DNA Barcodes

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DNA Barcodes and Biodiversity
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DNA Barcoding Rationale
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Conventional Genomics - All Genes, One Species
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Gaining Barcode Closure for Animals
Horizontal Genomics - One Gene, All Species
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Horizontal Genomics for Biodiversity
Identifying Life conservation, management,
bioprospecting Discovering Life new species,
species ages, geographic patterns Evolutionary
Rules rate variation, shifts in nucleotide
usage, protein diversification
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Horizontal Genomics for Biodiversity - DNA
Barcoding
DNA Barcode short standardized sequence enabling
species discrimination in a large block of life
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DNA Barcoding Prospects
Barcoding Products and Life
415 1 Billion
1011 100 Billion
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DNA Barcoding Prospects
Prospects for Diagnosing Species with DNA Barcodes
Average species lifespan in fossil record 4
million years Rate of sequence change 1 per
million years Amount of sequence change 40
changes per 1000 bp
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DNA Barcoding in Animals
Gaining Barcode Closure for Animals
An Internal ID System for All Animals
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DNA Barcoding in Animals
Barcode Target 648 bp of COI
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DNA Barcoding in Animals
The Analytical Chain From Specimen to Database
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Barcode of Life Database
Barcode of Life Database
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Its not science. - Rodman, June 2003 Too
bad it wont deliver. - Sperling, October
2003 DNA barcoding is wanting in rationale,
methodology and interpretation of results. -
Will and Rubinoff, June 2004 There is nothing
fundamentally new in barcoding, except scale and
proposed standardization. - Moritz Cicero,
September 2004
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This pioneering effort in DNA barcoding will set
in motion the single most significant project in
biology that I know today. - Janzen, July
2003 Fashionable DNA-barcoding methods are a
breakthrough for identification. - Wheeler,
Raven Wilson, January 2004 I believe that the
problem of species numbers will be solved by
taking small pieces of organisms and sticking
them in a hand-held machine which analyses their
DNA. - Lord May, April 2004 There is
little doubt that large-scale and standardized
sequencing, when integrated with existing
taxonomic practice, can contribute significantly
to the challenges of identifying individuals and
increasing the rate of discovering biological
diversity. - Moritz Cicero, September 2004
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Resolving Species Through DNA Barcoding
Humans and Our Relatives
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Resolving Species Through DNA Barcoding
COI Divergences () in Closely Related Animals
1.0
0.9
0.8
0.7
0.6
Proportion of Species Pairs
0.5
0.4
0.3
0.2
0.1
0
2
4
8
16
32
64
Sequence Divergence
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Resolving Species Through DNA Barcoding
Sensitivity Analysis on Large Phyla
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Resolving Species Through DNA Barcoding
Sensitivity Analysis
Rates of Evolution
G C (3rd position)
.00
.05
.10
.15
.20
.25
.30
1x
2x
3x
4x
5x
6x
7x
8x
9x
10x
Lepidoptera
Lepidoptera
Hymenoptera
Hymenoptera
Ephemeroptera
Ephemeroptera
.20
.25
.30
.35
.40
.45
.50
1x
2x
3x
4x
5x
Aves
Aves
Mammals
Mammals
Osteichthyes
Osteichthyes
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Resolving Species Through DNA Barcoding
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Resolving Species Through DNA Barcoding
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Resolving Species Through DNA Barcoding
Bird Identification Through DNA Barcodes
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Resolving Species Through DNA Barcoding
Bird Identification Through DNA Barcodes
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Resolving Species Through DNA Barcoding
Birds of North America
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Resolving Species Through DNA Barcoding
Decapod Identification Through DNA Barcodes
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Resolving Species Through DNA Barcoding
Tropical Biodiversity
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Resolving Species Through DNA Barcoding
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Resolving Species Through DNA Barcoding
COI Divergences ()
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Resolving Species Through DNA Barcoding
Barcoding Animals (10 million species)

• Effective in varied geographic settings
• Effective in varied taxonomic groups
• gt99.99 resolution

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Resolving Species Through DNA Barcoding
Barcode Repository (10 000 data pits)
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Resolving Species Through DNA Barcoding
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Resolving Species Through DNA Barcoding
COI Divergence in Eukaryotes
Fungi
Eubacteria
Animalia
Kinetoplastida
Chlorophyceae
Land Plants
Euglenophyta
Apicomplexa
Chloroarachniophyta
Dinoflagellata
Xanthophyceae
Prymnesiophyta
Rhodophyta
Eustigmatophyceae
Bacillarioophyceae
Cryptophyta
Chlorophyceae
Phaeophyceae
Ciliata
20 aa
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Resolving Species Through DNA Barcoding
Algae Identification Through DNA Barcodes
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Barcodes Developing a ReferenceLibrary for
Known Species

• Master key
• ID all life stages
• IDs cheap fast
• Residual taxonomic uncertainty low

Alpheus heterochelis
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DNA Barcodes Can We Use Them to Recognize New
Species?
There is a close correspondence between species
recognized by sequence thresholds and those
revealed by traditional taxonomic approaches.
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Automating Species Discovery Moths
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Barcodes A Lead Role inSpecies Discovery?

• Sequence thresholds reveal gt95 of species
• Barcode counts counts throughconventional
  taxonomy
• Rapid draft counts through barcodes
• Total evidence is the goal

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DNA Barcoding Toward Global Acivation
Taxonomy, DNA, and the Barcode of Life
Imagine a world in which any person, anywhere, at
any time can identify any species at little or no
cost. That world is techno- logically upon us.
This report addresses the formative stages of an
Initiative to bring this to society sooner rather
than later.
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DNA Barcoding Towards Global Activation
First International Barcode of Life Conference
Feb 5-8, 2005
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DNA Barcoding Toward Global Activaion

• CBOL launched April, 2004.
• Active memberships in 25 countries (and
  growing).
• Projects to barcode all birds and all fishes on
  Earth.
• Estimated cost to barcode all animal life 1
  billion.

Guelph
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The Future of DNA Barcoding
Gaining Barcode Closure for Animals
Gaining Closure for All Animals
10 million species x 10 barcodes each 100
million barcodes
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The Future of DNA Barcoding
Barcoding A Field Guide for the Third Millenium
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• Global Bio-ID System
• Evolutionary Rules
• Conserving Life
• Bio-Management

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Acknowledgements
Laboratory
Database
Sujeevan Ratnasingham
Jeremy DeWaard
Rob Dooh
Nataly Ivanova
Pia Marquardt
Stephanie Kirk
Janet Topan
Funders
Angela Holliss
Gordon and Betty Moore Foundation
Collaborators
45 colleagues in
NSERC CFI OIT
8 nations
Canada Research Chairs Program
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