Ecology of Aquaculture Species and Enhancement of Stocks
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A Solution for Universal Classification of Species Based on Genomic
Hindawi Publishing Corporation International Journal of Plant Genomics Volume 2007, Article ID 27894, 8 pages doi:10.1155/2007/27894 Research Article A Solution for Universal Classification of Species Based on Genomic DNA Mariko Kouduka,1 Daisuke Sato,1 Manabu Komori,1 Motohiro Kikuchi,2 Kiyoshi Miyamoto,3 Akinori Kosaku,3 Mohammed Naimuddin,1, 4 Atsushi Matsuoka,5 and Koichi Nishigaki1, 6 1 Department of Functional Materials Science, Saitama University, Saitama, Japan 2 Chitose Salmon Aquarium Chitose, Youth Educational Foundation, Chitose, Hokkaido, Japan 3 Institute of Medical Science, Dokkyo Medical University, Tochigi, Japan 4 Biol. Res. and Functions, National Inst. AIST, Tsukuba, Ibaraki, Japan 5 Department of Geology, Niigata University, Niigata, Japan 6 Rational Evolutionary Design of Advanced Biomolecules, Saitama Small Enterprise Promotion Corporation, SKIP City, Saitama, Japan Received 22 July 2006; Revised 8 October 2006; Accepted 8 October 2006 Recommended by Cheng-Cang Wu Traditionally, organisms have been classified on the basis of their phenotype. Recently, genotype-based classification has become possible through the development of sequencing technology. However, it is still difficult to apply sequencing approaches to the analysis of a large number of species due to the cost and labor. In most biological fields, the analysis of complex systems compris- ing various species has become an important theme, demanding an effective method for handling a vast number of species. In this paper, we have demonstrated, using plants, fish, and insects, that genome profiling, a compact technology for genome analysis, can classify organisms universally. Surprisingly, in all three of the domains of organisms tested, the phylogenetic trees generated from the phenotype topologically matched completely those generated from the genotype. -
Cottus Poecilopus Heckel, 1836, in the River Javorin- Ka, the Tatra
Oecologia Montana 2018, Cottus poecilopus Heckel, 1836, in the river Javorin- 27, 21-26 ka, the Tatra mountains, Slovakia M. JANIGA, Jr. In Tatranská Javorina under Muráň mountain, a small fish nursery was built by Christian Kraft von Institute of High Mountain Biology University of Hohenlohe around 1930. The most comprehensive Žilina, Tatranská Javorina 7, SK-059 56, Slovakia; studies on fish from the Tatra mountains were writ- e-mail:: [email protected] ten by professor Václav Dyk (1957; 1961), Dyk and Dyková (1964a,b; 1965), who studied altitudinal distribution of fish, describing the highest points where fish were found. His studies on fish were likely the most complex studies of their kind during that period. Along with his wife Sylvia, who illus- Abstract. This study focuses on the Cottus poe- trated his studies, they published the first realistic cilopus from the river Javorinka in the north-east studies on fish from the Tatra mountains including High Tatra mountains, Slovakia. The movement the river Javorinka (Dyk and Dyková 1964a). Feri- and residence of 75 Alpine bullhead in the river anc (1948) published the first Slovakian nomenclature were monitored and carefully recorded using GPS of fish in 1948. Eugen K. Balon (1964; 1966) was the coordinates. A map representing their location in next famous ichthyologist who became a recognised the river was generated. This data was collected in expert in the fish fauna of the streams of the Tatra the spring and summer of 2016 and in the autumn mountains, the river Poprad, and various high moun- of 2017. Body length and body weight of 67 Alpine tain lakes. -
(Sea of Okhotsk, Sakhalin Island): 2. Cyclopteridae−Molidae Families
ISSN 0032-9452, Journal of Ichthyology, 2018, Vol. 58, No. 5, pp. 633–661. © Pleiades Publishing, Ltd., 2018. An Annotated List of the Marine and Brackish-Water Ichthyofauna of Aniva Bay (Sea of Okhotsk, Sakhalin Island): 2. Cyclopteridae−Molidae Families Yu. V. Dyldina, *, A. M. Orlova, b, c, d, A. Ya. Velikanove, S. S. Makeevf, V. I. Romanova, and L. Hanel’g aTomsk State University (TSU), Tomsk, Russia bRussian Federal Research Institute of Fishery and Oceanography (VNIRO), Moscow, Russia cInstitute of Ecology and Evolution, Russian Academy of Sciences (IPEE), Moscow, Russia d Dagestan State University (DSU), Makhachkala, Russia eSakhalin Research Institute of Fisheries and Oceanography (SakhNIRO), Yuzhno-Sakhalinsk, Russia fSakhalin Basin Administration for Fisheries and Conservation of Aquatic Biological Resources—Sakhalinrybvod, Aniva, Yuzhno-Sakhalinsk, Russia gCharles University in Prague, Prague, Czech Republic *e-mail: [email protected] Received March 1, 2018 Abstract—The second, final part of the work contains a continuation of the annotated list of fish species found in the marine and brackish waters of Aniva Bay (southern part of the Sea of Okhotsk, southern part of Sakhalin Island): 137 species belonging to three orders (Perciformes, Pleuronectiformes, Tetraodon- tiformes), 31 family, and 124 genera. The general characteristics of ichthyofauna and a review of the commer- cial fishery of the bay fish, as well as the final systematic essay, are presented. Keywords: ichthyofauna, annotated list, conservation status, commercial importance, marine and brackish waters, Aniva Bay, southern part of the Sea of Okhotsk, Sakhalin Island DOI: 10.1134/S0032945218050053 INTRODUCTION ANNOTATED LIST OF FISHES OF ANIVA BAY The second part concludes the publication on the 19. -
Introduction to Environmental Microbiology
Reviewers Andrzej Noworyta Zdzisław Szulc The publication was prepared based on delivered materials © Copyright by Oficyna Wydawnicza Politechniki Wrocławskiej, Wrocław 2006 ISBN 83-7085-880-5 Oficyna Wydawnicza Politechniki Wrocławskiej Wybrzeże Wyspiańskiego 27, 53-370 Wrocław http://www.oficyna.pwr.wroc.pl [email protected] INTRODUCTION TO ENVIRONMENTAL MICROBIOLOGY The INTRODUCTION TO ENVIRONMENTAL MICROBIOLOGY has been developed by academic teachers from Wroclaw University of Technology, Poland in the frame of international project Socrates Minerva CELL TALK–88091–CP-BE-2000-Minerva-ODL realized together with partners from Belgium, Ireland, Bulgaria, Portugal and Netherlands. The project was coordinated by prof. Chris van Keer from Katholieke Hogeschool Sint Lieven in Gent, Belgium. The book is addressed to students of environmental engineering, biology, biotechnology, biochemistry and to students of other specializations interested in increasing their knowledge about microorganisms living in environment and in solving environmental problems with the use of microorganisms capable of degrading xenobiotics. Authors Barbara Kołwzan graduated from the University of Economics in Poznan, the Food Commodity Science specialization. She received her Ph.D. at the Wroclaw University of Technology, the Institute of Environment Protection Engineering. She worked as a research assistant at the Toxicology Laboratory at the Institute of Environment Protection Engineering and as a research and didactic assistant at the Biology and Ecology Group. At present she is a head of Research associate at the Biology and Ecology Group, Institute of Environment Protection Engineering. barbara. [email protected] Waldemar Adamiak received his M.Sc. degree in biology from the Wroclaw University. Now he works as a lecturer on the Department of Environmental Engineering at the Technical University of Wroclaw. -
Analysis of Petroleum Hydrocarbons in Soil from View of Bioremediation Process
█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████ ANALYSIS OF PETROLEUM HYDROCARBONS IN SOIL FROM VIEW OF BIOREMEDIATION PROCESS R. Mračnová1, L. Soják1, R. Kubinec1, A. Kraus2, A. Eszényiová3, I. Ostrovský1 1Chemical Institute, Faculty of Natural Sciences, Comenius University, Mlynska dolina CH-2, 842 1 5 Bratislava (Slovakia), e-mail: [email protected] 2Institut of Analytical and Environmental Chemistry, Martin Luther University, 061 20 Halle (Germany) 3Slovnaft Ltd., Research Institute of Petroleum and Hydrocarbon Gases, Vlcie hrdlo, 82412 Bratislava (Slovakia) ABSTRACT The pollution of the environment by petroleum hydrocarbons is the most often pollution of them all. Nevertheless, hydrocarbons present in environment can be not only of petroleum or anthropogenic origin, but of biogenic as well. Typically the hydrocarbons are presented in the environment as very complex mixtures of individual compounds with very different chemical structure, wide range of the boiling points ( ≈ 800 oC) as well as with the wide range of the number of carbon atoms. Immediately they are spread in any environmental matrix the complex physical, chemical and biochemical reactions start. A lot of methods have been developed and new are permanently in progress for the monitoring and control of petroleum hydrocarbons contamination and/or soils bioremediation. Generally, all methods by whose the hydrocarbons contaminants are determined in GC-FID system do not satisfied recommendations for enough accurate and precise results. Hyphenation of capillary gas chromatography and mass selective de- tector operated in the selective ion monitoring mode essentially allows detai- led specification of non-polar extractable hydrocarbons. Isoprenoid alkanes, alkylhomologues of aromatic hydrocarbons and polycyclic alkanes hopanes- like were investigated as markers for recognition of petroleum and biogenic contamination. -
