DNA Barcoding and the Consortium for the Barcode of Life

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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_at_si.edu http//www.barcoding.si.edu
• 202/633-0812 fax [phone]

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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

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

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

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The Mitochondrial Genome

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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

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Current Norm High throughput
Large capacity PCR and sequencing reactions
ABI 3100 capillary automated sequencer
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Future Norm?

• A taxonomic GPS
• Link to reference database
• Usable by non-specialists.

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Consortium for the Barcode of Life (CBOL)

• An international affiliation of
• 80 Members Orgs, 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

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CBOL Member Organizations(as of May 2005)
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CBOLs 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

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CBOLs 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

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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

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Barcode Section of GenBank
Voucher Specimen
Species Name
Specimen Metadata
Indices - Catalog of Life - GBIF/ECAT Nomenclato
rs - Zoo Record - IPNI NameBank Publication
links - New species
GeoreferenceHabitatCharacter setsImagesBehavio
rOther genes
Barcode Sequence
Trace files
Other Databases
Literature(link to content or citation)
PhylogeneticPopn GeneticsEcological