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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 ANNEXES 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 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. QLRI-CT-2002-02755 FishTrace ANNEX I Annex I: 1st FishTrace Plenary Meeting. Madrid, 12-14 February, 2003. 1st FISHTRACE MEETING 12-14 February 2003 Madrid, Spain Held at NH Prisma Hotel, and Department of Biochemistry and Molecular Biology IV, UCM Meeting Participants Participant 1 (UCM): José M. Bautista, Amalia Diez, Gema González, Susana Schönhuth, Rafael González, Faye Taylor; Participant 2 (EC-JRC-IPSC): Philippe Carreau; Participant 3 (NRM): Sven Kullander, Michael Noren; Participant 4 (ICCM): Jose Antonio González, Ignacio Lozano, Fernanda Marreo, Montserrat Gimeno; Participant 5 (IFREMER): Monique Etienne, Veronique Verrez-Bagnis, Marc Jerome; Participant 6 (RIVO): Hilde van Pelt; Participant 7 (IMAR): Mafalda Freitas, Rosa Pestana; Participant 9 (NAGREF): Grigorius Krey; Alexis Tsangridis; Participant 10 (MNHN): Guy Duhamel, Patrice Pruvost. Meeting Agenda: 1st DAY, February 12 – Wednesday 1. Introduction to FishTrace 2. Presentation of participant teams 3. Workpackages structure and information flow. 4. Schedules: General, Workpackages, Participant teams, Milestones and deliverables 5. Visit to the molecular biology laboratories at UCM and demonstrations on sampling for taxonomy, genetics and museums. 2nd DAY, February 13 - Thursday 6. WP1: Standardization of Methods and Legal Aspects 7. WP2: Sampling and Taxonomy. 8. WP3: Molecular Genetic Identification. 9. WP4: Biogeographical Molecular Haplotyping. 10. WP5: Biological Reference Collections. 11. WP6: Database Development. 12. WP7: Validation in Database. 13. WP 8: Implementation of WWW Technologies. 3rd DAY, February 14 - Friday 14. WP 9: Dissemination and Applicability. 15. Organization of practical work and information flow (Taxonomic, genetic and Collections Data Blocks: Research teams involved and flow) 16. Information flow at each geographical location and to the database 17. Implementation of the overviewing performance and periodical progress reports 18.. Financial and administrative matters. 19. Next Meetings. MEETING MINUTES 1.- Introduction to FishTrace: The meeting started at 09:30 hours at the NH Prisma Hotel. The coordinator for the project, Dr José Bautista, welcomed the participants and presented the origins and general structure of the project, as well as the European dimension in terms of coverage of the geographic areas. 2.- Presentation of participant teams: 10:00 - 11:15: All participants did a presentation of the scientific groups participating in the project. They included details on their institutions; experience and other projects in which they participate; personnel assigned to this project, their performance and responsibilities, including the geographical area of their analysis (sampling, genetics and/or collections), and a briefing of the Workpackages in which the institution participates. Following are the names of those who presented each institution: Participant 1 (UCM): Amalia Diez Participant 2 (EC-JRC-IPSC): Philippe Carreau Participant 3 (NRM): Sven Kullander Participant 4 (ICCM): Jose Antonio González Participant 5 (IFREMER): Monique Etienne Participant 6 (RIVO): Hilde V Pelt Participant 7 (IMAR): Mafalda Freitas Participant 9 (NAGREF): Grigorius Krey Participant 10 (MNHN): Guy Duhamel Ignacio Lozano did the presentation on behalf of Participant 8 (TFMC) and informed the participants that Dr. Sebastian Jimenez, the scientist in charge of this group, could not attend the meeting. 3. Workpackages structure and information flows. At 11:45: Dr Bautista presented the general objectives of the project drawn over each Workpackage structure and how the success on the project depends on the maintenance of the information flow among Workpackages. At the general discussion on this topic, it was pointed out the urgent need for a quick standardization of all methods to start the tasks for Workpackages 2 and 3, and a detailed definition of the database fields in order to make them compatible with other cross-linked databases of interest for FishTrace. Keeping the right of use on photographs and sequences for specific purposes (books, publications, tools for genetic identification) was also discussed with the understanding that the project is founded to make it available to the public. In this respect it was also observed the need to start Workpackage 9, dissemination, as soon as possible with the coordination activity of IFREMER to detect possible interested parties in our complete set of information (sequences, photographs, etc). 4. Schedules: General, Workpackages, Participant teams, Milestones and deliverables At 12:30 : there was a definition of the project schedules indicating the timetables to be covered. The context of the project planning including each Workpackage, the contribution of each participant institution, the milestones to be reached and the deliverables during the time course of the project. 5. Visit to molecular biology laboratories at UCM and demonstrations on sampling for taxonomy, genetics and museums. At 15:30: there was a visit to the coordinating group’s laboratory at the Universidad Complutense de Madrid. There was a demonstration on taxonomy sampling, for genetics and museums. Tentative protocols for sampling and molecular genetics were given to each participant. 2nd Day 6. WP1: Standardization of Methods and Legal Aspects At 09:30 Dr Van Pelt presented the tasks covered by Wordpackage 1 (standardization) for which RIVO is the leader. In the presentation a list of subjects to standardize was shown, making special emphasis in those aspects of sampling, DNA, PCR and sequencing, data compilation, images and collection. Particular attention was given to legal aspects on public access to the database; patents and exchange flow of biological samples. The list of standardized methods of FishTrace will be available through the FishTrace web site, so all groups are able to provide identical data quality. A “legal committee” formed by Hilde van Pelt (RIVO), Guy Duhamel (MNHN), Monique Etienne (IFREMER) and Philippe Carreau (EJC) will help and research to advise on legal questions related to data releasing from FrishTrace. During the discussion it was agreed that the protocols for standardization must circulate form the Workpackage leader of each standardized tasks to the other contributors in the same Worpackage. Finally, RIVO will act as a referee for all method standarization and produce the definitive standardized protocol. 7. WP2: Sampling and Taxonomy. At 10:15 Dr Kullander presented the tasks covered by Workpackage 2 (Sampling + Taxonomy) for which NRM is the Workpackage leader. Within the objectives of this Workpackage it was described the sampling procedure and the corresponding data and material to be obtained from each sample. Particular emphasis was given to the systematic work, and the relationship with possible different haplotypes detected in Workpackage 4 from the different geographical locations. The need for a standardization and agreement on the systematic by all groups contributing was clear during the discussion, in particular related to the fields in the database. Issues related to regional data compilation and literature was also raised. This is expected to maintain a certain degree of originality in terms of discovering the most local particularities and not to download from other databases. It was also mentioned that fish photos must retain the copyright of the photographer but them will be freely released among the participants of the project. The need for agreements on what
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