The DNA Barcode of Life
What is a DNA Barcode?
• A fingerprint for identification
• A short, easily and universally amplifiable,
and reasonably variable piece of DNA
• Current barcode markers:
– Animals: 650 bp of the CO1 gene
– Fungi: nuclear ITS
– Plants: not decided
What is the point?
• Method of identification, particularly for nonexperts
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Import/export and pest control
Fisheries management
Water and habitat quality assessment
Partial or fragmentary sample analysis
Associating different life stages
• Biodiversity Exploration
– Discovery of sibling species
– Quick assessment of local genetic diversity
– “DNA assisted alpha taxonomy”
What constitutes a DNA Barcode?
• Sequence is from a expertly-identified, vouchered
specimen
• Voucher meta-information required: GPS
coordinates, photographs (in situ, in some cases),
collector and identifier data
• DNA sequence is high quality (minimum length,
minimum coverage, minimum “quality scores”
• Raw data (chromatograms) publicly available
Where does the Data Go?
BOLD
http://barcoding.life.org
Consortium for the Barcode of
Life (CBoL)
Univ. Guelph
(Hebert’s Lab)
Taiwan
Australia
?
SI
Multi-institutional:
DNA Working Group, Plant Working Group, Database Working
Group, Analysis Working GroupAncient/Formalin Working Group
Leading Labs:
Protocols, equipment loans, laboratory space, training
Current Products:
BOLD, BioCorder Field Management Application, LIMS, TaxTube
Collecting
Methods
Specimen
Handling
Suction
sponges
flatworms
Electroshock
Protocols
Rubble
Brushing
jellies
Malaise Trap
worms
Glass fiber
Plankton
Tows
Beating
Baited
Traps
TaxTube
Sand
Sieving
organic
DNA Extraction
Primers
& PCR
Metadata
& LIMS
Permits
ferns
portable
Kits
QuickTime™ and a
TIFF (LZW) decompressor
are needed to see this picture.
crabs
snails
tunicates
Extraction Specimen
fishes
lizards
Controversies Swirling Around
DNA Barcoding - 2 causes
• Cause 1: Thoughtless and ill-chosen
words, arrogance, over-sell
– “Will replace taxonomists”
– “Species named based on levels of
sequence divergence”
– “Phylogenetic relationships discovered”
– “Will uncover the meaning of life and
everything”
Controversies - Cause 2
• Potential for failure of identification, or
mis-identification, etc.
– Population and evolutionary history
– Practical methodological issues
Valid Concerns:
1. Evolutionary History
• Hybridization (plastid genomes)
• Pseudogenes
• Heteroplasmy or multiple copies (nuclear
markers)
• Lineage sorting, recent speciation
• Slow rates of sequence divergence
Valid Concerns:
2. Practical considerations
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Lack of universality
Co-amplification
Incomplete sampling
Lack of taxonomic experts
DNA Barcoding at the Labs of Analytical
Biology
(L.A.B.)
National Museum of Natural History
My Barcoding Philosophy
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1.
2.
I’m not “discovering” species, not making trees
Collaboration with taxonomic experts
Train students, interns, other researchers
Assist colleagues with lab setup, protocol
development, etc.
3. Create a “lending library” of high quality, wellvouchered DNAs
L.A.B. Projects:
1. Saving the world
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Bird Strike Identification (w/ USAF, FAA)
Economically Important Plants of the World (ofW)
Tephritid fruit flies ofW
Mosquitoes ofW; mosquitoes of Korea (w/ US Army)
Stream monitoring through aquatic insect larvae (w/
EPA)
• Just what is that fish fillet? (w/ USFW, USDA, FDA)
• Wasp parasites of drosophilid fruit fles
• Invasive Tunicates and Bryozoans (w/ SERC)
Traditional Species Identification:
Size, shape, color, feathers, etc.
easy
harder
impossible?
L.A.B. Projects:
2. Exploring Biodiversity
• Association of larval and adult fish - Caribbean;
spawning patterns and chronology
• Frogs of Central America - pre and post chytrid fungal
invasion
• Plants of Panama
• Tunicates of the Mediterranean and Red Sea
• All Bocas Barcoding Alliance (ABBA)
• Ophiurids of the Antarctic
• Deep-sea isopods
• Gastropods of Vanuatu
• Biocode Moorea
Identification of Larval Caribbean
Fishes:
Association of adult with larva
Carrie Bow Cay, Belize
Association of larval photographs and DNA “barcodes”
with identified and barcoded adults
EASY
DIFFICULT
Identification of Larval Caribbean Fishes:
Association of adults with larva
All Bocas Barcode Alliance (ABBA)
Sponges
July 2006
Octocorals
July 2007
Tunicates
August 2006
2008
•Algae (also 2007)
•Shrimp
Hydroids
August 2006
Nudibranchs
August 2006
•Nematodes
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A South Pacific Coral Reef:
BioCode Moorea
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Barcode of Life
• Valuable Resource
– Loss of taxonomic expertise
– Need for identification, practical and exploratory
– Rapid survey methods valuable
• Requirements
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Pitfalls acknowledged, explored, tested
Collaboration
Good curation
Public availability
Additional molecular markers a no-brainer.