:19PM Via Free Access 202 RAUCH ET AL
Contributions to Zoology 88 (2019) 201-235 CTOZ brill.com/ctoz Shrimps of the genus Periclimenes (Crustacea, Decapoda, Palaemonidae) associated with mushroom corals (Scleractinia, Fungiidae): linking DNA barcodes to morphology Cessa Rauch Department of Taxonomy & Systematics, Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands Department of Natural History, Section of Taxonomy and Evolution, University Museum of Bergen, University of Bergen, PB7800, 5020 Bergen, Norway Bert W. Hoeksema Department of Taxonomy & Systematics, Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands Bambang Hermanto Technical Implementation Unit for Marine Biota Conservation, Research Centre for Oceanog- raphy (RCO-LIPI), Bitung, Indonesia Charles H.J.M. Fransen Department of Taxonomy & Systematics, Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands [email protected] Abstract Most marine palaemonid shrimp species live in symbiosis with invertebrates of various phyla. These as- sociations range from weak epibiosis to obligatory endosymbiosis and from restricted commensalism to semi-parasitism. On coral reefs, such symbiotic shrimps can contribute to the associated biodiversity of reef corals. Among the host taxa, mushroom corals (Cnidaria: Anthozoa: Fungiidae) are known to harbour various groups of symbionts, including shrimps. Some but not all of these associated species are host-specific. Because data on the host specificity of shrimps on mushroom corals are scarce, shrimp spe- cies of the genus Periclimenes were collected from mushroom corals during fieldwork in Lembeh Strait, © RAUCH ET AL., 2019 | doi:10.1163/18759866-20191357 This is an open access article distributed under the terms of the prevailing cc-by license at the time of publication. -
A Molecularly Based Phylogeny Reconstruction of Mushroom Corals
Contributions to Zoology, 80 (2) 107-132 (2011) A molecularly based phylogeny reconstruction of mushroom corals (Scleractinia: Fungiidae) with taxonomic consequences and evolutionary implications for life history traits Arjan Gittenberger1, 2, Bastian T. Reijnen1, Bert W. Hoeksema1, 3 1 Department of Marine Zoology, Netherlands Centre for Biodiversity Naturalis, PO Box 9517, 2300 RA Leiden, The Netherlands 2 Institute for Environmental Sciences and Institute for Biology, Leiden University, PO Box 9516, 2300 RA Leiden, The Netherlands 3 E-mail: [email protected] Key words: COI, evolutionary history, ITS 1 & 2, maximum coral size, polystomatism, reproduction strategy Abstract Sequence alignment and phylogenetic analyses ............. 112 Evolution of life history traits ............................................. 113 The phylogenetic relationships of the Fungiidae, a family of pre- Results ............................................................................................. 113 dominantly free-living, zooxanthellate, reef corals, were studied Molecular phylogeny reconstructions .............................. 113 by sequencing a part of the mitochondrial Cytochrome Oxidase Evolutionary trends in morphology and life I (COI) and the complete ribosomal Internal Transcribed Spacers history traits ............................................................................. 114 (ITS) I & II of specimens from various locations in the Indo- Discussion ..................................................................................... -
Cop18 Doc. 99 A6
CoP18 Doc. 99 Annex 6 (English only / seulement en anglais / únicamente en inglés) Annex 6 to CoP18 Doc. 99 Nomenclature document – proposed changes in the published literature concerning nomenclature of CITES-listed animal species for which the Animals Committee, at the time of CoP18 document submission, has not yet reached a recommendation on adoption or rejection for CITES purposes. For ease of navigation, this Annex is divided into seven sections: Annex 6A: Mammals pages 2 - 8 Annex 6B: Birds (to be reviewed in conjunction with Annex 5) pages 9-36 Annex 6C: Reptiles pages 37-44 Annex 6D: Amphibians pages 45-46 Annex 6E: Cartilaginous and bony Fishes pages 47-48 Annex 6F: Invertebrates other than corals pages 49-50 Annex 6G: Corals pages 51-86 In the column ‘Appendix’, the CITES Appendix in which the species or higher taxon is listed is given; in many but not all cases, the Annex in which the species is placed in EU regulation (A, B or C) is also listed. In Annexes 6A, 6C, 6D, 6E and 6F, multiple references are sometimes cited that each document the described nomenclatural change; in those cases, individual references within the table cell are separated by ‘##’. In Annexes 6B and 6G specific symbols are used to indicate nomenclatural splits, lumps and other changes, as follows: The symbol '<' is used to indicate species lumps, i.e. taxa currently recognised as separate, but that have been grouped together as synonym or subspecies under another name in the associated reference. The symbol '>' is used to indicate species splits, i.e. -
