DNA Barcoding and the Information Infrastructure of Taxonomy

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DNA Barcoding and the Information Infrastructure
of Taxonomy

• David E. Schindel, Executive Secretary
• Consortium for the Barcode of Life
• National Museum of Natural History
• Smithsonian Institution
• Schindeld_at_si.edu http//www.barcoding.si.edu
• 202/633-0812 fax [phone]

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Biodiversity InformaticsFragmented, Unconnected
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Growth of Biodiversity Databases
Museum databases of associated data
Authority files of taxonomic names
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What? Where? When?
Distributed Database serving data through nodes
and partners
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Census of Marine Life (CoML)and the Ocean
Biogeographic Information System (OBIS)
Museum databases of associated data
Databases of species occurrences and distribution
Authority files of taxonomic names
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DNA BarcodesA Key Variable for Biodiversity
Informatics
Museum databases of associated data
Databases of species occurrences and distribution
(OBIS)
Authority files of taxonomic names
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• Background on
• DNA Barcoding
• The DNA Barcode Initiative
• Consortium for the Barcode of Life (CBOL)
• Current and planned activities
• Data standards for barcode data
• Impact on the information infrastructure of
  taxonomy

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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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Characteristics of Barcode Regions

• 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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When species have disjunct ranges of variation,
barcodes are an efficient diagnostic tool
From Meyer and Paulay, PLoS Biology, 2005
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The Mitochondrial Genome

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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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Uses of DNA Barcodes

• Applied tool for identifying regulated species
• Disease vectors, agricultural pests, invasives
• Environmental indicators, protected species
• Using minimal samples, damaged specimens, gut
  contents, droppings
• Research tool for improving species-level
  taxonomy
• Associating all life history stages, genders
• Testing species boundaries, finding new variants
• Triage tool for flagging potential new species
• Undescribed and cryptic species

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Uses of DNA Barcodes

• Applied tool for identifying regulated species
• Disease vectors, agricultural pests, invasives
• Environmental indicators, protected species
• Using minimal samples, damaged specimens, gut
  contents, droppings
• Research tool for improving species-level
  taxonomy
• Associating all life history stages, genders
• Testing species boundaries, finding new variants
• Triage tool for flagging potential new species
• Undescribed and cryptic species

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Associating Life Stages, Processed Parts,
Dimorphic Genders
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Steatogenini until the early 90s
Hypopygus lepturus Hoedeman 1962
Steatogenys elegans Steatogenys duidae
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Color patterns in Hypopygus
Nijssen Isbrüker 1972
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Steatogenini during the 90s
Hypopygus lepturus Hoedeman 1962
Hypopygus neblinae Mago-Leccia 1994
Steatogenys
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Steatogenini during the 90s / today
Hypopygus lepturus Hoedeman 1962
Hypopygus neblinae Mago-Leccia 1994
Stegostenopos Triques 1997
Steatogenys
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R. Bernhard, 2004
8a
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RAG 1 MP/ML/Dist
Stegostenopus
Hypopygus neblinae
A
H. lepturus
C
D
Steatogenys
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12S16S Strict of ML/MP/Dist
Stegostenopus
H. neblinae
A
C
H. lepturus
D
E
Steatogenys
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D-loop MP/ML/Dist
H. lepturus
D
E
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COI - BARCODE MP
H. lepturus
Eigenmannia sp.
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Uses of DNA Barcodes

• Applied tool for identifying regulated species
• Disease vectors, agricultural pests, invasives
• Environmental indicators, protected species
• Using minimal samples, damaged specimens, gut
  contents, droppings
• Research tool for improving species-level
  taxonomy
• Associating all life history stages, genders
• Testing species boundaries, finding new variants
• Triage tool for flagging potential new species
• Undescribed and cryptic species

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Using DNA Barcodes

• Establish reference library of barcodes from
  identified voucher specimens
• If necessary, revise species limits
• Then
• Identify unknowns by searching against reference
  sequences
• Look for matches (mismatches) against library on
  a chip
• Before long Analyze relative abundance in
  multi-species samples

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Analytical chain

• Databasing
• Labeling
• Imaging
• Tissue sampling
• DNA extraction
• PCR
• PCR check
• Sequencing reaction
• Sequencing cleanup
• Sequencing
• Trace editing submission

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Methods
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Barcode of Life Database
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Analytical chain

• Databasing
• Labeling
• Imaging
• Tissue sampling
• DNA extraction
• PCR
• PCR check
• Sequencing reaction
• Sequencing cleanup
• Sequencing
• Trace editing submission

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Current Norm High throughput
Large capacity PCR and sequencing reactions
ABI 3100 capillary automated sequencer
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Cost of Reagents and Disposables

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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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Producing Barcode Data 2010?Barcode data
anywhere, instantly

• Data in seconds to minutes
• Pennies per sample
• Link to reference database
• A taxonomic GPS
• Usable by non-specialists

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Methods
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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
• Barcoding can help to create a 21st century
  research environment for taxonomy

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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
• BUTBarcoding can help to create a 21st century
  research environment for taxonomy

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Consortium for the Barcode of Life (CBOL)

• First barcoding publications in 2002
• Cold Spring Harbor planning workshops in 2003
• Sloan Foundation grant, launch in May 2004
• Secretariat opens at Smithsonian, September 2004
• First international conference February 2005
• Now an international affiliation of
• 120 Members Orgs, 40 countries, 6 continents
• Natural history museums, biodiversity
  organizations
• Users e.g., government agencies
• Private sector biotech companies, database
  providers

