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Genetic Catalogue, Biological Reference Collections and Online Database of European Marine Fishes

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Genetic Catalogue, Biological Reference Collections and Online Database of European Marine Fishes QUALITY OF LIFE AND MANAGEMENT OF LIVING RESOURCES PROGRAMME (1998-2002) Genetic Catalogue, Biological Reference Collections and Online Database of European Marine Fishes FINAL REPORT PROJECT IDENTIFICATION + FINAL SCIENTIFIC REPORT Contract number: QLRI-CT-2002-02755 Project acronym: FishTrace QoL action line: Area 14.1, Infrastructures Reporting period: 01/01/03 - 30/06/06 QUALITY OF LIFE AND MANAGEMENT OF LIVING RESOURCES PROGRAMME (1998-2002) Genetic Catalogue, Biological Reference Collections and Online Database of European Marine Fishes FINAL REPORT PROJECT IDENTIFICATION Contract number: QLRI-CT-2002-02755 Project acronym: FishTrace QoL action line: Area 14.1, Infrastructures Reporting period: 01/01/03 - 30/06/06 PROJECT IDENTIFICATION FishTrace QLRI-CT-2002-02755 PROJECT IDENTIFICATION Title of the project Genetic Catalogue, Biological Reference Collections and Online Database of European Marine Fishes Acronym of the project FishTrace Type of contract Total project costs (in euro) Thematic network 2000000 € Contract number Period covered by the Final Report QLRI-CT-2002-02755 (e.g. 1 February 2000 – 31 January 2001) 1 January 2003 – 30 June 2006 PROJECT COORDINATOR Name Title Address José M. Bautista Professor Facultad de Veterinaria. Ciudad Universitaria. 28040. Madrid. Spain Telephone: Telefax: E-mail address + 34 91 394 3823 + 34 91 394 3824 [email protected] Key words (5 maximum - Please include specific keywords that best describe the project.) Genetics, Fish, Database World wide web address (the project’s www address ) www. fishtrace.org / www. fishtrace.com List of participants Provide all partners’ details including their legal status in the contract i.e.,contractor, assistant contractor (to which contractor?) PARTICIPANT No.1: UCM (Coordinator) Name: Dr. José M. Bautista Organization/Institution: Universidad Complutense of Madrid. Address: Facultad de Veterinaria, Ciudad Universitaria, E-28040 Madrid, Spain Telephone: + 34 91 394 3823 Fax: + 34 91 394 3824 e-mail: [email protected] PARTICIPANT No. 2: JRC Name: Ms. Naouma Kourti Organization/Institution: European Commission, Joint Research Centre, Address: Via Enrico Fermi 1, 21020 Ispra (Va). Italy Telephone: + 39 0332 786045 Fax: + 39 0332 789658 e-mail: [email protected] Page 1 PROJECT IDENTIFICATION FishTrace QLRI-CT-2002-02755 PARTICIPANT No. 3: NRM Name: Dr. Sven Kullander Organization/Institution: Swedish Museum of Natural History Address: Frescativaegen 40, PO Box 50007, SE-104 05, Stockholm, Sweden Telephone: + 46 8 51954116 Fax: + 46 8 51954212 e-mail: [email protected] PARTICIPANT No. 4: ICCM Name: Dr. José A. González Organization/Institution: Goverment of the Canary Islands- Canarian Institute of Marine Sciences Address: Carretera de Taliarte s/n, P.O. Box 56. E-35200 Telde (Las Palmas), Canary Islands, Spain Telephone: + 34 928 13 29 00 (ext. 220) Fax: + 34 928 13 2908 e-mail: [email protected] PARTICIPANT No. 5: IFREMER Name: Dr. Véronique Verrez-Bagnis Organization/Institution: French Research Institute for the Exploitation of the Sea - IFREMER Address: Ifremer – Centre de Nantes Rue de l'île d'Yeu, 44311, Nantes Cedex 3 France Telephone: + 33 2 40374081 Fax: + 33 2 40374071 e-mail: [email protected] PARTICIPANT No. 6: RIVO Name: Dr. Hilde van Pelt-Heerschap Organization/Institution: Netherlands Institute for Fisheries Research. Address: Haringkade 1,1970 AB Ijmuiden,The Netherlands Telephone: + 31 2 55564792 Fax: + 31 2 55564644 e-mail: [email protected] PARTICIPANT No. 7: IMAR Name: Dr. Manuel J. Biscoito Organization/Institution: Instituto do Mar Address: Rua da Mouraria, 31, 9004-546 Funchal, Madeira, Portugal Telephone: + 351 291700360 Fax: + 351 291766339 e-mail: [email protected] Page 2 PROJECT IDENTIFICATION FishTrace QLRI-CT-2002-02755 PARTICIPANT No. 8: TFMC Name: Dr. Sebastián Jiménez Organization/Institution: Organismo Autónomo de Museos y Centros Address: Fuente Morales s/n, P.O. Box 856, E-38001. Santa Cruz de Tenerife, Spain Telephone: + 34 922 532739 Fax: + 34 922 279353 e-mail: [email protected] PARTICIPANT No. 9: NAGREF Name: Dr. Grigorios Krey Organization/Institution: National Agricultural Research Foundation Address: Nea Peramos, Kavala, GR-64007, Greece Telephone: + 30 25940 29035 Fax: + 30 25940 22222 e-mail: [email protected] PARTICIPANT No. 10: MNHN Name: Prof. Guy Duhamel Organization/Institution: Muséum National d'Histoire Naturelle Address: 57, rue Cuvier. 