6 附录2 中国造礁石珊瑚同物异名对照表appendix 2 Comparison Of
黄林韬, 黄晖, 江雷. 中国造礁石珊瑚分类厘定. 生物多样性, 2020, 28 (4): 515–523. http://www.biodiversity-science.net/CN/10.17520/biods. 2019384 附录2 中国造礁石珊瑚同物异名对照表 Appendix 2 Comparison of synonyms of Chinese hermatypic corals 旧种名 Old species 新种名 New species 文献依据 Basis of 旧物种来源文献 Original description names names record Hoeksema & Cairns, Acanthastrea faviaformis Dipsastraea matthaii Zhao et al, 2017 2020 Acanthastrea hillae Homophyllia bowerbanki Dai & Horng, 2009b Arrigoni et al, 2016 Acanthastrea Micomussa lordhowensis 陈乃观等, 2005 Arrigoni et al, 2016 lordhowensis Hoeksema & Cairns, Acrhelia horrescens Galaxea horrescens 邹仁林, 2001 2020 Acropora aff. Guppyi Acropora humilis Д.В.纳乌莫夫等, 1960 邹仁林, 2001 Acropora affinis Acropora florida 邹仁林等, 1975 Wallace, 1999 Acropora armata Acropora cytherea 于登攀和邹仁林, 1996; 邹仁林, 2001 邹仁林, 2001 Acropora azurea Acropora nana Dai & Horng, 2009a; 潘子良, 2017 Wallace, 1999 Wallace et al, 2007; Dai Acropora brueggemanni Isopora brueggemanni 邹仁林, 2001 & Horng, 2009a Acropora complanata Acropora clathrata Yang & Dai, 1981 Wallace, 1999 邹仁林等, 1975; 于登攀和邹仁林, Wallace, 1999; 邹仁林, Acropora conferta Acropora hyacinthus 1996 2001 Acropora corymbosa Acropora cytherea 邹仁林等, 1975, 2001 Wallace, 1999 Acropora crateriformis Isopora crateriformis 黄晖等, 2011 Wallace et al, 2007 Wallace et al, 2007; Dai Acropora cuneata Isopora cuneata 黄晖等, 2011 & Horng, 2009a Acropora danai Acropora abrotanoides Dai & Horng, 2009a, b Wallace, 1999 Wallace, 1999; 邹仁林, Acropora decipiens Acropora robusta 邹仁林等, 1975 2001 Acropora Acropora selago 邹仁林等, 1975 Wallace, 1999 deliculatadelicatula -
Evolutionary Trends in Onshore-Offshore Distribution Patterns of Mushroom Coral Species (Scleractinia: Fungiidae)
Contributions to Zoology, 81 (4) 199-221 (2012) Evolutionary trends in onshore-offshore distribution patterns of mushroom coral species (Scleractinia: Fungiidae) Bert W. Hoeksema1, 2 1 Department of Marine Zoology, Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands 2 E-mail: [email protected] Key words: competitive exclusion, ecophylogenetics, environmental gradients, habitat partitioning, niche differen- tiation, phylogenetic ecology Abstract Species co-occurrences based on abundance and incidence data ............................................................... 209 A phylogenetically based comparative analysis of onshore-off- Ordination of species co-occurrences ............................. 209 shore distribution patterns of mushroom coral species (Sclerac- Discussion ...................................................................................... 214 tinia: Fungiidae) was made to reconstruct an evolutionary sce- Onshore-offshore patterns ................................................. 214 nario for differentiation in fungiid shelf habitats. This phylo- Spatial partitioning and co-existence ............................. 214 ecological study integrates data on fungiid distribution patterns Phylogenetic ecology ........................................................... 215 along environmental gradients on the Spermonde Shelf, SW Acknowledgements ...................................................................... 217 Sulawesi, with a recently published phylogeny reconstruction of References -
Recent Changes in Scleractinian Coral Nomenclature and Classification