Preliminary Researches on the Effect of Essential Oils on Moulds Isolated
Popa G. O. et al./Scientific Papers: Animal Science and Biotechnologies, 2018, 51 (2) SaMSTNb23 and SaMSTNb33: Emerging Markers for Growth Traits in Huchen (Hucho hucho, Linnaeus, 1758) 1, 1, 1 1 Gina–Oana Popa ‡, *, Ramona Nechifor ‡, Alexandru Burcea , Maria Samu , Andreea Dudu1, Marieta Costache1, Marilena Maereanu2, Sergiu Emil Georgescu1 1University of Bucharest, Faculty of Biology, Department of Biochemistry and Molecular Biology, 91-95 Splaiul Independenței, 050095, Bucharest, Romania 2S.C. Danube Research-Consulting S.R.L., 89bis Câmpia Libertății Street, 825200, Isaccea, Romania ‡The first two authors contributed equally to this work. Abstract Huchen or Danube salmon (Hucho hucho, Linnaeus, 1758) is an economically and ecologically valuable salmonid species, among the most endangered fish species inhabiting the Danube basin. Consequently, appropriate conservation measures are required to prevent the species extinction. Although H. hucho is a poorly studied species, there are several studies on other salmonid species regarding fast growth markers. Following these studies, the main purpose of the current study was to determine growth-related SNPs in myostatin gene in H. hucho. Therefore, we analysed 20 aquaculture individuals of same age separated in two groups according length and weight, by sequencing the amplification product of SaMSTNb23 and SaMSTNb33 primers pairs. We also statistically analysed the differences in the development of individuals over time regarding total length, weight and head length. Significantly variations were observed (p < 0.001) for the measured traits in both groups. Regarding the genetic analysis, we observed nine SNPs in the mstn gene structure. Considering these results, it appears that the analysed markers are not appropriate for genetic analysis of growth traits in H. -
Huchen (Hucho Hucho) ERSS
Huchen (Hucho hucho) Ecological Risk Screening Summary U.S. Fish & Wildlife Service, April 2011 Revised, January 2019, February 2019 Web Version, 4/30/2019 Photo: Liquid Art. Licensed under CC-SA 4.0 International. Available: https://commons.wikimedia.org/wiki/File:Danube_Salmon_-_Huchen_(Hucho_hucho).jpg. (January 2019). 1 Native Range and Status in the United States Native Range From Froese and Pauly (2019): “Europe: Danube drainage [Austria, Bosnia and Herzegovina, Bulgaria, Croatia, Germany, Hungary, Italy, Romania, Serbia, Slovakia, Slovenia, Switzerland, and Ukraine].” “Population has declined [in Slovenia] due to pollution and river regulation. Conservation measures include artificial propagation and stocking [Povz 1996]. Status of threat: Regionally extinct [Bianco and Ketmaier 2016].” 1 “Considered locally extinct (extirpated) in 1990 [in Switzerland] [Vilcinskas 1993].” “Extinct in the wild in 2000 [in Czech Republic] [Lusk and Hanel 2000]. This species is a native species in the basin of the Black Sea (the rivers Morava and Dyje). At present, its local and time- limited occurrence depends on the stocking material from artificial culture. Conditions that will facilitate the formation of a permanent population under natural conditions are not available [Lusk et al. 2004]. […] Status of threat: extinct in the wild [Lusk et al. 2011].” From Freyhof and Kottelat (2008): “The species is severely fragmented within the Danube drainage, where most populations exclusively depend on stocking and natural reproduction is very limited due to habitat alterations and flow regime changes.” From Grabowska et al. (2010): “The exceptional case is huchen (or Danubian salmon), Hucho hucho. The huchen’s native range in Poland was restricted to two small rivers (Czarna Orawa and Czadeczka) of the Danube River basin, […]” Status in the United States Froese and Pauly (2019) report an introduction to the United States between 1870 and 1874 that did not result in an established population. -
Paralabrax, Pisces, Serranidae)
