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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.

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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
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
slide3

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
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.)
slide5

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

uses of dna barcodes
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
slide7

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
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
slide9

Current Norm: High throughput

Large capacity PCR and

sequencing reactions

ABI 3100 capillary

automated sequencer

future norm
Future Norm?
  • A taxonomic GPS
  • Link to reference database
  • Usable by non-specialists.
consortium for the barcode of life cbol
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
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
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
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
slide17

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