Linking Barcode Data to Multiple Users David E. Schindel, Executive Secretary National Museum of Natural History Smithsonian Institution / ; fax 202/

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

The Mitochondrial Genome Cyt b D-Loop ND5 H-strand ND4 ND4L ND3 CO III CO I L-strand ND6 CO I ND2 ND1 CO II Small ribosomal RNA Large ribosomal RNA ATPase subunit 8 ATPase subunit 6

The Barcode Assembly Line Freshly collected specimens Frozen tissue Young museum specimens BOLD GenBank BARCODE Records Users with unidentified specimens Taxonomic Identifications and BARCODE Data Standards

Promote barcoding as a global standard Build participation Working Groups BARCODE standard International Conferences Increase production of public BARCODE records Projects, Networks, Organizations

Uses of DNA Barcodes Research tool for species-level taxonomy, ecology: 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 “Triage” tool for flagging potential new species: Undescribed and cryptic species Undescribed and cryptic species Taxonomic groups with few morphological features Taxonomic groups with few morphological features

New Sources of Taxonomic/Ecological Data Immature stages, damaged specimens Immature stages, damaged specimens Trophic webs from gut contents Trophic webs from gut contents Fecal droppings Fecal droppings Non-invasive sampling (catch/release, shed feathers, moults, fin clips) Non-invasive sampling (catch/release, shed feathers, moults, fin clips) Rapid ecological sampling and ecosystem assessment Rapid ecological sampling and ecosystem assessment Ecogenomic mixtures Ecogenomic mixtures

Uses of DNA Barcodes Research tool for species-level taxonomy, ecology: 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 “Triage” tool for flagging potential new species: Undescribed and cryptic species Undescribed and cryptic species Taxonomic groups with few morphological features Taxonomic groups with few morphological features

Uses of DNA Barcodes Research tool for species-level taxonomy, ecology: 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 “Triage” tool for flagging potential new species: Undescribed and cryptic species Undescribed and cryptic species Taxonomic groups with few morphological features Taxonomic groups with few morphological features

Species sampled Specimens per species Total # specimens sequenced # gene regions Total sequence length per species DNA barcoding Tree of Life Genomics Eco- genomics (?) NA - no vouchers ?NA

What DNA Barcoding is NOT Barcoding is not DNA taxonomy; no single gene (or character) is adequate Barcoding is not DNA taxonomy; no single gene (or character) is adequate Barcoding is not Tree of Life; barcode clusters are not phylogenetic trees Barcoding is not Tree of Life; barcode clusters are not phylogenetic trees Barcoding is not just COI; standardizing on one region has benefits and limits Barcoding is not just COI; standardizing on one region has benefits and limits Molecules in taxonomy is not new; but large-scale and standardization are new Molecules in taxonomy is not new; but large-scale and standardization are new

What DNA Barcoding is NOT Barcoding is not DNA taxonomy; no single gene (or character) is adequate Barcoding is not DNA taxonomy; no single gene (or character) is adequate Barcoding is not Tree of Life; barcode clusters are not phylogenetic trees Barcoding is not Tree of Life; barcode clusters are not phylogenetic trees Barcoding is not just COI; standardizing on one region has benefits and limits Barcoding is not just COI; standardizing on one region has benefits and limits Molecules in taxonomy is not new; but large-scale and standardization are new Molecules in taxonomy is not new; but large-scale and standardization are new

CBOL’s History Sloan Foundation support for two Banbury planning workshops in 2003 Sloan Foundation support for two Banbury planning workshops in 2003 Sloan 2-year inaugural CBOL grant, May 2004 Sloan 2-year inaugural CBOL grant, May 2004 Secretariat opens at Smithsonian, September 2004 Secretariat opens at Smithsonian, September 2004 International conference London, February 2005 International conference London, February 2005 $1.55 million 2-year renewal in April 2006 $1.55 million 2-year renewal in April 2006 Now an international affiliation of: Now an international affiliation of: Natural history museums, biodiversity organizations Natural history museums, biodiversity organizations Users: e.g., government agencies Users: e.g., government agencies Private sector biotech companies, database providers Private sector biotech companies, database providers

CBOL Member Organizations: Member organizations, 50 countries 54 Member organizations from 23 developing countries

CBOL’s Mission: Promoting DNA Barcoding as a Global Standard 1. Developing/raising community standards 2. Barcode projects to populate database 3. Global participation and coordination 4. Acceptance by taxonomic community 5. Adoption by regulatory agencies 6. Excitement in other fields of science 7. Product development by private companies

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 Georeference Habitat Character sets Images Behavior Other genes Trace files Other Databases Phylogenetic Pop’n Genetics Ecological Primers Databases - Provisional sp.