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Consortium for the Barcode of Life
(CBOL)Smithsonian Institution/Sloan
Foundation125 Member Organizations, 40 Countries
as of June 2006
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Outreach Activities

• Regional meetings in
• Cape Town, South Africa, 7-8 April 2006, SANBI
• Nairobi, Kenya, 18-19 October 2006
• Brazil, February 2007
• Taiwan, September 2007
• Second International Barcode Conference
• Taiwan, September 2007
• Support from CBOL, host governments and
  international development agencies

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Goals of Regional Meetings

• Raise awareness
• Explore potential applications in the region
• Assess greatest needs and opportunities in the
  region
• Identify highest priorities, construct national
  and regional action plans
• Start intra-regional networks and
  intercontinental partnerships

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CBOL-Initiated Projects

• Fish Barcode of Life (FISH-BOL)
• 30,000 marine/freshwater species by 2010
• All Birds Barcoding Initiative (ABBI)
• 10,000 species by 2010
• Tephritid fruit flies
• 2,000 pest/beneficial species and relatives by
  2008
• Mosquitoes
• 3,300 species by 2008
• African Scale Insects
• Endangered vertebrates (bushmeat)

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Projects initiated by others

• CMarZ Marine habitat, multiple taxa
• All-Leps Multiple regions/habitats, single taxon
• BioCode, Moorea Single location, multiple
  habitats, multiple taxa

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CBOLs Working Groups

• Database Designing/constructing the Barcode
  Section of GenBank
• DNA Protocols for formalin-fixed and old museum
  specimens Producing LIMS for dissemination
• Data Analysis Beyond phenetic methods
  population genetics perspective
• Plants Identify gene region(s) for barcoding

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Barcode Data Standards

• Consensus results of Front Royal meeting
• GBIF ? ITIS ? GRIN
• NBII ? Species2000 ? IPNI
• ICZN ? ZooRecord ? OBIS
• Structured link to voucher specimen
• Species name selected from authority
• Online access to metadata
• Trace files and quality scores
• Minimum sequence length

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BARCODE Records in INSDC
Voucher Specimen
Species Name
Specimen Metadata
GeoreferenceHabitatCharacter setsImagesBehavio
rOther genes
Indices - Catalog of Life - GBIF/ECAT Nomenclato
rs - Zoo Record - IPNI - NameBank Publication
links - New species Databases - Provisional sp.
Barcode Sequence
Trace files
Primers
Other Databases
Literature(link to content or citation)
PhylogeneticPopn GeneticsEcological
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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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CBOLs Working Groups

• Database Designing/constructing the Barcode
  Section of GenBank
• DNA Protocols for formalin-fixed and old museum
  specimens Producing LIMS for dissemination
• Data Analysis Beyond phenetic methods
  population genetics perspective
• Plants Identify gene region(s) for barcoding

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CBOL Formalin Workshop

• May 8-9 workshop in Washington, National Research
  Council
• Chemists, biochemists, biophysicists, biomedical
  researchers
• Literature survey of DNA recovery protocols from
  formalin-fixed specimens
• Create a new research agenda
• Workshop report in July
• Follow-on with SPNHC as major partner

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The Barcode Assembly Line 2008Opening the
museum treasure-trove
Freshly collected specimens
Formalin-fixed specimens
Older museum specimens
Young museum specimens
Frozen tissue
DNA Barcode Data
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CBOLs Working Groups

• Database Designing/constructing the Barcode
  Section of GenBank
• DNA Protocols for formalin-fixed and old museum
  specimens Producing LIMS for dissemination
• Data Analysis Beyond phenetic methods
  population genetics perspective
• Plants Identify gene region(s) for barcoding

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Some Technical Challenges

• Using character-based barcodes
• Optimizing sample size
• Specimen identification versus species
  discovery
• Measuring confidence
• Shrinking the barcode

Workshop, July 2006, NMNH Paris Rutgers/DIMACS,
European Science Fn.
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CBOLs Working Groups

• Database Designing/constructing the Barcode
  Section of GenBank
• DNA Protocols for formalin-fixed and old museum
  specimens Producing LIMS for dissemination
• Data Analysis Beyond phenetic methods
  population genetics perspective
• Plants Identify gene region(s) for barcoding
  by December 2006

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Progress toward Plant Barcode

• Kress 2005 proposal for ITS and trnh-psbA
• Kew Garden receives Sloan/Moore Foundation
  support
• Phase 1 screens 100 genes across 50 sibling
  species pairs
• Phase 2 tests of matK, rpcoC1, rpoB, ndhJ, and
  accD
• Canadian proposal for rbcL
• CBOL protocols for approving barcode regions

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Wider Impacts of Barcoding

• Catalyzing interoperability of databases
• Barcode data standards link sequences, specimens,
  species names and publications
• Improving the information infrastructure
• Digital library initiative in taxonomy
• Renewing the mission of museums
• DNA recovery from formalin-fixed specimens
• Promoting the growth of DNA banks
• Expanding analytical toolbox for taxonomy

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Taipei Barcode Conference

• Academia Sinica, week of 17 September
• Second International Barcode Conference
• Regional Barcode Meeting for South/SE Asia
• CBOL Working Groups
• FISH-BOL/Marine Fisheries workshop
• Short course on biodiversity informatics