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Linking Barcode Data to Multiple Users

Linking Barcode Data to Multiple Users. David E. Schindel, Executive Secretary National Museum of Natural History Smithsonian Institution SchindelD@si.edu ; http://www.barcoding.si.edu 202/633-0812; fax 202/633-2938.

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Linking Barcode Data to Multiple Users

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  1. Linking Barcode Data to Multiple Users David E. Schindel, Executive Secretary National Museum of Natural History Smithsonian Institution SchindelD@si.edu;http://www.barcoding.si.edu 202/633-0812; fax 202/633-2938

  2. A DNA barcode is a short gene sequence taken from standardized portions of the genome, used to identify species

  3. D-Loop Small ribosomal RNA Large ribosomal RNA Cyt b ND1 ND6 COI COI ND5 L-strand ND2 H-strand ND4 COI ND4L COII ND3 ATPase subunit 8 COIII ATPase subunit 6 The Mitochondrial Genome

  4. The Barcode Assembly Line Taxonomic Identifications and BARCODE Data Standards Freshly collected specimens Frozen tissue Young museum specimens BOLD Users with unidentified specimens GenBank BARCODE Records

  5. Projects, Networks, Organizations • Promote barcoding as a global standard • Build participation • Working Groups • BARCODE standard • International Conferences • Increase production of public BARCODE records

  6. Uses of DNA Barcodes Research tool for species-level taxonomy, ecology: • Associating all life history stages, genders • Testing species boundaries, finding new variants Applied tool for identifying regulated species: • Disease vectors, agricultural pests, invasives • Environmental indicators, protected species “Triage” tool for flagging potential new species: • Undescribed and cryptic species • Taxonomic groups with few morphological features

  7. New Sources of Taxonomic/Ecological Data • Immature stages, damaged specimens • Trophic webs from gut contents • Fecal droppings • Non-invasive sampling (catch/release, shed feathers, moults, fin clips) • Rapid ecological sampling and ecosystem assessment • Ecogenomic mixtures

  8. Uses of DNA Barcodes Research tool for species-level taxonomy, ecology: • Associating all life history stages, genders • Testing species boundaries, finding new variants Applied tool for identifying regulated species: • Disease vectors, agricultural pests, invasives • Environmental indicators, protected species “Triage” tool for flagging potential new species: • Undescribed and cryptic species • Taxonomic groups with few morphological features

  9. Uses of DNA Barcodes Research tool for species-level taxonomy, ecology: • Associating all life history stages, genders • Testing species boundaries, finding new variants Applied tool for identifying regulated species: • Disease vectors, agricultural pests, invasives • Environmental indicators, protected species “Triage” tool for flagging potential new species: • Undescribed and cryptic species • Taxonomic groups with few morphological features

  10. What DNA Barcoding is NOT • Barcoding is not DNA taxonomy; no single gene (or character) is adequate • Barcoding is not Tree of Life; barcode clusters are not phylogenetic trees • Barcoding is not just COI; standardizing on one region has benefits and limits • Molecules in taxonomy is not new; but large-scale and standardization are new

  11. What DNA Barcoding is NOT • Barcoding is not DNA taxonomy; no single gene (or character) is adequate • Barcoding is not Tree of Life; barcode clusters are not phylogenetic trees • Barcoding is not just COI; standardizing on one region has benefits and limits • Molecules in taxonomy is not new; but large-scale and standardization are new

  12. CBOL’s History • Sloan Foundation support for two Banbury planning workshops in 2003 • Sloan 2-year inaugural CBOL grant, May 2004 • Secretariat opens at Smithsonian, September 2004 • International conference London, February 2005 • $1.55 million 2-year renewal in April 2006 • Now an international affiliation of: • Natural history museums, biodiversity organizations • Users: e.g., government agencies • Private sector biotech companies, database providers

  13. CBOL Member Organizations: 2007 • 160+ Member organizations, 50 countries • 54 Member organizations from 23 developing countries