CBOL’s Mission: Promoting DNA Barcoding as a Global Standard 1. Developing/raising community standards 2. Barcode projects to populate database 3. Global participation and coordination 4. Acceptance by taxonomic community 5. Adoption by regulatory agencies 6. Excitement in other fields of science 7. Product development by private companies

CBOL-Initiated Projects Tephritid fruit flies (USDA) Tephritid fruit flies (USDA) 2,000 pest/beneficial species and relatives by ,000 pest/beneficial species and relatives by 2008 Mosquitoes 3,300 species by 2008 Mosquitoes 3,300 species by 2008 Fish Barcode of Life, FISH-BOL Fish Barcode of Life, FISH-BOL 30,000 marine/freshwater species by ,000 marine/freshwater species by 2010 All Birds Barcoding Initiative (aviation agencies) All Birds Barcoding Initiative (aviation agencies) 10,000 species by ,000 species by 2010 Water quality assessment (USEPA) Water quality assessment (USEPA) Scale insects, commercial fish, hardwood Scale insects, commercial fish, hardwood

CBOL’s Mission: Promoting DNA Barcoding as a Global Standard 1. Developing/raising community standards 2. Barcode projects to populate database 3. Global participation and coordination 4. Acceptance by taxonomic community 5. Adoption by regulatory agencies 6. Excitement in other fields of science 7. Product development by private companies

Geographic Outreach Activities Regional meetings in: Regional meetings in: Cape Town, South Africa, 7-8 April 2006, SANBI Cape Town, South Africa, 7-8 April 2006, SANBI Nairobi, Kenya, October 2006 Nairobi, Kenya, October 2006 Brazil, February 2007 Brazil, February 2007 Taiwan, September 2007 Taiwan, September 2007 Assess technical/scientific capacity Assess technical/scientific capacity Identify high-priority barcoding projects Identify high-priority barcoding projects Initiate regional networks, partnerships Initiate regional networks, partnerships Partnership with BioNET-INTERNATIONAL Partnership with BioNET-INTERNATIONAL

Leading Lab Network Taipei Short Course, September 2007 BioCode STRISI-LAB CCDB BOLDGenBank

New CBOL Activities, Leading Lab Network Leading Lab Network “Phase 2” support for regional networks “Phase 2” support for regional networks Offer to promote Fungal Barcoding Initiative Offer to promote Fungal Barcoding Initiative Outreach to west/central Africa, India, China Outreach to west/central Africa, India, China More direct communication with Member Organizations More direct communication with Member Organizations Promote acceptance by CBD, developing countries Promote acceptance by CBD, developing countries Expand partnerships with GBIF, Encyclopedia of Life, Census of Marine Life, Catalog of Life Expand partnerships with GBIF, Encyclopedia of Life, Census of Marine Life, Catalog of Life

CBOL’s Mission: Promoting DNA Barcoding as a Global Standard 1. Developing/raising community standards 2. Barcode projects to populate database 3. Global participation and coordination 4. Acceptance by taxonomic community 5. Adoption by regulatory agencies 6. Excitement in other fields of science 7. Product development by private companies

Adoption by Regulators US Federal Aviation Administration – All Birds US Federal Aviation Administration – All Birds US Environmental Protection Agency US Environmental Protection Agency $250K pilot test, water quality bioassessment $250K pilot test, water quality bioassessment US Food and Drug Administration US Food and Drug Administration Reference barcodes for commercial fish Reference barcodes for commercial fish FISH-BOL and fish regulatory agencies FISH-BOL and fish regulatory agencies CBOL workshop in Taipei, September 2007 CBOL workshop in Taipei, September 2007 FAO International Plant Protection Commission FAO International Plant Protection Commission Proposal for Diagnostic Protocols for fruit flies Proposal for Diagnostic Protocols for fruit flies CITES, National Agencies, Conservation NGOs CITES, National Agencies, Conservation NGOs International Steering Committee, identifying pilot projects International Steering Committee, identifying pilot projects

CBOL’s Mission: Promoting DNA Barcoding as a Global Standard 1. Developing/raising community standards 2. Barcode projects to populate database 3. Global participation and coordination 4. Acceptance by taxonomic community 5. Adoption by regulatory agencies 6. Excitement in other fields of science 7. Product development by private companies

Intellectual Outreach Activities BOLI/Assembling the Tree of Life meeting BOLI/Assembling the Tree of Life meeting Building operational collaborations Building operational collaborations Seeking database interoperability Seeking database interoperability Identifying research opportunities Identifying research opportunities EMBO Workshop on Molecular Biodiversity and DNA Barcodes EMBO Workshop on Molecular Biodiversity and DNA Barcodes Behavior of molecular markers across taxa Behavior of molecular markers across taxa Banbury 3 workshop on molecular evolution Banbury 3 workshop on molecular evolution Barcode data in research on speciation, phylogeography, DNA dynamics Barcode data in research on speciation, phylogeography, DNA dynamics