BUTLER ET AL.: DEVELOPMENTAL STAGES OF THREE SEA BASSES CalCOFI Rep., Vol. XXm, 1982 DEVELOPMENTAL STAGES OF THREE CALIFORNIA SEA BASSES (PARALABRAX, PISCES, SERRANIDAE) JOHN L BUTLER, H. GEOFFREY MOSER, GREGORY S. HAGEMAN. AND LAYNE E. NORDGREN National Oceanic and Atmospheric Administraticm Depaltrnent of Biological Suencas National Marine Fisheries Service Universiiy of Southern CaMornia thnhwest Fishecies Center universily Park La Jdla, California 92038 Lw Angeles, California 90007 ABSTRACT was known from Cedros Island south to Cab San Eggs, larvae, and juveniles of kelp bass, Parala- Lucas and the Gulf of California (Fitch and Shultz bra clathratus, barred sand bass, P. nebulifer, and 1978). Larvae of Paralabrax sp. have been illustrated spotted sand bass, P. rnaculatofasciatus, are described by Kendall (1979) from CalCOFI specimens, which from specimens reared in the laboratory and from we have identified as P. clathratus. All three species specimens collected in the field. Eggs of spotted sand are found in nearshore areas from the surface to about bass'are 0.80-0.89 mm in diameter; eggs of kelp bass 600 feet (Miller and Lea 1972). and barred sand bass are 0.94-0.97 mm in diameter. The kelp and sand basses combined rank second in Larvae and juveniles of the three species may be dis- the California sport fish catch (Oliphant 1979). Iden- tinguished by differences in pigmentation during most tifying these three species in ichthyoplankton collec- stages of development. Larvae of the two species of tions may be important in monitoring population sand bass are indistinguishable during notochord changes and assessing the impact of human activities flexion. -
Marine Reconnaissance Survey of Proposed Sites for a Small Boat Harbor in Agat Bay, Guam
Ii MARINE RECONNAISSANCE SURVEY OF PROPOSED SITES FOR A SMALL BOAT HARBOR IN AGAT BAY, GUAM Mitchell 1. Chernin, Dennis R. Lassuy, Richard "E" Dickinson, and John W. Shepard II Submitted to !i U. S. Army Corps of Engineers Contract No. DACWB4-77-C-0061 I! I ~ Technical Report No. 39 University of Guam Marine Laboratory September 1977 , ,; , TABLE OF CONTENTS Page INTRODUCTION 1 METHODS 3 RESULTS AND DISCUSSION 5 Description of Study Sites 5 Macro-invertebrates 7 Marine Plants 13 Corals 22 Fishes 29 Currents 38 Water Quality 40 CONCLUSIONS AND RECOMMENDATIONS 47 LITERATURE CITED 49 APPENDIX 50 LIST OF FIGURES 1. General location map for the Agat Bay study areas. 2. Map indicating general topographical features at the Nimitz and Ta1eyfac study sites. 6 3. Map indicating general topographical features at the Bangi site. 17 4. Current movement along three transects at the Bangi site at low tide. 41 5. Current movement along two transects at the Bangi site at high tide. 42 6. Current movement on the Northern (Tr.IV) and Center (Tr.V) reef flats and Nimitz Channel during high tide. 43 7. Current movement on the Northern and Center reef flats and Nimitz Channel during a falling tide. 44 8. Current movement on the Taleyfac reef flat and Ta1eyfac Bay during a falling tide. 45 9. Current movement on the Ta1eyfac reef flat (Tr.VI) and Taleyfac Bay during a rising tide. 46 A-1. Location of two fish transects at the Gaan site 51 A-2. Density of fishes in each 2D-meter transect interval of Transect A (Fig. -
Genomic, Ecological, and Morphological Approaches to Investigating Species Limits: a Case Study in Modern Taxonomy from Tropical Eastern Pacific Surgeonfishes
Received: 28 November 2018 | Revised: 13 February 2019 | Accepted: 13 February 2019 DOI: 10.1002/ece3.5029 ORIGINAL RESEARCH Genomic, ecological, and morphological approaches to investigating species limits: A case study in modern taxonomy from Tropical Eastern Pacific surgeonfishes William B. Ludt1 | Moisés A. Bernal2 | Erica Kenworthy3 | Eva Salas4 | Prosanta Chakrabarty3 1National Museum of Natural History, Smithsonian Institution, Abstract Washington, District of Columbia A wide variety of species are distinguished by slight color variations. However, mo- 2 Department of Biological Sciences, 109 lecular analyses have repeatedly demonstrated that coloration does not always cor- Cooke Hall, State University of New York at Buffalo, Buffalo, New York respond to distinct evolutionary histories between closely related groups, suggesting 3Ichthyology Section, 119 Foster Hall, that this trait is labile and can be misleading for species identification. In the present Museum of Natural Science, Department of Biological Sciences, Louisiana State