75231 Paris cedex 05, France Telephone: + 33 1 40 793755 Fax: + 33 1 40 795642 e-mail: [email protected] Page 3 QUALITY OF LIFE AND MANAGEMENT OF LIVING RESOURCES PROGRAMME (1998-2002) Genetic Catalogue, Biological Reference Collections and Online Database of European Marine Fishes FINAL SCIENTIFIC REPORT Contract number: QLRI-CT-2002-02755 Project acronym: FishTrace QoL action line: Area 14.1, Infrastructures Reporting period: 01/01/03 - 30/06/06 QLRI-CT-2002-02755 FishTrace INDEX INDEX FINAL REPORT 1.- Introduction 6 2.- Objectives 11 3.- Material and Methods 14 3.1.- Standardization of experimental procedures 14 3.2.- Sampling and taxonomic identification of targeted fish species 15 3.3.- Biological collections from target species 26 3.4.- Molecular genetics procedures 28 3.5.- Molecular analysis of fish populations 33 3.6.- Data validation 34 3.7.- Database implementation 37 3.8.- Public web interface 39 4.- Results 40 4.1.- Standardization of experimental procedures 40 4.2.- Sampling and Taxonomy 41 4.3.- Biological Reference Collections 45 4.4.- Genetic Catalogue of European marine fishes 46 4.5.- Population structure of six European marine fish species 54 4.6.- Validation of taxonomic and genetic data 60 4.7.- Database 64 4.8.- Public web interface 74 5.- Discussion 82 6.- Conclusions 101 7.- Exploitation and dissemination of results 103 8.- Policy related benefits 109 9.- Future actions 110 10.- Action requested to the Commission 111 11.- Tables and Figures 112 12.- References 205 13.- World Wide Web Links 223 14.- Abbreviations 224 Page 4 QLRI-CT-2002-02755 FishTrace INDEX Annexes Annex I: 1st FishTrace Plenary Meeting. Madrid, 12-14th February, 2003. Annex II: FishTrace Database Structuration Meeting. Paris, 13-14th May, 2003. Annex III: FishTrace Standardization Meeting. Stockholm, 4-7th June, 2003. Annex IV: 2nd FishTrace Plenary Meeting. Las Palmas de Gran Canaria (Spain), 19-21st November, 2003. Annex V: FishTrace Meeting on Data Validation. Ispra, Italy. 15-16th April, 2004. Annex VI: 3rd FishTrace Plenary Meeting. Paris, 25-27th November, 2004. Annex VII: FishTrace Database & Web Interface Meeting. Madrid, 11th March, 2005. Annex VIII: 4th FishTrace Plenary Meeting. Funchal (Portugal), 24-26th October, 2005. Annex IX: FishTrace Concluding Meeting. Kavala (Greece), May 10-12th, 2006. Annex X: Sampling and Taxonomy (WP2) Protocol. Annex XI: Results from Molecular Genetic Procedures Standardisation. Annex XII: Molecular identification and DNA barcoding (WP3). Protocol and PCR conditions. Annex XIII: Phylogenetic Validation of Sequences. Guidelines. Annex XIV: Preparing sequence files for the Sequin tool. Annex XV: Reference Collections (WP5) Protocol, Loan Request Form and Invoice of Specimens. Annex XVI: Guidelines for Validation purposes (WP7) including a protocol defining format for the Validation tasks. Annex XVII: Concise Protocol for the online validation process. Annex XVIII: The Bibliography Module in the FishTrace Database. Annex XIX: Results from the genetic population structure analysis. Annex XX: Results from haplotype connectivity network analysis. Annex XXI: Final Report on Validation and Missing Data. Annex XXII: Control Data Validation Flow Document. Annex XXIII: Leaflet presenting the FishTrace project. Page 5 QLRI-CT-2002-02755 FishTrace INTRODUCTION 1.- Introduction Taxonomy and systematics of most animal species have been described in sufficient detail to permit the classification of practically any organism and, in particular, may be of use in the identification of the species and subspecies for the fish trade and ecological concerns regarding fisheries. However, before FishTrace started there was a lack of fast reference tools that hindered the efficient identification and differentiation of teleosts required in fisheries management, biological and ecological research, and human consumption. This problem could affect several of the socio-economic activities related to Fisheries Policies and therefore, the constitution of a database for identification of fish species of commercial, ecological and zoological interest for the European countries was clearly necessary. Thus, the FishTrace network has catalysed during the last years the pooling of biological material and sequence data corresponding to more than 220 European marine fish species with commercial, ecological and zoological interest. These species have been ad hoc sampled from most European sea areas as well as from some extra-European areas. Moreover, the sampling of species overlapping different geographical areas has allowed the morphological and genetic comparison of specimens from widespread species across the European seas. FishTrace has achieved a critical mass of expertise by joining the efforts of sample collectors, ichthyologists, curators, molecular biologists, and database developers. The workplan was designed to directly confront the problem of reliable fish species identification and differentiation through the creation of a public online database containing a genetic catalogue of marine teleosts which could be used
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