DNA Barcoding and the Consortium for the Barcode of Life

1. DNA Barcoding and the Consortium for the Barcode of Life Scott Miller Smithsonian Institution http://www.barcoding.si.edu

2. Why systematics and taxonomy? Basic tool for describing and explaining biological diversity Historical framework for biocontrol, biogeography, ecology, evolution, etc. -predictive value of phylogeny- Communication of knowledge

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

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

5. Small ribosomal RNA The Mitochondrial Genome D-Loop mtDNA DNA Cytochrome b ND1 ND6 ND5 COI ND2 COI L-strand H-strand Typical Animal Cell ND4 ND4L COII ND3 COIII ATPase subunit 8 ATPase subunit 6 Mitochondrion Barcoding for Animals - COI

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

7. Associating Life Stages, Processed Parts, Dimorphic Genders

8. Consortium for the Barcode of Life (CBOL) • First barcoding publications in 2002 • Cold Spring Harbor planning workshops in 2003 • Sloan Foundation 2-year grant for $800K May 2004 • Secretariat opens at Smithsonian, September 2004 • First international conference February 2005 • $1.55 million 2-year renewal in April 2006 • Now an international affiliation of: • Natural history museums, biodiversity organizations • Users: e.g., government agencies • Private sector biotech companies, database providers

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

10. CBOL’s Strategy • Collaborate with existing biodiversity initiatives • Work to connect existing systems with new data standards; avoid “reinventing the wheel” • Rely on GenBank, EMBL and DDBJ as archival data repositories • BOLD as LIMS and barcode database/analysis • Global participation • Engage taxonomists and applied user communities • Set tangible, realistic goals, near-term results

11. Linking to International Initiatives through CBOL • Global Biodiversity Information Facility (GBIF) • ISIS/ZIMS (zoos) • Taxonomic databases (Species 2000, ITIS) • Voucher specimen databases (EMu) • Biodiversity Heritage Library • Genbank/EMBL/DDBJ partnership • Encyclopedia of Life (new – www.eol.org)

12. CBOL Taxon Focused 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

13. CBOL’s Working Groups • Database: Designing/constructing the Barcode Section of GenBank • DNA: Protocols for formalin-fixed and old museum specimens; Producing LIMS for dissemination • Data Analysis: Beyond phenetic methods; population genetics perspective • Plants: Identify gene region(s) for barcoding

14. Driving Cultural Change • Integrating databases: • Sequences, vouchers, species names • Accelerating taxonomic outputs • Digital libraries, Encyclopedia of Life • Species registration, ZooBank • Promoting open access to data • The barcode “data commons” • Creating a reward system for data publication • PLoS One “data release” papers • Community feedback for data curation

15. CBOL Formalin Workshop • May 8-9, 2006 workshop in Washington, U.S. National Research Council • Chemists, biochemists, biophysicists, biomedical researchers • Literature survey of DNA recovery protocols from formalin-fixed specimens • Create a new research agenda • Follow-on with SPNHC as major partner

16. CBOL Outreach Activities • Regional meetings in: • Cape Town, South Africa, 7-8 April 2006, SANBI • Nairobi, Kenya, 18-19 October 2006 • Brazil, February 2007 • Taiwan, September 2007 • Second International Barcode Conference • Taiwan, September 2007 • Support from CBOL, host governments and international development agencies

17. Goals of Regional Meetings • Raise awareness • Explore potential applications in the region • Assess greatest needs and opportunities in the region • Identify highest priorities, construct national and regional action plans • Start intra-regional networks and intercontinental partnerships

18. 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

19. Methods

20. Producing Barcode Data: 2006 • Hundreds of samples per day • Dimes to dollars per sample Polymerase Chain Reaction Amplification units ABI 3100 capillary automated sequencer

21. Producing Barcode Data: 2008 Faster, more portable: Hundreds of samples per hour Integrated DNA microchips Table-top microfluidic systems

22. Producing Barcode Data: 2010?Barcode data anywhere, instantly • Data in seconds to minutes • Pennies per sample • Link to reference database • A taxonomic GPS • Usable by non-specialists

23. What DNA Barcoding is NOT • Barcoding is not DNA taxonomy; no single gene (or character) is adequate • Barcoding is not “Tree of Life”; we focus on species diagnosis not phylogeny • 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 • Barcoding can help to create a 21st century research environment for taxonomy

24. For additional information, seewww.barcoding.si.eduMore CBOL members welcome!