Recent changes in Scleractinian coral nomenclature and classification. (A practical guide for coral and reef ecologists) Michel Pichon Adjunct Professor, James Cook University Australia Honorary Associate, Museum of Tropical Queensland, Townsville The following document provides information on changes which were introduced recently in the classification and nomenclature of scleractinian corals. Such changes stem to a large extent from the research activity and the syntheses carried out by the members of the international “Scleractinian Systematics Working Group” (SSWG) over the last few years. They are the result of a multi-pronged approach combining the information provided by the implementation of relatively new techniques, which have only recently been applied to scleractinian coral taxonomy. Such new tools include, inter alia, morphometrics, microstructural analyses, anatomy of soft parts and molecular genetics. The changes thus made to the nomenclature and classification of scleractinian corals underlie a move towards a classification reflecting more and more the phylogeny of various taxa, and as a result may place side by side morphologically very dissimilar species. Furthermore, such a move will require a re-definition of numerous genera (and of some families, which from a practical viewpoint is less critical) in accordance with the rules set out in the International Code of Zoological Nomenclature. Such a work is still to be done and a number of genera remain to this day without an adequate revised diagnostic morphological characterization. Several important studies are still in progress and one may expect additional changes in the near future. The present document, therefore, does not pretend to represent a complete revision of scleractinian coral taxonomy. -
Host Relations and DNA Reveal a Cryptic Gall Crab Species (Crustacea: Decapoda: Crypto Chiridae) Associated with Mushroom Corals (Scleractinia: Fungiidae)
Contributions to Zoology, 84 (1) 39-57 (2015) Host relations and DNA reveal a cryptic gall crab species (Crustacea: Decapoda: Crypto chiridae) associated with mushroom corals (Scleractinia: Fungiidae) Sancia E.T. van der Meij1, 2 1 Department of Marine Zoology, Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands 2 E-mail: [email protected] Key words: cryptic species, Fungicola, host specificity, Indo-West Pacific region, Tropical Eastern Pacific region, Scleractinia Abstract with a distribution ranging from the Red Sea and east- ern Africa to the west coast of Central America (Hoek- Mushroom corals of the Indo-West Pacific Fungiidae (Sclerac- sema, 1989). Several species have been recorded in tinia) provide habitats for a rich associated fauna, including three association with these fungiids (Hoeksema et al., 2012). species of gall crabs (Cryptochiridae). During the course of the Most of the associated fauna consists of crustaceans present study gall crabs were sampled from many different fungiid hosts. Based on this ‘reversed’ approach - by studying and molluscs, but fishes have also been recorded to live coral symbionts from a host perspective - a previously unnoticed in symbiosis with fungiids (Bos, 2012; Hoeksema et al., host specificity pattern was detected. The sampling of gall crab 2012). Such heterospecific associations between a host fauna per host coral combined with molecular analyses of H3 and an associated organism can range from brief fac- nDNA, 16S and COI mtDNA revealed a cryptic gall crab species ultative encounters to lifelong obligate partnerships closely related to Fungicola fagei. This new species, described hereafter as Fungicola syzygia sp. -
Patterns of Coral Species Richness and Reef Connectivity in Malaysia
Patterns of coral species richness and reef connectivity in Malaysia Waheed, Z. Patterns of coral species richness and reef connectivity in Malaysia PhD thesis, Leiden University Cover design: Yee Wah Lau Printed by: Gildeprint, Enschede ISBN: 978 94 6233 460 1 © 2016 by Z. Waheed, all rights reserved. Funding. This thesis was accomplished with financial support from the Ministry of Higher Education Malaysia, with additional support from Universiti Malaysia Sabah, WWF-Malaysia, the A.M. Buitendijkfonds, and TREUB-maatschappij (Society for the Advancement of Research in the Tropics). Disclaimer. Following the recommendation of Article 8.2 of the International Code of Zoological Nomenclature, I declare that this publication is not issued for public and permanent scientific record, or for purposes of zoological nomenclature, and therefore not published within the meaning of the Code. Patterns of coral species richness and reef connectivity in Malaysia Proefschrift ter verkrijging van de graad van Doctor aan de Universiteit Leiden, op gezag van de Rector Magnificus prof. mr. C.J.J.M. Stolker, volgens besluit van het College voor Promoties te verdedigen op dinsdag 22 november 2016 klokke 13:45 door Zarinah Waheed geboren te Kota Kinabalu, Maleisië in 1978 Promotiecommissie Prof. dr. L.M. Chou (National University of Singapore, Singapore) Prof. dr. M. Schilthuizen (Universiteit Leiden & Naturalis Biodiversity Center) Prof. dr. H.P. Spaink (Universiteit Leiden) Prof. dr. P.C. van Welzen (Universiteit Leiden & Naturalis Biodiversity Center) Dr. F. Benzoni (University of Milano-Bicoca, Italy) Dr. C.H.J.M. Fransen (Naturalis Biodiversity Center) Promoter Prof. dr. E. Gittenberger (Universiteit Leiden & Naturalis Biodiversity Center) Copromoter Dr. -
