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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 • 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
Taxonomists The Practice of Taxonomy The Uses of Taxonomy Socioeconomic Decisions Taxonomic Decision-Making Distributions of Character Variation Concerns/ Regulations Characters Specimens Specimens
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.)
A DNA barcode is a short gene sequence taken from standardized portions of the genome, used to identify species
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
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
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
Current Norm: High throughput Large capacity PCR and sequencing reactions ABI 3100 capillary automated sequencer
Future Norm? • A taxonomic GPS • Link to reference database • Usable by non-specialists.
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
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
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
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
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