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Consortium for the Barcode of Life (CBOL): Linking Molecules to the Catalogue of Life

Consortium for the Barcode of Life (CBOL): Linking Molecules to the Catalogue of Life. 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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Consortium for the Barcode of Life (CBOL): Linking Molecules to the Catalogue of Life

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  1. Consortium for the Barcode of Life (CBOL): Linking Molecules to the Catalogue of Life 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. Species Identification Matters • Basic research on evolution, ecology • Endangered/protected species • Agricultural pests/beneficial species • Invasive species • Disease vectors/pathogens • Hazards (e.g., bird strikes on airplanes) • Environmental quality indicators • Managing for sustainable harvesting • Fidelity of cell lines/culture collections

  3. Infrastructure of Taxonomy:Fragmented, Disconnected • Collections and databases of specimens • Seedbanks, culture/cell line collections • Compilations of taxonomic names • Floristic and faunistic surveys/inventories • Monographs, Taxonomic revisions • Data repositories (gene sequences, characters, images, trees) • The (undigitized) Taxonomic Literature

  4. Biodiversity Informatics:Fragmented, Unconnected Type specimens Varied species concepts: - BSC (hard to apply) - Typology - Genetic lineages

  5. Growth of Biodiversity Databases Museum databases of associated data Authority files of taxonomic names

  6. Databases of Species Distributions Museum databases of associated data Databases of species occurrences and distribution Authority files of taxonomic names

  7. DNA Barcodes:A Key Variable for Biodiversity Informatics Museum databases of associated data Databases of species occurrences and distribution (OBIS) Authority files of taxonomic names

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

  9. Uses of DNA Barcodes Research tool for improving species-level taxonomy: • 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 • Using minimal samples, damaged specimens, gut contents, droppings “Triage” tool for flagging potential new species: • Undescribed and cryptic species

  10. Uses of DNA Barcodes Research tool for improving species-level taxonomy: • 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 • Using minimal samples, damaged specimens, gut contents, droppings “Triage” tool for flagging potential new species: • Undescribed and cryptic species

  11. Uses of DNA Barcodes Research tool for improving species-level taxonomy: • 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 • Using minimal samples, damaged specimens, gut contents, droppings “Triage” tool for flagging potential new species: • Undescribed and cryptic species

  12. CBOL Member Organizations: 2007 • 150+ Member organizations, 45 countries • 30+ Member organizations from 20+ developing countries

  13. CBOL’s Strategy • Collaborate with existing biodiversity initiatives • Work to connect existing systems with new data standards; avoid creating new databases • Rely on GenBank, EMBL and DDBJ as stable data repositories • Global participation • Engage taxonomists and applied user communities • Set tangible, realistic goals, near-term results

  14. Taxonomy in GenBank • Species names provided by submitters • Names added to Taxonomy Browser • Only recently checked against compilations • Submitters informed of errors but not forced to make corrections

  15. Barcode Data Standards • Consensus results of Front Royal meeting • GBIF  ITIS  GRIN • NBII  Species2000  IPNI • ICZN  ZooRecord  OBIS • Structured link to voucher specimen • Species name selected from authority • Online access to metadata • Trace files and quality scores • Minimum sequence length

  16. 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 Databases - Provisional sp. Barcode Sequence Trace files Primers Other Databases Literature(link to content or citation) PhylogeneticPop’n GeneticsEcological

  17. CBOL-Initiated Projects • Fish Barcode of Life (FISH-BOL) • 30,000 marine/freshwater species by 2010 • All Birds Barcoding Initiative (ABBI) • 10,000 species by 2010 • Tephritid fruit flies • 2,000 pest/beneficial species and relatives by 2008 • Mosquitoes • 3,300 species by 2008 • African scale insects, lake fish, stem-borers

  18. Taipei Barcode Conference • Second International Barcode Conference • Academia Sinica, week of 17 September • Regional Barcode Meeting for South/SE Asia • CBOL Working Groups • FISH-BOL/Marine Fisheries workshop • Short course on biodiversity informatics

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