Phylogenetic Ecology of Gall Crabs (Cryptochiridae) As Associates of Mushroom Corals (Fungiidae) Sancia E
Phylogenetic ecology of gall crabs (Cryptochiridae) as associates of mushroom corals (Fungiidae) Sancia E. T. van der Meij1,2, Charles H. J. M. Fransen1, Leon R. Pasman1 & Bert W. Hoeksema1 1Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands 2Oxford University Museum of Natural History, Parks Road, Oxford, OX1 3PW, UK Keywords Abstract Cospeciation, Dacryomaia, Fungicola, host specificity, Indo-Pacific, new associations. Coral-associated fauna is a relatively understudied topic. Hence, the nature of the relationship between an associated organism and its host is usually Correspondence unknown. In the present study, the obligate associations between gall crabs Sancia E. T. van der Meij, Naturalis (Decapoda: Cryptochiridae) and mushroom corals (Scleractinia: Fungiidae) are Biodiversity Center, Darwinweg 2, 2333 CR reviewed from a phylogenetic perspective. Based on field surveys, examination Leiden, The Netherlands. of museum material and a literature review, a total of 35 fungiid species have Tel: +31(0)717519613; Fax: + 31(0)717519666; been found that act as hosts for four gall crab species. Fungiid-associated gall E-mail: [email protected] crabs appear to be more geographically widespread than previously known, with new records showing their occurrences from the Red Sea and western Funding Information Indian Ocean all the way to the central Pacific Ocean. The obligate nature of Netherlands Foundation for the the association between cryptochirids and their hosts makes them an ideal Advancement of Tropical Research WOTRO model taxon to test for possible cospeciation events. The congruence between (Grant W77-96), Van Tienhoven Foundation their phylogenies was tested by using the program Jane 4.0, resulting in cospeci- for International Nature Protection, Stichting ation and duplication events between the crabs and their host corals. -
MARINE PROFILING of MARUDU BAY, SABAH, MALAYSIA Coastal and Marine Resources Management in the Coral Triangle-Southeast Asia (TA 7813-REG)
MARINE PROFILING OF MARUDU BAY, SABAH, MALAYSIA Coastal and Marine Resources Management in the Coral Triangle-Southeast Asia (TA 7813-REG) Tehcnical Report FINAL REPORT: MARINE PROFILING OF MARUDU BAY, SABAH MARINE PROFILING OF MARUDU BAY, SABAH, MALAYSIA Final Report1 1 Manjaji-Matsumoto, B.M., Saleh, E., Waheed, Z., Muhammad Ali, S.H., and Madin, J., eds. 2017. Marine Profiling of Marudu Bay, Sabah: Final Report. Prepared for PRIMEX. May 2017. Borneo Marine Research Institute, Universiti Malaysia Sabah. COASTAL AND MARINE RESOURCES MANAGEMENT IN THE CORAL TRIANGLE: SOUTHEAST ASIA, INDONESIA, MALAYSIA, PHILIPPINES (TA 7813-REG) FINAL REPORT: MARINE PROFILING OF MARUDU BAY, SABAH Page i TABLE OF CONTENTS Page LIST OF TABLES ....................................................................................................................... ii LIST OF FIGURES .................................................................................................................... iii LIST OF PHOTOS ..................................................................................................................... iv LIST OF ABBREVIATIONS ........................................................................................................ v ACKNOWLEDGMENTS ...........................................................................................................vii EXECUTIVE SUMMARY .........................................................................................................viii I. INTRODUCTION ...........................................................................................................