  14. CBOL’s Mission:Promoting DNA Barcoding as a Global Standard • Developing/raising community standards • Barcode projects to populate database • Global participation and coordination • Acceptance by taxonomic community • Adoption by regulatory agencies • Excitement in other fields of science • Product development by private companies

  15. BARCODE Records in INSDC Specimen Metadata Voucher Specimen Species Name GeoreferenceHabitatCharacter setsImagesBehaviorOther genes Indices - Catalogue of Life - GBIF/ECAT Nomenclators - Zoo Record - IPNI - NameBank Publication links - New species Barcode Sequence Trace files Primers Other Databases Literature(link to content or citation) PhylogeneticPop’n GeneticsEcological Databases - Provisional sp.

  16. CBOL’s Mission:Promoting DNA Barcoding as a Global Standard • Developing/raising community standards • Barcode projects to populate database • Global participation and coordination • Acceptance by taxonomic community • Adoption by regulatory agencies • Excitement in other fields of science • Product development by private companies

  17. CBOL-Initiated Projects • Tephritid fruit flies (USDA) • 2,000 pest/beneficial species and relatives by 2008 • Mosquitoes 3,300 species by 2008 • Fish Barcode of Life, FISH-BOL • 30,000 marine/freshwater species by 2010 • All Birds Barcoding Initiative (aviation agencies) • 10,000 species by 2010 • Water quality assessment (USEPA) • Scale insects, commercial fish, hardwood

  18. CBOL’s Mission:Promoting DNA Barcoding as a Global Standard • Developing/raising community standards • Barcode projects to populate database • Global participation and coordination • Acceptance by taxonomic community • Adoption by regulatory agencies • Excitement in other fields of science • Product development by private companies

  19. Geographic Outreach Activities • Regional meetings in: • Cape Town, South Africa, 7-8 April 2006, SANBI • Nairobi, Kenya, 18-19 October 2006 • Brazil, February 2007 • Taiwan, September 2007 • Assess technical/scientific capacity • Identify high-priority barcoding projects • Initiate regional networks, partnerships • Partnership with BioNET-INTERNATIONAL

  20. Leading Lab NetworkTaipei Short Course, September 2007 STRI SI-LAB BOLD GenBank CCDB BioCode

  21. New CBOL Activities, 2008-2009 • Leading Lab Network • “Phase 2” support for regional networks • Offer to promote Fungal Barcoding Initiative • Outreach to west/central Africa, India, China • More direct communication with Member Organizations • Promote acceptance by CBD, developing countries • Expand partnerships with GBIF, Encyclopedia of Life, Census of Marine Life, Catalog of Life

  22. CBOL’s Mission:Promoting DNA Barcoding as a Global Standard • Developing/raising community standards • Barcode projects to populate database • Global participation and coordination • Acceptance by taxonomic community • Adoption by regulatory agencies • Excitement in other fields of science • Product development by private companies

  23. Adoption by Regulators • US Federal Aviation Administration – All Birds • US Environmental Protection Agency • $250K pilot test, water quality bioassessment • US Food and Drug Administration • Reference barcodes for commercial fish • FISH-BOL and fish regulatory agencies • CBOL workshop in Taipei, September 2007 • FAO International Plant Protection Commission • Proposal for Diagnostic Protocols for fruit flies • CITES, National Agencies, Conservation NGOs • International Steering Committee, identifying pilot projects

  24. CBOL’s Mission:Promoting DNA Barcoding as a Global Standard • Developing/raising community standards • Barcode projects to populate database • Global participation and coordination • Acceptance by taxonomic community • Adoption by regulatory agencies • Excitement in other fields of science • Product development by private companies

  25. Intellectual Outreach Activities • BOLI/Assembling the Tree of Life meeting • Building operational collaborations • Seeking database interoperability • Identifying research opportunities • EMBO Workshop on Molecular Biodiversity and DNA Barcodes • Behavior of molecular markers across taxa • Banbury 3 workshop on molecular evolution • Barcode data in research on speciation, phylogeography, DNA dynamics

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