Download Schindel - EPA-RTP - 8 Apr 08

From DNA Barcoding to the
Encyclopedia of Life:
Initiatives in Biodiversity
Informatics
David E. Schindel, Executive Secretary
National Museum of Natural History
Smithsonian Institution
[email protected];
http://www.barcoding.si.edu
202/633-0812; fax 202/633-2938
Species Identification Matters
Environmental quality indicators
Managing for sustainable harvesting
Consumer protection, ensuring food quality
Endangered/protected species
Invasive species (e.g., in ballast water)
Basic research on evolution, ecology
Agricultural pests/beneficial species
Disease vectors/pathogens
Fidelity of cell lines/culture collections
EPA/RTP – 8 April 08
Encyclopedia of Life
Taxonomic revisions, biotic surveys
Published species descriptions
Public database records
Description/revision not yet
published
Data not yet released
Not yet described
Not yet in specimen catalog
Not yet examined
Not yet curated
Not yet collected
EPA/RTP – 8 April 08
Infrastructure of Taxonomy
Collections and databases of specimens
Seedbanks, culture/cell line collections
Compilations of taxonomic names
Floristic and faunistic surveys/inventories
Monographs, Taxonomic revisions
Data repositories (gene sequences,
characters, images, trees)
The (undigitized) Taxonomic Literature
EPA/RTP – 8 April 08
Biodiversity Informatics:
Fragmented, Unconnected
Specimens
Journal
Publications
Species
Names
EPA/RTP – 8 April 08
Data providers:
DNA data: Barcoding
Specimens: Specify, KE-EMu, ARCTOS
Publications: Biodiversity Heritage Library
Tools and Value-adders:
Improving georeference data: BioGeomancer
Collecting, preparing data: EDIT ScratchPads
Building consensus taxonomies: CATE
Aggregators
Reviewed lists of taxonomic names: ITIS, Species2000
Assembling occurrence reports: OBIS
One-stop access to distributed data: GBIF
EOL – Knowledge space
EPA/RTP – 8 April 08
Biodiversity Heritage Library
www.biodiversitylibrary.org
Scanning and OCR converting the out-ofcopyright taxonomic literature
Now Online: 7,660 volumes; 2,942,044 pages
American Museum of Natural History (New
York)
Field Museum (Chicago)
Natural History Museum (London)
Smithsonian Institution (Washington)
Missouri Botanical Garden (St. Louis)
New York Botanical Garden (New York)
Royal Botanic Garden, Kew
Botany Libraries, Harvard University
Ernst Mayr Library of the Museum of
Comparative Zoology, Harvard University
Marine Biological Laboratory / Woods Hole
Oceanographic Institution
James Dwight Dana
Zoophytes. Atlas, 1849
EPA/RTP – 8 April 08
Growth of Biodiversity Databases
Voucher
Specimen
Biodiversity
Heritage
Library
Journal
Publication
Museum
databases of
associated data
Species
Name
Authority files
of taxonomic
names
EPA/RTP – 8 April 08
What?
Where?
When?
Distributed
Database
serving data
through
nodes and
partners
Census of Marine Life (CoML)
and the Ocean Biogeographic
Information System (OBIS)
Voucher
Specimen
Museum
databases of
associated data
Databases of species
occurrences and
distribution
Journal
Publication
Species
Name
Authority files
of taxonomic
names
EPA/RTP – 8 April 08
EPA/RTP – 8 April 08
Global Biodiversity Information
Facility (GBIF)
Voucher
Specimen
Museum
databases of
associated data
Databases of species
occurrences and
distribution
Journal
Publication
Species
Name
Authority files
of taxonomic
names
EPA/RTP – 8 April 08
www.eol.org
On-line resource—plants,
animals, microorganisms
Web pages for all 1.8 million
known species
Plus millions more yet to be
described
Common format
Customizable by user
Freely available
Accessible from a common portal
Never completed
EPA/RTP – 8 April 08
Components of the
Encyclopedia of Life (EOL)
Each site consists of several components
– Species page for the general public
Draft pages assembled via mashup technology
Drafts authenticated by experts (“curators”) using
controlled wikis
Information submitted by public
– Anyone can comment on the information and or suggest
things to add
– Curators will examine these suggestions and may move
some of the information to the protected part
EPA/RTP – 8 April 08
EPA/RTP – 8 April 08
DNA Barcodes:
A Key Variable for Biodiversity
Informatics
Voucher
Specimen
Museum
databases of
associated data
Databases of species
occurrences and
distribution (OBIS)
Barcode
Sequence
Journal
Publication
Species
Name
Authority files
of taxonomic
names
EPA/RTP – 8 April 08
A DNA barcode is a
short gene sequence
taken from
standardized portions
of the genome,
used to identify species
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.”
