Overview of DNA Barcoding

1. Overview of DNA Barcoding David E. Schindel, Executive Secretary Consortium for the Barcode of Life National Museum of Natural History Smithsonian Institution Schindeld@si.edu; http://www.barcoding.si.edu 202/633-0812; fax 202/633-2938 ABBI/FISH-BOL meeting, Buenos Aires, March 2007

2. DNA Barcodes:A Key Variable for Biodiversity Informatics Museum databases of associated data Databases of species occurrences and distribution (OBIS) Authority files of taxonomic names ABBI/FISH-BOL meeting, Buenos Aires, March 2007

3. Background on • DNA Barcoding • The DNA Barcode Initiative • Consortium for the Barcode of Life (CBOL) • Current and planned activities • Data standards for barcode data • Challenges to CBOL projects • Support from CBOL ABBI/FISH-BOL meeting, Buenos Aires, March 2007

4. A DNA barcode is a short gene sequence taken from standardized portions of the genome, used to identify species ABBI/FISH-BOL meeting, Buenos Aires, March 2007

5. Reactions to Barcoding: 2004 • From ecologists and other users:“This is what we need! How soon can we get started?” • From traditional taxonomists:“Species should be based on lots of characters, not just barcodes” • From forward-looking taxonomists:“Using molecular data as species diagnostics isn’t new, but standardization and broad implementation are great!” • From barcoding practitioners:“I had my doubts at the beginning, but it really works as a tool for identification (96% accurate in a recent mollusc paper) and it is at least as good as traditional approaches to discovering new species.” ABBI/FISH-BOL meeting, Buenos Aires, March 2007

6. 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 ABBI/FISH-BOL meeting, Buenos Aires, March 2007

7. Associating Life Stages, Processed Parts, Dimorphic Genders ABBI/FISH-BOL meeting, Buenos Aires, March 2007

8. 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 ABBI/FISH-BOL meeting, Buenos Aires, March 2007

9. 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 ABBI/FISH-BOL meeting, Buenos Aires, March 2007

10. Using a Million Barcodes A critical mass of standardized data for: • Biogeographic patterns, habitat dynamics • Phylogeography • Niche modelling • Ecological relationships • Dynamics of molecular evolution • Complementing Tree of Life • Long-term biodiversity monitoring • Understanding and preserving biodiversity ABBI/FISH-BOL meeting, Buenos Aires, March 2007

11. What DNA Barcoding is NOT • 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 just COI; standardizing on one region has benefits and limits • Molecules in taxonomy is not new; but large-scale and standardization are new ABBI/FISH-BOL meeting, Buenos Aires, March 2007

12. ABBI/FISH-BOL meeting, Buenos Aires, March 2007

13. ABBI/FISH-BOL meeting, Buenos Aires, March 2007

14. What DNA Barcoding is NOT • 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 just COI; standardizing on one region has benefits and limits • Molecules in taxonomy is not new; but large-scale and standardization are new ABBI/FISH-BOL meeting, Buenos Aires, March 2007

15. Consortium for the Barcode of Life (CBOL) • First barcoding publications in 2002 • Cold Spring Harbor planning workshops in 2003 • Sloan Foundation grant, launch in May 2004 • Secretariat opens at Smithsonian, September 2004 • First international conference February 2005 • Now an international affiliation of: • 150 Members Org’s, 45 countries, 6 continents • Natural history museums, biodiversity organizations • Users: e.g., government agencies • Private sector biotech companies, database providers ABBI/FISH-BOL meeting, Buenos Aires, March 2007

16. Consortium for the Barcode of Life (CBOL)Smithsonian Institution/Sloan Foundation150 Member Organizations, 45 Countries as of March 07 ABBI/FISH-BOL meeting, Buenos Aires, March 2007

