schindel

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

Species Identification Matters: 

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

Infrastructure of Taxonomy:Fragmented, Disconnected: 

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

Biodiversity Informatics:Fragmented, Unconnected: 

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

Growth of Biodiversity Databases: 

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

Databases of Species Distributions: 

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

DNA Barcodes:A Key Variable for Biodiversity Informatics: 

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)

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

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

Uses of DNA Barcodes: 

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

Uses of DNA Barcodes: 

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

Uses of DNA Barcodes: 

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

Slide16: 

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

CBOL’s Strategy: 

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

Taxonomy in GenBank: 

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

Barcode Data Standards: 

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

Slide20: 

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

CBOL-Initiated Projects: 

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

Taipei Barcode Conference: 

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