EPA/RTP – 8 April 08
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
EPA/RTP – 8 April 08
Projects, Networks, Organizations
• Promote barcoding
as a global standard
• Build participation
• Working Groups
• BARCODE standard
• International
Conferences
• Increase production
of public BARCODE
records
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
EPA/RTP – 8 April 08
Associating Life Stages, Processed Parts,
Dimorphic Genders
The Barcoding Pipeline
Building the reference library:
– Well-identified specimen
– Tissue subsample
– DNA extraction, PCR amplification
– DNA sequencing
– Data submission to GenBank
Using the reference library:
– Unidentified specimen
– Tissue, DNA, sequencing
– Comparison with reference sequences
EPA/RTP – 8 April 08
Producing Barcode Data: 2008
Faster, more portable: Hundreds of samples per hour
Integrated DNA microchips
Table-top microfluidic systems
EPA/RTP – 8 April 08
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 nonspecialists
EPA/RTP – 8 April 08
Consortium for the
Barcode of Life (CBOL)
First barcoding publications in 2002
Cold Spring Harbor planning workshops in 2003
Sloan Foundation 2-year grant for $800K May 2004
Secretariat opens at Smithsonian, September 2004
First international conference February 2005
$1.55 million 2-year renewal in April 2006
Now an international affiliation of:
– Natural history museums, biodiversity organizations
– Users: e.g., government agencies
– Private sector biotech companies, database providers
EPA/RTP – 8 April 08
CBOL Member Organizations: 2007
• 150+ Member organizations, 45 countries
• 30+ Member organizations from 20+ developing countries
EPA/RTP – 8 April 08
CBOL’s Mission:
Promoting DNA Barcoding
as a Global Standard
1.
2.
3.
4.
5.
6.
7.
Developing/raising community standards
Barcode projects to populate database
Global participation and coordination
Adoption by regulatory agencies
Acceptance by taxonomic community
Excitement in other fields of science
Product development by private companies
EPA/RTP – 8 April 08
BARCODE Records in INSDC
Specimen
Metadata
Georeference
Habitat
Character sets
Images
Behavior
Other genes
Other
Databases
Phylogenetic
Pop’n Genetics
Ecological
Voucher
Specimen
Barcode
Sequence
Trace files
Primers
Literature
(link to content or
citation)
Species
Name
Indices
- Catalogue of Life
- GBIF/ECAT
Nomenclators
- Zoo Record
- IPNI
- NameBank
Publication links
- New species
Databases
- Provisional sp.
EPA/RTP – 8 April 08
Structured Link to Vouchers
Institutional
Acronym
:
Collection
Code
:
Catalog
ID
EPA/RTP – 8 April 08
Link from GenBank to Museums
EPA/RTP – 8 April 08
CBOL’s Mission:
Promoting DNA Barcoding
as a Global Standard
1.
2.
3.
4.
5.
6.
7.
Developing/raising community standards
Barcode projects to populate database
Global participation and coordination
Adoption by regulatory agencies
Acceptance by taxonomic community
Excitement in other fields of science
Product development by private companies
EPA/RTP – 8 April 08
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, lake fish, stem-borers
EPA/RTP – 8 April 08
CBOL’s Mission:
Promoting DNA Barcoding
as a Global Standard
1.
2.
3.
4.
5.
6.
7.
Developing/raising community standards
Barcode projects to populate database
Global participation and coordination
Adoption by regulatory agencies
Acceptance by taxonomic community
Excitement in other fields of science
Product development by private companies
EPA/RTP – 8 April 08
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
EPA/RTP – 8 April 08
CBOL’s Mission:
Promoting DNA Barcoding
as a Global Standard
1.
2.
3.
4.
5.
6.
7.
Developing/raising community standards
Barcode projects to populate database
Global participation and coordination
Adoption by regulatory agencies
Acceptance by taxonomic community
Excitement in other fields of science
Product development by private companies
EPA/RTP – 8 April 08
Adoption by Regulators
Environmental Protection Agency
– $250K pilot test, water quality bioassessment
Food and Drug Administration
– Reference barcodes for commercial fish
NOAA/NMFS
– $100K for Gulf of Maine pilot project
– FISH-BOL workshop with agencies, Taipei, Sept 2007
Federal Aviation Administration – $500K for birds
FAO International Plant Protection Commission
– Proposal for Diagnostic Protocols for fruit flies
CITES, National Agencies, Conservation NGOs
– International Steering Committee, identifying pilot projects
EPA/RTP – 8 April 08
US Wadeable Streams Assessment
• National assessment of the condition of wadeable streams
• 10 different taxonomic ID laboratories
• 749 stream macroinvertebrate samples (sites)
• All organisms identified to genus only
• 10% random re-identification by independent taxonomist
• Data quality objective – 85% repeatability
Credible environmental
decision-making
depends on objectivity
and repeatability of
taxonomic results
EPA/RTP – 8 April 08
EPA Advanced Monitoring Initiative
Mark Bagley, USEPA/ORD, Cincinnati
Project Goals
•
•
•
Develop a DNA barcode library for important aquatic
indicator species (EPT)
Ephemeroptera (Mayflies)
Plecoptera (Stoneflies)
Trichoptera (Caddisflies)
Compare DNA barcodes to traditional bioassessments for
EPT taxa from Maryland stream survey
Cost, Speed, Objectivity, Accuracy, Precision
How important is increased taxonomic precision?
Determine how to efficiently incorporate DNA barcodes into
a state bioassessment program