17. Outreach Activities • Regional meetings in: • Cape Town, South Africa, 7-8 April 2006, SANBI • Nairobi, Kenya, 18-19 October 2006 • Brazil, March 2007 • Taiwan, September 2007 • Support from CBOL, host governments and international development agencies • Second International Barcode Conference • Taiwan, September 2007 ABBI/FISH-BOL meeting, Buenos Aires, March 2007

18. 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 ABBI/FISH-BOL meeting, Buenos Aires, March 2007

19. 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 • Endangered vertebrates (bushmeat) ABBI/FISH-BOL meeting, Buenos Aires, March 2007

20. Projects initiated by others • CMarZ: Marine habitat, multiple taxa • All-Leps: Multiple regions/habitats, single taxon • BioCode, Moorea: Single location, multiple habitats, multiple taxa ABBI/FISH-BOL meeting, Buenos Aires, March 2007

21. 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 ABBI/FISH-BOL meeting, Buenos Aires, March 2007

22. 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 ABBI/FISH-BOL meeting, Buenos Aires, March 2007

23. BARCODE Records in INSDC Specimen Metadata Voucher Specimen Species Name GeoreferenceHabitatCharacter setsImagesBehaviorOther genes Indices - Catalog of Life - GBIF/ECAT Nomenclators - Zoo Record - IPNI - NameBank Publication links - New species Databases - Provisional sp. Barcode Sequence Trace files Primers Other Databases Literature(link to content or citation) PhylogeneticPop’n GeneticsEcological ABBI/FISH-BOL meeting, Buenos Aires, March 2007

24. Digitizing Taxonomic Literature • CBOL’s catalytic efforts: • Library-Laboratory meeting in London, 2005, on electronic access to taxonomic literature • Led to formation of Biodiversity Heritage Library initiative • Proactive steps with PubMed to add taxonomic journals to online abstracts • Aggressive negotiation with publishers of barcoding papers • Involvement in Encyclopedia of Life ABBI/FISH-BOL meeting, Buenos Aires, March 2007

25. 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 ABBI/FISH-BOL meeting, Buenos Aires, March 2007

26. CBOL Formalin Workshop • May 8-9, 2006 workshop in Washington, 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 ABBI/FISH-BOL meeting, Buenos Aires, March 2007

27. 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 ABBI/FISH-BOL meeting, Buenos Aires, March 2007

28. 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 by December 2006 ABBI/FISH-BOL meeting, Buenos Aires, March 2007

29. Progress toward Plant Barcode • Kress 2005 proposal for ITS and trnh-psbA • Kew Garden receives Sloan/Moore Foundation support, early 2005 • Phase 1 screens 100 genes across 50 sibling species pairs • Phase 2 tests of matK, rpcoC1, rpoB, ndhJ, and accD • Canadian proposal for rbcL • CBOL protocols for approving barcode regions ABBI/FISH-BOL meeting, Buenos Aires, March 2007

30. Wider Impacts of Barcoding • Catalyzing interoperability of databases • Barcode data standards link sequences, specimens, species names and publications • Improving the information infrastructure • Digital library initiative in taxonomy • Expanding analytical toolbox for taxonomy • Renewing the mission of museums • DNA recovery from formalin-fixed specimens • Promoting the growth of DNA banks ABBI/FISH-BOL meeting, Buenos Aires, March 2007

31. Major Challenges • Lack of funding to acquire, identify, curate specimens • Assembling, managing, editing, QA for BARCODE-compliant data are labor-intensive • Technical problems with data transfer to BOLD • GenBank’s BarSTool is new • Aversion to sharing data pre-publication ABBI/FISH-BOL meeting, Buenos Aires, March 2007

32. Support from CBOL • ABBI and FISH-BOL get $50K per year • Internships for data management • Travel/consulting by taxonomists for specimen identification • Assistance in proposal writing • Formalin project • “Leading Lab” initiative to improve lab and data management protocols ABBI/FISH-BOL meeting, Buenos Aires, March 2007

33. 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 ABBI/FISH-BOL meeting, Buenos Aires, March 2007