Transcript Taxonomic Value Chain (in rough sequence)

Overview of
DNA Barcoding and the
Barcode of Life Initiative
Scott E. Miller, Chair, CBOL Executive
Committee
National Museum of Natural History
Smithsonian Institution
[email protected]; http://www.barcoding.si.edu
Scott Miller – SANBI, 7 April 2006
Poor representation of systematics
infrastructure in Africa
Scott Miller – SANBI, 7 April 2006
Human resources
also thinly distributed
• Stuckenberg (1964): most systematics done
outside of Africa, but only 7% of world
entomologists working on Africa
• Gaston & May (1992): only 4% of ecologists & 7%
of systematists in Africa
• Surveys by CABI (1993), ICIPE (1996),
SAFRINET (1998) show same trends
Scott Miller – SANBI, 7 April 2006
Outreach to Africa
• South Africa and Kenya involved from
beginning of CBOL in May 2004
• Southern African regional workshop now
• Eastern and Western regional workshops
under discussion
• African involvement in global campaigns
(e.g., birds, fish, mosquitos, fruit flies)
Scott Miller – SANBI, 7 April 2006
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.”
Scott Miller – SANBI, 7 April 2006
A DNA barcode is a
short gene sequence
taken from
standardized portions
of the genome,
used to identify species
Scott Miller – SANBI, 7 April 2006
The Mitochondrial Genome
D-Loop
Small ribosomal RNA
Large
ribosomal RNA
Cyt b
ND1
ND6
ND5
L-strand
COI
COI
ND2
H-strand
ND4
COI
ND4L
ND3
COIII
COII
ATPase subunit 8
ATPase subunit 6
Scott Miller – SANBI, 7 April 2006
Uses of DNA Barcodes
Applied tool for identifying regulated species:
• Disease vectors, agricultural pests, invasives
• Environmental indicators, protected species
Research tool for assigning specimens to known
species, including:
• Life history stages, damaged specimens, gut
contents, droppings
“Triage” tool for flagging potential new species:
• Undescribed and cryptic species
Scott Miller – SANBI, 7 April 2006
Species Identification Matters
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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
Scott Miller – SANBI, 7 April 2006
Uses of DNA Barcodes
Research tool for assigning specimens to
known species, including:
• Life history stages, damaged specimens, gut
contents, droppings
Scott Miller – SANBI, 7 April 2006
Uses of DNA Barcodes
Applied tool for identifying regulated species:
• Disease vectors, agricultural pests, invasives
• Environmental indicators, protected species
Research tool for assigning specimens to
known species, including:
• Life history stages, damaged specimens, gut
contents, droppings
“Triage” tool for flagging potential new species:
• Undescribed and cryptic species
23% marine species in Pearl Harbor are alien or cryptogenic
Scott Miller – SANBI, 7 April 2006
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
• NEVERTHELESS, Barcoding is helping
to create a 21st century research
environment for taxonomy
Scott Miller – SANBI, 7 April 2006
Wider Impacts of Barcoding: 2008
• Catalyzing interoperability of databases
– Barcode data standards link sequences,
specimens, species names and publications
• Renewing the mission of museums
– DNA recovery from formalin-fixed specimens
– Promoting the growth of DNA banks
• Expanding analytical toolbox for taxonomy
• Improving the information infrastructure
– Digital library initiative in taxonomy
Scott Miller – SANBI, 7 April 2006
Digitizing Taxonomic Literature
• CBOL’s catalytic efforts:
– Library-Laboratory meeting in London on
electronic access to taxonomic literature
– Led to formation of Biodiversity Heritage
Library initiative
– Proactive steps with PubMed to add
taxonomic journals to online abstracts
– Aggressive negotiation with publishers of
barcoding papers
Scott Miller – SANBI, 7 April 2006
The Vision:
Enabling research, product
development,
and dissemination
Ideally, all data should be accessible:
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From any location
In formats appropriate to users
With a single query for each data type
Using simple links
Interoperable across data sets
… digitally
Scott Miller – SANBI, 7 April 2006
Species web pages
Scott Miller – SANBI, 7 April 2006
Collaborating with
International Initiatives
• Global Biodiversity Information Facility (GBIF)
• Global Taxonomy Initiative (GTI) of Convention on
Biological Diversity
• BioNet International
• Projects such as SABONET
• Digital library
• Genbank/EMBL/DDBJ
• Leveraging “north” and “south” funding?
Scott Miller – SANBI, 7 April 2006
Planned Outreach
• Regional meetings in:
– Cape Town, South Africa, 7-8 April 2006, SANBI
– Brazil, 2nd quarter 2006
– Southern Asia, mid-2007
– Nairobi, Kenya, October 2006
• Second International Barcode Conference
– Southeast Asia, February 2007
• Support from CBOL, host governments and
international development agencies
Scott Miller – SANBI, 7 April 2006