study, we analyze the evolutionary history of sister species of Prionurus surgeon- University, Baton Rouge, Louisiana fishes in the Tropical Eastern Pacific (TEP), which are distinguished by the presence 4 FISHBIO, Santa Cruz, California or absence of dark spots on their body. We examined the species limits in this system Correspondence using comparative specimen‐based approaches, a mitochondrial gene (COI), more William B. Ludt, National Museum of than 800 nuclear loci (Ultraconserved Elements), and abiotic niche comparisons. The Natural History, Smithsonian Institution, Washington, DC. results indicate there is a complete overlap of meristic counts and morphometric Email: [email protected] measurements between the two species. Further, we detected multiple individuals Funding information with intermediate spotting patterns suggesting that coloration is not diagnostic. -
Venom Evolution Widespread in Fishes: a Phylogenetic Road Map for the Bioprospecting of Piscine Venoms
Journal of Heredity 2006:97(3):206–217 ª The American Genetic Association. 2006. All rights reserved. doi:10.1093/jhered/esj034 For permissions, please email: [email protected]. Advance Access publication June 1, 2006 Venom Evolution Widespread in Fishes: A Phylogenetic Road Map for the Bioprospecting of Piscine Venoms WILLIAM LEO SMITH AND WARD C. WHEELER From the Department of Ecology, Evolution, and Environmental Biology, Columbia University, 1200 Amsterdam Avenue, New York, NY 10027 (Leo Smith); Division of Vertebrate Zoology (Ichthyology), American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024-5192 (Leo Smith); and Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024-5192 (Wheeler). Address correspondence to W. L. Smith at the address above, or e-mail: [email protected]. Abstract Knowledge of evolutionary relationships or phylogeny allows for effective predictions about the unstudied characteristics of species. These include the presence and biological activity of an organism’s venoms. To date, most venom bioprospecting has focused on snakes, resulting in six stroke and cancer treatment drugs that are nearing U.S. Food and Drug Administration review. Fishes, however, with thousands of venoms, represent an untapped resource of natural products. The first step in- volved in the efficient bioprospecting of these compounds is a phylogeny of venomous fishes. Here, we show the results of such an analysis and provide the first explicit suborder-level phylogeny for spiny-rayed fishes. The results, based on ;1.1 million aligned base pairs, suggest that, in contrast to previous estimates of 200 venomous fishes, .1,200 fishes in 12 clades should be presumed venomous. -
The Global Trade in Marine Ornamental Species
From Ocean to Aquarium The global trade in marine ornamental species Colette Wabnitz, Michelle Taylor, Edmund Green and Tries Razak From Ocean to Aquarium The global trade in marine ornamental species Colette Wabnitz, Michelle Taylor, Edmund Green and Tries Razak ACKNOWLEDGEMENTS UNEP World Conservation This report would not have been The authors would like to thank Helen Monitoring Centre possible without the participation of Corrigan for her help with the analyses 219 Huntingdon Road many colleagues from the Marine of CITES data, and Sarah Ferriss for Cambridge CB3 0DL, UK Aquarium Council, particularly assisting in assembling information Tel: +44 (0) 1223 277314 Aquilino A. Alvarez, Paul Holthus and and analysing Annex D and GMAD data Fax: +44 (0) 1223 277136 Peter Scott, and all trading companies on Hippocampus spp. We are grateful E-mail: [email protected] who made data available to us for to Neville Ash for reviewing and editing Website: www.unep-wcmc.org inclusion into GMAD. The kind earlier versions of the manuscript. Director: Mark Collins assistance of Akbar, John Brandt, Thanks also for additional John Caldwell, Lucy Conway, Emily comments to Katharina Fabricius, THE UNEP WORLD CONSERVATION Corcoran, Keith Davenport, John Daphné Fautin, Bert Hoeksema, Caroline MONITORING CENTRE is the biodiversity Dawes, MM Faugère et Gavand, Cédric Raymakers and Charles Veron; for assessment and policy implemen- Genevois, Thomas Jung, Peter Karn, providing reprints, to Alan Friedlander, tation arm of the United Nations Firoze Nathani, Manfred Menzel, Julie Hawkins, Sherry Larkin and Tom Environment Programme (UNEP), the Davide di Mohtarami, Edward Molou, Ogawa; and for providing the picture on world’s foremost intergovernmental environmental organization.