Overview of DNA Barcoding and the Barcode of Life Initiative

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Overview of DNA Barcoding and the Barcode of
Life Initiative

• Scott E. Miller, Chair, CBOL Executive Committee
• National Museum of Natural History
• Smithsonian Institution
• MillerS_at_si.edu http//www.barcoding.si.edu

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Poor representation of systematics infrastructure
in Africa
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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

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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)

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

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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

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Species Identification Matters

• 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

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Uses of DNA Barcodes

• Research tool for assigning specimens to known
  species, including
• Life history stages, damaged specimens, gut
  contents, droppings

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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

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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

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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

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Digitizing Taxonomic Literature

• CBOLs 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

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The Vision Enabling research, product
development, and dissemination

• Ideally, all data should be accessible
• From any location
• In formats appropriate to users
• With a single query for each data type
• Using simple links
• Interoperable across data sets
• digitally

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Species web pages
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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?

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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