catalogue of life, reading, uk, 29 march 2007 consortium for the barcode of life (cbol): linking...
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Catalogue of Life, Reading, UK, 29 March 2007
Consortium for the Consortium for the Barcode of Life Barcode of Life (CBOL): Linking (CBOL): Linking Molecules to the Molecules to the Catalogue of LifeCatalogue of Life
David E. Schindel, Executive David E. Schindel, Executive SecretarySecretary
National Museum of Natural HistoryNational Museum of Natural HistorySmithsonian InstitutionSmithsonian Institution
[email protected]@si.edu;; http://www.barcoding.si.eduhttp://www.barcoding.si.edu202/633-0812; fax 202/633-2938202/633-0812; fax 202/633-2938
Catalogue of Life, Reading, UK, 29 March 2007
Species Identification Species Identification MattersMatters
Basic research on evolution, ecologyBasic research on evolution, ecology Endangered/protected species Endangered/protected species Agricultural pests/beneficial speciesAgricultural pests/beneficial species Invasive speciesInvasive species Disease vectors/pathogensDisease vectors/pathogens Hazards (e.g., bird strikes on airplanes)Hazards (e.g., bird strikes on airplanes) Environmental quality indicatorsEnvironmental quality indicators Managing for sustainable harvestingManaging for sustainable harvesting Fidelity of cell lines/culture collectionsFidelity of cell lines/culture collections
Catalogue of Life, Reading, UK, 29 March 2007
Infrastructure of Taxonomy:Infrastructure of Taxonomy:Fragmented, DisconnectedFragmented, Disconnected
Collections and databases of specimensCollections and databases of specimens Seedbanks, culture/cell line collectionsSeedbanks, culture/cell line collections Compilations of taxonomic namesCompilations of taxonomic names Floristic and faunistic Floristic and faunistic
surveys/inventoriessurveys/inventories Monographs, Taxonomic revisionsMonographs, Taxonomic revisions Data repositories (gene sequences, Data repositories (gene sequences,
characters, images, trees)characters, images, trees) The (undigitized) Taxonomic LiteratureThe (undigitized) Taxonomic Literature
Catalogue of Life, Reading, UK, 29 March 2007
Biodiversity Informatics:Biodiversity Informatics:Fragmented, UnconnectedFragmented, Unconnected
Journal Publication
Species Name
Voucher Specimen
??
Type specimens
Varied species concepts: - BSC (hard to apply) - Typology - Genetic lineages
Catalogue of Life, Reading, UK, 29 March 2007
Growth of Biodiversity DatabasesGrowth of Biodiversity Databases
Journal Publication
Species Name
Voucher Specimen
Authority files of taxonomic
names
Museum databases of
associated data
Catalogue of Life, Reading, UK, 29 March 2007
Catalogue of Life, Reading, UK, 29 March 2007
Catalogue of Life, Reading, UK, 29 March 2007
Catalogue of Life, Reading, UK, 29 March 2007
Databases of Species Databases of Species DistributionsDistributions
Journal Publication
Species Name
Voucher Specimen
Authority files of taxonomic
names
Museum databases of
associated dataDatabases of species
occurrences and distribution
Catalogue of Life, Reading, UK, 29 March 2007
Catalogue of Life, Reading, UK, 29 March 2007
DNA Barcodes:DNA Barcodes:A Key Variable for Biodiversity A Key Variable for Biodiversity
InformaticsInformatics
Journal Publication
Species Name
Voucher Specimen
Barcode Sequence
Authority files of taxonomic
names
Museum databases of
associated dataDatabases of species
occurrences and distribution (OBIS)
Catalogue of Life, Reading, UK, 29 March 2007
A DNA barcode is a A DNA barcode is a short gene sequence short gene sequence
taken from taken from standardized portions standardized portions
of the genome,of the genome, used to identify used to identify
speciesspecies
Catalogue of Life, Reading, UK, 29 March 2007
Uses of DNA BarcodesUses of DNA BarcodesResearch tool for improving species-level Research tool for improving species-level
taxonomy:taxonomy: Associating all life history stages, gendersAssociating all life history stages, genders Testing species boundaries, finding new Testing species boundaries, finding new
variantsvariants
Applied tool for identifying regulated species:Applied tool for identifying regulated species: Disease vectors, agricultural pests, invasivesDisease vectors, agricultural pests, invasives Environmental indicators, protected species Environmental indicators, protected species Using minimal samples, damaged specimens, Using minimal samples, damaged specimens,
gut contents, droppingsgut contents, droppings
““Triage” tool for flagging potential new species:Triage” tool for flagging potential new species: Undescribed and cryptic speciesUndescribed and cryptic species
Catalogue of Life, Reading, UK, 29 March 2007
Uses of DNA BarcodesUses of DNA BarcodesResearch tool for improving species-level Research tool for improving species-level
