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DNA Barcoding: An Emerging Global Standard for Species Identification. Consortium for the Barcode of Life National Museum of Natural History Smithsonian Institution http://www.barcoding.si.edu 202/633-0808; fax 202/633-2938.

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dna barcoding an emerging global standard for species identification

DNA Barcoding: An Emerging Global Standard for Species Identification

Consortium for the Barcode of Life

National Museum of Natural History

Smithsonian Institution

http://www.barcoding.si.edu

202/633-0808; fax 202/633-2938

slide2

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

slide3

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

uses of dna barcodes
Uses of DNA Barcodes

Applied tool for identifying regulated species:

  • Disease vectors, agricultural pests, invasives
  • Environmental indicators, protected species
  • Using minimal samples, damaged specimens, gut contents, droppings

Research tool for improving species-level taxonomy:

  • Associating all life history stages, genders
  • Testing species boundaries, finding new variants

“Triage” tool for flagging potential new species:

  • Undescribed and cryptic species
using dna barcodes
Using DNA Barcodes
  • Establish reference library of barcodes from identified voucher specimens
  • If necessary, revise species limits
  • Then:
    • Identify unknowns by searching against reference sequences
    • Look for matches (mismatches) against ‘library on a chip’
    • Before long: Analyze relative abundance in multi-species samples
reactions to barcoding 2004
Reactions to Barcoding: 2004
  • 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 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.”
what dna barcoding is not
What DNA Barcoding is NOT
  • 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 just COI; standardizing on one region has benefits and limits
  • Molecules in taxonomy is not new; but large-scale and standardization are new
  • Barcoding can help to create a 21st century research environment for taxonomy
what dna barcoding is not10
What DNA Barcoding is NOT
  • 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 just COI; standardizing on one region has benefits and limits
  • Molecules in taxonomy is not new; but large-scale and standardization are new
  • BUT…Barcoding can help to create a 21st century research environment for taxonomy
slide11

BARCODE Data Standard

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

Primers

Other Databases

Literature(link to content or citation)

PhylogeneticPop’n GeneticsEcological

slide12

Current Norm: High throughput

Large capacity PCR and

sequencing reactions

ABI 3100 capillary

automated sequencer

producing barcode data 2008 faster more portable hundreds of samples per hour
Producing Barcode Data: 2008 Faster, more portable: Hundreds of samples per hour

Integrated DNA microchips

Table-top microfluidic systems

reference vs micro barcodes
Reference vs. Micro-Barcodes
  • BARCODE reference records
    • Adhere to data standards
    • Bidirectional reads, 500+ bp long
    • Linked to voucher, species name
  • Query barcode records
    • Used in BLAST or other searches
    • Often single pass reads
    • Often very short – 100+ bp for good IDs
    • Can cost less than $2, take less than 6 hours
producing barcode data 2010 barcode data anywhere instantly
Producing Barcode Data: 2010?Barcode data anywhere, instantly
  • Data in seconds to minutes
  • Pennies per sample
  • Link to reference database
  • A taxonomic GPS
  • Usable by non-specialists
consortium for the barcode of life cbol
Consortium for the Barcode of Life (CBOL)
  • 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
  • Now an international affiliation of:
    • 130+ Members Org’s, 40 countries, 6 continents
    • Natural history museums, biodiversity organizations
    • Users: e.g., government agencies
    • Private sector biotech companies, database providers
cbol s underlying principles
CBOL’s Underlying Principles
  • Standardization, cost-effectiveness
  • Minimalism (scientific) – short sequence
  • Global participation
  • Tangible, realistic goals, near-term results
  • Respond to applied user communities
  • Minimalisim (organizational) – Coordination/Facilitation of Bottom-Up activities, build on existing activities, avoid new ones
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; advice to new labs
  • Data Analysis: Beyond phenetic methods; population genetics perspective
  • Plants: Identify gene region(s) for barcoding
outreach to developing countries
Outreach to Developing Countries
  • Regional meetings in:
    • Cape Town, South Africa, 7-8 April 2006, SANBI
    • Nairobi, Kenya, 18-19 October 2006, NMK
    • Sao Paolo, Brazil, February 2007, INPA
    • Southern Asia, 2nd quarter 2007
  • Second International Barcode Conference
    • Singapore, 13-15 June 2007
  • Support from CBOL, host governments and international development agencies
goals of regional meetings
Goals of Regional Meetings
  • Raise awareness
  • Explore potential applications in the region
  • Assess greatest needs and opportunities in the region
  • Identify highest priorities, construct national and regional action plans
  • Start intra-regional networks and intercontinental partnerships
current and planned projects
Current and Planned Projects
  • Four Working Groups
  • FishBOL and All Birds Initiatives
  • Developing “Demonstrator Systems by 2008
  • African Scale Insect Barcoding Initiative (planned at Cape Town Regional Meeting)
  • International Network for Barcoding Invasive and Pest Species (INBIPS)
  • Forming a Conservation Committee
demonstrator development
Demonstrator Development

GOAL: By June 2008, create an operational system for global ID of an important group

  • Mosquitoes (disease vectors)
    • Barcode 85% (2932) of 3449 known species
    • Minimum 5 specimens per species
    • Reliance on archival collections
  • Tephritid fruit flies (agricultural pests)
    • Barcode 2000 species of 4500, 5 per species
    • All pests and beneficials, with closest relatives
    • Invasive non-destructive sampling of existing collections
abbi and fish bol
ABBI and FISH-BOL
  • Global initiatives to create reference library
  • Enable users to adopt barcode ID systems
  • All-species barcode database will:
    • Strengthen specimen/species data
    • Improve collections, tissue/DNA resources
    • Attract users to barcoding for specimen IDs
  • Regional Working Groups
  • Small Steering Committee and CBOL
bold data system
BoLD Data System
  • Developed/hosted by Univ. Guelph
  • Workbench for most barcode projects
  • Laboratory Information Management System (LIMS) for assembling data
  • Management and Analysis System
  • Identification system for matching unknowns to reference records
  • Uploading to GenBank
launching cbol projects
Launching CBOL Projects

Assembling Steering Committee

    • Users
    • Taxonomists, collection curators
    • Service providers (BoLD, analytical labs)
  • Plan for scope, timetable, logistics
  • Pilot tests of primers, PCR amplification
  • Assemble pipeline of specimens to lab
slide31

DNA from identified voucher

Create BARCODE reference record

Refine taxonomy of group

ID unknowns

DNA from unidentified immature specimen

Create BARCODE reference records

Associate immatures with names

DNA from identified adult voucher

Repository of provisional vouchers

ID unknowns

Add names to vouchered immatures

Refine taxonomy of group