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

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

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

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

5. ABBI/FISH-BOL meeting, Buenos Aires, March 2007 Reactions to Barcoding: 2004 From ecologists and other users: “This is what we need! How soon can we get started?” 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 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 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.” 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.”

6. ABBI/FISH-BOL meeting, Buenos Aires, March 2007 Uses of DNA Barcodes Research tool for improving species-level taxonomy: 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 Using minimal samples, damaged specimens, gut contents, droppings Using minimal samples, damaged specimens, gut contents, droppings “Triage” tool for flagging potential new species: Undescribed and cryptic species Undescribed and cryptic species

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

8. ABBI/FISH-BOL meeting, Buenos Aires, March 2007 Uses of DNA Barcodes Research tool for improving species-level taxonomy: 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 Using minimal samples, damaged specimens, gut contents, droppings Using minimal samples, damaged specimens, gut contents, droppings “Triage” tool for flagging potential new species: Undescribed and cryptic species Undescribed and cryptic species

9. ABBI/FISH-BOL meeting, Buenos Aires, March 2007 Uses of DNA Barcodes Research tool for improving species-level taxonomy: 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 Using minimal samples, damaged specimens, gut contents, droppings Using minimal samples, damaged specimens, gut contents, droppings “Triage” tool for flagging potential new species: Undescribed and cryptic species Undescribed and cryptic species

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

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

12. 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 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

15. ABBI/FISH-BOL meeting, Buenos Aires, March 2007 Consortium for the Barcode of Life (CBOL) First barcoding publications in 2002 First barcoding publications in 2002 Cold Spring Harbor planning workshops in 2003 Cold Spring Harbor planning workshops in 2003 Sloan Foundation grant, launch in May 2004 Sloan Foundation grant, launch in May 2004 Secretariat opens at Smithsonian, September 2004 Secretariat opens at Smithsonian, September 2004 First international conference February 2005 First international conference February 2005 Now an international affiliation of: Now an international affiliation of: 150 Members Org’s, 45 countries, 6 continents150 Members Org’s, 45 countries, 6 continents Natural history museums, biodiversity organizationsNatural history museums, biodiversity organizations Users: e.g., government agenciesUsers: e.g., government agencies Private sector biotech companies, database providersPrivate sector biotech companies, database providers

16. ABBI/FISH-BOL meeting, Buenos Aires, March 2007 Consortium for the Barcode of Life (CBOL) Smithsonian Institution/Sloan Foundation 150 Member Organizations, 45 Countries as of March 07

17. ABBI/FISH-BOL meeting, Buenos Aires, March 2007 Outreach Activities Regional meetings in: 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 Support from CBOL, host governments and international development agencies Second International Barcode Conference Second International Barcode Conference -Taiwan, September 2007

18. ABBI/FISH-BOL meeting, Buenos Aires, March 2007 Goals of Regional Meetings Raise awareness Raise awareness Explore potential applications in the region Explore potential applications in the region Assess greatest needs and opportunities in the region Assess greatest needs and opportunities in the region Identify highest priorities, construct national and regional action plans Identify highest priorities, construct national and regional action plans Start intra-regional networks and intercontinental partnerships Start intra-regional networks and intercontinental partnerships

19. ABBI/FISH-BOL meeting, Buenos Aires, March 2007 CBOL-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 flies Tephritid fruit flies 2,000 pest/beneficial species and relatives by 20082,000 pest/beneficial species and relatives by 2008 Mosquitoes Mosquitoes 3,300 species by 20083,300 species by 2008 African Scale Insects African Scale Insects Endangered vertebrates (bushmeat) Endangered vertebrates (bushmeat)

