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Overview of DNA Barcoding and the Barcode of Life Initiative

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DNA Barcoding and the Barcode of Life ... Undescribed and cryptic species 23% marine ... October 2006 Second International Barcode Conference Southeast Asia, ... – PowerPoint PPT presentation

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Title: Overview of DNA Barcoding and the Barcode of Life Initiative


1
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

2
Poor representation of systematics infrastructure
in Africa
3
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

4
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)

5
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.

6
A DNA barcode is a short gene sequence taken
from standardized portions of the genome, used
to identify species
7
The Mitochondrial Genome

8
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

9
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

10
Uses of DNA Barcodes
  • Research tool for assigning specimens to known
    species, including
  • Life history stages, damaged specimens, gut
    contents, droppings

11
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

12
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

13
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

14
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

15
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

16
Species web pages
17
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?

18
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
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