A1261864813WnZfE

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Potencials of DNA Barcoding in South America
19-20 March 2007
What is DNA Barcoding? And What is it Not?
Robert Hanner, PhD Database Working Group Chair,
CBOL Global Campaign Coordinator,
FISH-BOL Associate Director, Canadian Barcode of
Life Network Biodiversity Institute of Ontario,
University of Guelph, Canada
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If you needed to identify something
how would you do it?
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Consult the Literature?
March 15, 2007
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Or use a DNA Barcode?
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The Practice of Taxonomy
The Uses of Taxonomy
Socioeconomic Decisions
Taxonomists
Taxonomic Decision-Making
Distributions of Character Variation
Concerns/ Regulations
Characters
Specimens
Specimens
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Known speciesgt150,000
gt250,000 gt300,000
gt 30,000 flies, mosquitoes
flowering plants
beetles crabs,
lobsters
Why DNA-based identification?
Because There are many, many species
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And many species have a variety of life forms
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Identifying tiny bits and piecesBird hosts of
disease-carrying insects
MOLECULAR IDENTIFICATION OF BLOOD-MEAL SOURCES IN
CULISETA MELANURA AND CULISETA MORSITANS FROM AN
ENDEMIC FOCUS OF EASTERN EQUINE ENCEPHALITIS
VIRUS IN NEW YORK GOUDARZ MOLAEI, JOANNE
OLIVER, THEODORE G. ANDREADIS, PHILIP M.
ARMSTRONG, AND JOHN J. HOWARD The Connecticut
Agricultural Experiment Station, New Haven,
Connecticut Arthropod-Borne Disease Program, New
York State Department of Health Diagnostic
Laboratory, College of Veterinary Medicine,
Cornell University, Ithaca, New York
Arthropod-Borne Disease Program, New York State
Department of Health, Office of Public Health,
Syracuse, New York
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What is DNA barcoding? Distinguishing species
is the first step in understanding the living
world. Barcoding is a standardized approach to
identifying species by a short fragment of their
DNA.
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New tools for taxonomy
DNA Barcoding
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Barcoding Products and Life
415 1 Billion
1011 100 Billion
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Necessary Characteristics of a Target for DNA
Barcoding

• Low intraspecies variability
• Discontinuous variation between species
• Flanked by conserved regions
• Easy to amplify
• Long enough to work in all groups
• Short enough for single reads

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Combinatorial differences species ID tags
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Barcode Divergences and Species Boundaries
Within Species
None
Deep
Shallow
Shallow
Between Species
None
Deep
Shallow
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Barcode Divergences and Species Boundaries
Within Species
None
Deep
Shallow
Shallow
Between Species
None
Deep
Shallow
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Low Interspecific Divergences are rare
Cichlids
White-headed Gulls
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Barcoding All Eukaryotes
Fungi
Eubacteria
Animalia
Kinetoplastida
Chlorophyceae
Land Plants
Euglenophyta
Chloroarachniophyta
Apicomplexa
Dinoflagellata
Xanthophyceae
Rhodophyta
Prymnesiophyta
Eustigmatophyceae
Bacillarioophyceae
Cryptophyta
Chlorophyceae
Phaeophyceae
Ciliata
20 aa (COI)
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Barcoding Animals
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Helobdella triserialis Helobdella
papillornata Helobdella europaea Helobdella sp.
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Helobdella triserialis complex
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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 isnt 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.

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Microbes - 16S
Plants - RBCL
Animals - COI
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Vertical Genomics - All Genes, One Species
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Horizontal Genomics - One Read, All Species
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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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What is DNA barcoding? Horizontal genetic
transect What DNA barcoding is not?
Genomics -Genetic Prospecting -Biopiracy

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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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Producing Barcode Data 2008 Faster, more
portable Hundreds of samples per hour
Integrated DNA microchips
Table-top microfluidic systems
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The Future of DNA Barcoding
Microfabricated bioprocessor for integrated
nanoliter-scale Sanger DNA sequencing
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May 1954 Popular Mechanics
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A Field Guide for the Third Millennium?
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Barcodes Applied
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The Future of DNA Barcoding Environmental
Barcoding
Massively Parallel Pyrosequencing One reaction
120,000 sequence reads of 100-200 bp
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Acknowledgments

• Paul Hebert
• Mark Stockle
• David Schindel
• Mehrdad Hajibabaei
• Rob Dooh