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

21. ABBI/FISH-BOL meeting, Buenos Aires, March 2007 CBOL’s Working Groups Database: Designing/constructing the Barcode Section of GenBank Database: Designing/constructing the Barcode Section of GenBank DNA: Protocols for formalin-fixed and old museum specimens; Producing LIMS for dissemination DNA: Protocols for formalin-fixed and old museum specimens; Producing LIMS for dissemination Data Analysis: Beyond phenetic methods; population genetics perspective Data Analysis: Beyond phenetic methods; population genetics perspective Plants: Identify gene region(s) for barcoding Plants: Identify gene region(s) for barcoding

22. ABBI/FISH-BOL meeting, Buenos Aires, March 2007 Barcode Data Standards Consensus results of Front Royal meeting Consensus results of Front Royal meeting GBIF  ITIS  GRINGBIF  ITIS  GRIN NBII  Species2000  IPNINBII  Species2000  IPNI ICZN  ZooRecord  OBISICZN  ZooRecord  OBIS Structured link to voucher specimen Structured link to voucher specimen Species name selected from authority Species name selected from authority Online access to metadata Online access to metadata Trace files and quality scores Trace files and quality scores Minimum sequence length Minimum sequence length

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

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

25. ABBI/FISH-BOL meeting, Buenos Aires, March 2007 CBOL’s Working Groups Database: Designing/constructing the Barcode Section of GenBank Database: Designing/constructing the Barcode Section of GenBank DNA: Protocols for formalin-fixed and old museum specimens; Producing LIMS for dissemination DNA: Protocols for formalin-fixed and old museum specimens; Producing LIMS for dissemination Data Analysis: Beyond phenetic methods; population genetics perspective Data Analysis: Beyond phenetic methods; population genetics perspective Plants: Identify gene region(s) for barcoding Plants: Identify gene region(s) for barcoding

26. ABBI/FISH-BOL meeting, Buenos Aires, March 2007 CBOL Formalin Workshop May 8-9, 2006 workshop in Washington, National Research Council May 8-9, 2006 workshop in Washington, National Research Council Chemists, biochemists, biophysicists, biomedical researchers Chemists, biochemists, biophysicists, biomedical researchers Literature survey of DNA recovery protocols from formalin-fixed specimens Literature survey of DNA recovery protocols from formalin-fixed specimens Create a new research agenda Create a new research agenda Follow-on with SPNHC as major partner Follow-on with SPNHC as major partner

27. ABBI/FISH-BOL meeting, Buenos Aires, March 2007 CBOL’s Working Groups Database: Designing/constructing the Barcode Section of GenBank Database: Designing/constructing the Barcode Section of GenBank DNA: Protocols for formalin-fixed and old museum specimens; Producing LIMS for dissemination DNA: Protocols for formalin-fixed and old museum specimens; Producing LIMS for dissemination Data Analysis: Beyond phenetic methods; population genetics perspective Data Analysis: Beyond phenetic methods; population genetics perspective Plants: Identify gene region(s) for barcoding Plants: Identify gene region(s) for barcoding

28. ABBI/FISH-BOL meeting, Buenos Aires, March 2007 CBOL’s Working Groups Database: Designing/constructing the Barcode Section of GenBank Database: Designing/constructing the Barcode Section of GenBank DNA: Protocols for formalin-fixed and old museum specimens; Producing LIMS for dissemination DNA: Protocols for formalin-fixed and old museum specimens; Producing LIMS for dissemination Data Analysis: Beyond phenetic methods; population genetics perspective Data Analysis: Beyond phenetic methods; population genetics perspective Plants: Identify gene region(s) for barcoding by December 2006 Plants: Identify gene region(s) for barcoding by December 2006

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

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

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

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

33. ABBI/FISH-BOL meeting, Buenos Aires, March 2007 Taipei Barcode Conference Second International Barcode Conference Second International Barcode Conference Academia Sinica, week of 17 September Academia Sinica, week of 17 September Regional Barcode Meeting for South/SE Asia Regional Barcode Meeting for South/SE Asia CBOL Working Groups CBOL Working Groups FISH-BOL/Marine Fisheries workshop FISH-BOL/Marine Fisheries workshop Short course on biodiversity informatics Short course on biodiversity informatics