Catalogue of Life, Reading, UK, 29 March 2007 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 / ; fax 202/

Catalogue of Life, Reading, UK, 29 March 2007 Species Identification Matters Basic research on evolution, ecology Basic research on evolution, ecology Endangered/protected species Endangered/protected species Agricultural pests/beneficial species Agricultural pests/beneficial species Invasive species Invasive species Disease vectors/pathogens Disease vectors/pathogens Hazards (e.g., bird strikes on airplanes) Hazards (e.g., bird strikes on airplanes) Environmental quality indicators Environmental quality indicators Managing for sustainable harvesting Managing for sustainable harvesting Fidelity of cell lines/culture collections Fidelity of cell lines/culture collections

Catalogue of Life, Reading, UK, 29 March 2007 Infrastructure of Taxonomy: Fragmented, Disconnected Collections and databases of specimens Collections and databases of specimens Seedbanks, culture/cell line collections Seedbanks, culture/cell line collections Compilations of taxonomic names Compilations of taxonomic names Floristic and faunistic surveys/inventories Floristic and faunistic surveys/inventories Monographs, Taxonomic revisions Monographs, Taxonomic revisions Data repositories (gene sequences, characters, images, trees) Data repositories (gene sequences, characters, images, trees) The (undigitized) Taxonomic Literature The (undigitized) Taxonomic Literature

Catalogue of Life, Reading, UK, 29 March 2007 Biodiversity Informatics: Fragmented, Unconnected ?? Type specimens Varied species concepts: - BSC (hard to apply) - Typology - Genetic lineages

Catalogue of Life, Reading, UK, 29 March 2007 Growth of Biodiversity Databases Authority files of taxonomic names Museum databases of associated data

Catalogue of Life, Reading, UK, 29 March 2007

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

Catalogue of Life, Reading, UK, 29 March 2007

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

Catalogue of Life, Reading, UK, 29 March 2007 A DNA barcode is a short gene sequence taken from standardized portions of the genome, used to identify species

Catalogue of Life, Reading, UK, 29 March 2007 Uses of DNA Barcodes Research tool for improving species-level taxonomy: Associating all life history stages, genders Associating all life history stages, genders Testing species boundaries, finding new variants Testing species boundaries, finding new variants Applied tool for identifying regulated species: Disease vectors, agricultural pests, invasives Disease vectors, agricultural pests, invasives Environmental indicators, protected species Environmental indicators, protected species Using minimal samples, damaged specimens, gut contents, droppings Using minimal samples, damaged specimens, gut contents, droppings “Triage” tool for flagging potential new species: Undescribed and cryptic species Undescribed and cryptic species

Catalogue of Life, Reading, UK, 29 March 2007 Uses of DNA Barcodes Research tool for improving species-level taxonomy: Associating all life history stages, genders Associating all life history stages, genders Testing species boundaries, finding new variants Testing species boundaries, finding new variants Applied tool for identifying regulated species: Disease vectors, agricultural pests, invasives Disease vectors, agricultural pests, invasives Environmental indicators, protected species Environmental indicators, protected species Using minimal samples, damaged specimens, gut contents, droppings Using minimal samples, damaged specimens, gut contents, droppings “Triage” tool for flagging potential new species: Undescribed and cryptic species Undescribed and cryptic species

Catalogue of Life, Reading, UK, 29 March 2007 Uses of DNA Barcodes Research tool for improving species-level taxonomy: Associating all life history stages, genders Associating all life history stages, genders Testing species boundaries, finding new variants Testing species boundaries, finding new variants Applied tool for identifying regulated species: Disease vectors, agricultural pests, invasives Disease vectors, agricultural pests, invasives Environmental indicators, protected species Environmental indicators, protected species Using minimal samples, damaged specimens, gut contents, droppings Using minimal samples, damaged specimens, gut contents, droppings “Triage” tool for flagging potential new species: Undescribed and cryptic species Undescribed and cryptic species

Catalogue of Life, Reading, UK, 29 March 2007 CBOL Member Organizations: Member organizations, 45 countries 30+ Member organizations from 20+ developing countries

Catalogue of Life, Reading, UK, 29 March 2007 CBOL’s Strategy Collaborate with existing biodiversity initiatives Collaborate with existing biodiversity initiatives Work to connect existing systems with new data standards; avoid creating new databases Work to connect existing systems with new data standards; avoid creating new databases Rely on GenBank, EMBL and DDBJ as stable data repositories Rely on GenBank, EMBL and DDBJ as stable data repositories Global participation Global participation Engage taxonomists and applied user communities Engage taxonomists and applied user communities Set tangible, realistic goals, near-term results Set tangible, realistic goals, near-term results

Catalogue of Life, Reading, UK, 29 March 2007 Taxonomy in GenBank Species names provided by submitters Species names provided by submitters Names added to Taxonomy Browser Names added to Taxonomy Browser Only recently checked against compilations Only recently checked against compilations Submitters informed of errors but not forced to make corrections Submitters informed of errors but not forced to make corrections

Catalogue of Life, Reading, UK, 29 March 2007 Barcode Data Standards Consensus results of Front Royal meeting Consensus results of Front Royal meeting –GBIF  ITIS  GRIN –NBII  Species2000  IPNI –ICZN  ZooRecord  OBIS Structured link to voucher specimen Structured link to voucher specimen Species name selected from authority Species name selected from authority Online access to metadata Online access to metadata Trace files and quality scores Trace files and quality scores Minimum sequence length Minimum sequence length

Catalogue of Life, Reading, UK, 29 March 2007 Barcode Sequence Voucher Specimen Species Name Specimen Metadata Literature (link to content or citation) BARCODE Records in INSDC Indices - Catalogue of Life - GBIF/ECAT Nomenclators - Zoo Record - IPNI - NameBank Publication links - New species Databases - Provisional sp. Georeference Habitat Character sets Images Behavior Other genes Trace files Other Databases Phylogenetic Pop’n Genetics Ecological Primers

Catalogue of Life, Reading, UK, 29 March 2007 CBOL-Initiated Projects Fish Barcode of Life (FISH-BOL) Fish Barcode of Life (FISH-BOL) –30,000 marine/freshwater species by 2010 All Birds Barcoding Initiative (ABBI) All Birds Barcoding Initiative (ABBI) –10,000 species by 2010 Tephritid fruit flies Tephritid fruit flies –2,000 pest/beneficial species and relatives by 2008 Mosquitoes Mosquitoes –3,300 species by 2008 African scale insects, lake fish, stem-borers African scale insects, lake fish, stem-borers

Catalogue of Life, Reading, UK, 29 March 2007 Taipei Barcode Conference Second International Barcode Conference Second International Barcode Conference Academia Sinica, week of 17 September Academia Sinica, week of 17 September Regional Barcode Meeting for South/SE Asia Regional Barcode Meeting for South/SE Asia CBOL Working Groups CBOL Working Groups FISH-BOL/Marine Fisheries workshop FISH-BOL/Marine Fisheries workshop Short course on biodiversity informatics Short course on biodiversity informatics