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DNA Barcoding and the Consortium for the Barcode of Life

DNA Barcoding and the Consortium for the Barcode of Life. David E. Schindel, Executive Secretary National Museum of Natural History Smithsonian Institution SchindelD@si.edu ; http://www.barcoding.si.edu 202/633-0812; fax 202/633-2938. Species Identification Matters.

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DNA Barcoding and the Consortium for the Barcode of Life

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  1. DNA Barcoding and the Consortium for the Barcode of Life David E. Schindel, Executive Secretary National Museum of Natural History Smithsonian Institution SchindelD@si.edu; http://www.barcoding.si.edu 202/633-0812; fax 202/633-2938

  2. Species Identification Matters • Endangered/protected species • Agricultural pests • Invasive species • Disease vectors/pathogens • Hazards (e.g., bird strikes on airplanes) • Environmental quality indicators • Unsustainable harvesting • Fidelity of cell lines/culture collections

  3. Taxonomists The Practice of Taxonomy The Uses of Taxonomy Socioeconomic Decisions Taxonomic Decision-Making Distributions of Character Variation Concerns/ Regulations Characters Specimens Specimens

  4. The Problem… • Taxonomists are a limited resource • Taxonomic infrastructure is not widely available • Taxonomic decisions are difficult for non-specialists • Therefore, the practice of taxonomy does not scale up to meet the needs of society (or ecology, ecosystem studies, etc.)

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

  6. Uses of DNA Barcodes “Triage” tool for flagging potential new species: • Undescribed and cryptic species Research tool for assigning specimens to known species, including: • Life history stages, damaged specimens, gut contents, droppings Applied tool for identifying regulated species: • Disease vectors, agricultural pests, invasives • Protected species, CITES listed, trade-sensitive

  7. D-Loop Small ribosomal RNA Large ribosomal RNA Cyt b ND1 ND6 COI COI ND5 L-strand ND2 H-strand ND4 COI ND4L COII ND3 ATPase subunit 8 COIII ATPase subunit 6 The Mitochondrial Genome

  8. How much information is there in a DNA Barcode? • Human genome: • Contains 3 billion base-pairs • Identified by 648 bp COI barcode sequence • Content-to-label ratio: 5 X 106 • Oxford English Dictionary, 2nd Ed.,1989: • 20 volumes, 21,730 pages, 500,000 entries, 59 million words, 350 million print characters • Identified by 10-character ISBN • Content-to-label ratio: 4 X 107

  9. Current Norm: High throughput Large capacity PCR and sequencing reactions ABI 3100 capillary automated sequencer

  10. Future Norm? • A taxonomic GPS • Link to reference database • Usable by non-specialists.

  11. Consortium for the Barcode of Life (CBOL) • An international affiliation of: • 80+ Members Org’s, 35+ countries, 6 continents • Natural history museums, biodiversity organizations • Users: e.g., government agencies • Private sector biotech companies, database providers • 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

  12. CBOL Member Organizations(as of May 2005)

  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. CBOL’s Goals • Create a reference barcode database • Identify high-priority taxa and societal needs • Promote/facilitate barcoding projects and ‘CBOL campaigns’ • Improve methods, address shared obstacles through WGs • Populate database from collections • More portability, less time/expense • Improve taxonomic research environment

  15. Recent and Planned Activities • Data standards, Barcode records in GenBank • Launch of FishBOL, All Birds Initiatives • International Network for Barcoding Invasive and Pest Species (INBIPS) • APEC Workshop on Invasives, Beijing • Mosquitoes and disease vectors • Plans for CITES species, endangered Vertebrates, Bushmeat

  16. Barcode Section of GenBank Specimen Metadata Voucher Specimen Species Name GeoreferenceHabitatCharacter setsImagesBehaviorOther genes Indices - Catalog of Life - GBIF/ECAT Nomenclators - Zoo Record - IPNI NameBank Publication links - New species Barcode Sequence Trace files Other Databases Literature(link to content or citation) PhylogeneticPop’n GeneticsEcological

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