taxonomy:taxonomy: Associating all life history stages, gendersAssociating all life history stages, genders Testing species boundaries, finding new variantsTesting species boundaries, finding new variants
Applied tool for identifying regulated species:Applied tool for identifying regulated species: Disease vectors, agricultural pests, invasivesDisease vectors, agricultural pests, invasives Environmental indicators, protected species Environmental indicators, protected species Using minimal samples, damaged specimens, Using minimal samples, damaged specimens,
gut contents, droppingsgut contents, droppings
““Triage” tool for flagging potential new species:Triage” tool for flagging potential new species: Undescribed and cryptic speciesUndescribed and cryptic species
Catalogue of Life, Reading, UK, 29 March 2007
Uses of DNA BarcodesUses of DNA BarcodesResearch tool for improving species-level Research tool for improving species-level
taxonomy:taxonomy: Associating all life history stages, gendersAssociating all life history stages, genders Testing species boundaries, finding new variantsTesting species boundaries, finding new variants
Applied tool for identifying regulated species:Applied tool for identifying regulated species: Disease vectors, agricultural pests, invasivesDisease vectors, agricultural pests, invasives Environmental indicators, protected species Environmental indicators, protected species Using minimal samples, damaged specimens, Using minimal samples, damaged specimens,
gut contents, droppingsgut contents, droppings
““Triage” tool for flagging potential new species:Triage” tool for flagging potential new species: Undescribed and cryptic speciesUndescribed and cryptic species
Catalogue of Life, Reading, UK, 29 March 2007
CBOL Member Organizations: 2007
• 150+ Member organizations, 45 countries
• 30+ Member organizations from 20+ developing countries
Catalogue of Life, Reading, UK, 29 March 2007
CBOL’s StrategyCBOL’s Strategy Collaborate with existing biodiversity Collaborate with existing biodiversity
initiativesinitiatives Work to connect existing systems with new Work to connect existing systems with new
data standards; avoid creating new data standards; avoid creating new databasesdatabases
Rely on GenBank, EMBL and DDBJ as stable Rely on GenBank, EMBL and DDBJ as stable data repositoriesdata repositories
Global participationGlobal participation Engage taxonomists and applied user Engage taxonomists and applied user
communities communities Set tangible, realistic goals, near-term resultsSet tangible, realistic goals, near-term results
Catalogue of Life, Reading, UK, 29 March 2007
Taxonomy in GenBankTaxonomy in GenBank
Species names provided by Species names provided by submitterssubmitters
Names added to Taxonomy BrowserNames added to Taxonomy Browser Only recently checked against Only recently checked against
compilationscompilations Submitters informed of errors but not Submitters informed of errors but not
forced to make correctionsforced to make corrections
Catalogue of Life, Reading, UK, 29 March 2007
Barcode Data StandardsBarcode Data Standards Consensus results of Front Royal Consensus results of Front Royal
meetingmeeting– GBIFGBIF ITIS ITIS GRIN GRIN– NBIINBII Species2000 Species2000 IPNI IPNI– ICZNICZN ZooRecord ZooRecord OBIS OBIS
Structured link to voucher specimenStructured link to voucher specimen Species name selected from authoritySpecies name selected from authority Online access to metadataOnline access to metadata Trace files and quality scoresTrace files and quality scores Minimum sequence lengthMinimum 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.
GeoreferenceHabitat
Character setsImages
BehaviorOther genes
Trace filesOther
DatabasesPhylogenetic
Pop’n GeneticsEcological
Primers
Catalogue of Life, Reading, UK, 29 March 2007
CBOL-Initiated ProjectsCBOL-Initiated Projects Fish Barcode of Life (FISH-BOL)Fish Barcode of Life (FISH-BOL)
– 30,000 marine/freshwater species by 201030,000 marine/freshwater species by 2010 All Birds Barcoding Initiative (ABBI)All Birds Barcoding Initiative (ABBI)
– 10,000 species by 201010,000 species by 2010 Tephritid fruit fliesTephritid fruit flies
– 2,000 pest/beneficial species and relatives by 2,000 pest/beneficial species and relatives by 20082008
MosquitoesMosquitoes– 3,300 species by 20083,300 species by 2008
African scale insects, lake fish, stem-borersAfrican scale insects, lake fish, stem-borers
Catalogue of Life, Reading, UK, 29 March 2007
Taipei Barcode ConferenceTaipei Barcode Conference Second International Barcode Conference Second International Barcode Conference Academia Sinica, week of 17 SeptemberAcademia Sinica, week of 17 September Regional Barcode Meeting for South/SE Regional Barcode Meeting for South/SE
AsiaAsia CBOL Working GroupsCBOL Working Groups FISH-BOL/Marine Fisheries workshopFISH-BOL/Marine Fisheries workshop Short course on biodiversity informaticsShort course on biodiversity informatics