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

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

mailto:[email protected]

http://www.barcoding.si.edu/


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


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 surveys/inventoriesFloristic and faunistic surveys/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


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


Growth of Biodiversity DatabasesGrowth of Biodiversity Databases

Journal Publication

Species Name

Voucher Specimen

Authority files of taxonomic

names

Museum databases of

associated data


Databases of Species Databases of Species DistributionsDistributions

Journal Publication

Species Name

Voucher Specimen


names

Museum databases of

associated dataDatabases of species

occurrences and distribution


DNA Barcodes:DNA Barcodes:A Key Variable for Biodiversity A Key Variable for Biodiversity

InformaticsInformatics

Journal Publication

Species Name

Voucher Specimen

Barcode Sequence


names

Museum databases of

associated dataDatabases of species

occurrences and distribution (OBIS)


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


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


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 variantsApplied 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


CBOL Member Organizations: 2007

• 150+ Member organizations, 45 countries

• 30+ Member organizations from 20+ developing countries


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 databasesdata standards; avoid creating new databases 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


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


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


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


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


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

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

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