Download Taxonomic Value Chain (in rough sequence)

CBOL, DNA Barcoding and
Long-Term Ecological
Studies
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
“The GO network aims to
mainstream ecogenomic data into
next-generation Earth Observing
Systems, and improve and validate
models – at the local and global
levels – to better understand and
manage climate change and
ecosystem services.”
A sample should be more
than a sample
Long-term observation/monitoring
Understand long-term processes
Measure responses to forcing
functions:
–Climatic shifts
–Rare events (fire, flooding, drought)
–Land use changes
–Introductions, invasives, pathogens
–Experimental manipulation
Founding Philosophy
Environmental change is inevitable
Select a sentinel site (criteria vary)
Establish a longitudinal baseline
Wait for gradual shifts or rare events
[Or conduct perturbation experiments]
Document outcomes, impacts,
underlying processes on varied levels
Harvard Forest Long-Term Ecological Research Site
Smithsonian Environmental Research Center, Edgewater, MD
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•
•
•
•
What are (traditional)
Observatories?
Secure sites for long-term projects
Heavily instrumented
Environmental datastreams
Rarely have biorepositories for
voucher specimens
[Data standards for comparative
research]
Where to site Observatories?
Approaches to site selection and sampling:
– ATBIs for deep analysis of local richness
(repeated at sentinel sites?)
– Site-based long-term
ecological/ecosystem monitoring at
edges of habitat domains
– Virtual network: Compilations of projects
to document range/physiology shifts
– Bioblitzes as compromise
Why create Genome
Observatories (GOs)?
Genomic level closer to biological
responses (physiology, pop. variation)
Weaknesses of taxonomic names:
instability, non-standard protocols, string
data, cost and delay in data acquisition
Strengths of genetic data: standard
protocols; digital data; speed of data
acquisition; multiple uses: taxonomy,
phylogenetics, function, applications
GOs: How and Where?
Add to existing networks? (LTER,
NEON)?
Or
Should GOs be more mobile, work faster,
conduct shallower repeatable sampling?
Barcoding’s Contribution (1)
Taxonomy by non-taxonomists
Hidden splits
Difficult groups as MOTUs
Degraded, fragmental samples
Biotic lists from mixtures
Diet reconstruction from feces, gut
contents
Barcoding and NEON
Sentinel sites
Barcoding program with vouchers for:
– Mosquitoes
– Ground beetles
Prototype effort aims to:
– Evaluate barcoding methods
– Establish the DNA barcode library
– Develop workflow
Longer-term: Track species richness?
Biocode Inventory Progress
Fungi
Plants
unique species
Terrestrial Inverts
DNA barcoded
Specimens
Algae
Marine Invertebrates
Marine Verts
1
10
100
1000
10000
100000
June 2011
Arctic Canada Barcode ATBI
Michelle Van der Bank, Univ. of Johannesburg
Accepting Toyotas for South African Barcoding Blitzes
Barcodes in Ecology
Vouchers as communities of species,
samples of foodchains, not single taxon
Pathogens and bloodmeals in a mosquito
Pollen species on bees
Specialists versus generalists in:
– Insectivorous bats
– Phytophagous insects
Top herbivores and their impact on standing
diversity
Barcoding’s Contribution (2)
Data standard for large scale
– Standardized, calibrated unit of
similarity/variation
– Vouchering of specimens
– Traceability to
Vouchers in repositories
Raw sequence data in trace files
– Early data release for distributed data curation
New Standards Needed
Not just georeferenced
– Ecoreferenced – place in habitat, surrounding
organisms
– Bioreferenced – place in organism
Ecto/endoparasite?
Taken from what organ system?
Metadata on preservation methods used
Metadata on handling/sorting of mixtures
BARCODE Records in INSDC
Specimen
Metadata
Georeference
Habitat
Character sets
Images
Behavior
Other genes
Voucher
Specimen
Barcode
Sequence
Trace files
Literature
citation
Primers
Species
Name
Indices
- Catalogue of Life
- GBIF/ECAT
Nomenclators
- Zoo Record
- IPNI
- NameBank
Publication links
- New species
Record in
BOLD
Databases
- Provisional sp.
Voucher specimen
ID
Species ID
Identified by
Traditional
Taxonomy
GSC Minimum
Standards
(MI*)
XXX
XXX
XXX
XXX
X
X
XXX
XXX
DNA sequence
XXX
Gene region
Geographic origin
(country, ocean)
Latitude/Longitude
Collection date,
collector name
Trace files
Primer information
Traditional
GenBank
XXX
X
XXX
XXX
XXX
XXX
XXX
X
XX
XX
New Traceability Needed
Multiple proliferating generations of
offsprings:
– Tissue subsamples
DNA extracts
– PCR amplicons
Transfer of offsprings to new repositories
Retaining provenance data, ownership
documentation, MTA, restrictions on re-use
Synchronizing updates via BiSciCol
Compliance with Standard (1)
1.37 million records in BOLD
514,390 BARCODE records in INSDC
395,774 have ordinal name plus Barcode
Index Number for taxonomic ID
– Rapid data release versus time for annotation
– Exposure to data theft, risk of misidentification
– Added value of Linnean name
– Incidence of misidentifications in GenBank
– Danger of circular reasoning
Rod Page’s ‘Dark Taxa’
R. Page, iPhylo blogspot, 12 April 2011
Darwin Core Triplet
Structured Link to Vouchers
Institutional
Acronym
NHM
personal
:
:
:
Collection
Code
LEP
:
:
Catalog
ID
123456
DHJanzen : SRNP12345
CBOL/GBIF/NCBI
Registry of Biorepositories
www.biorepositories.org
Compliance with Standard (2)
514,390 BARCODE records in INSDC
– Traces, primers, length, country, and presence
of voucherID checked by GenBank
99.9% have entry for /specimen_voucher
13,151 have formatted voucher from 38
institutions
– 20 confirmed in biorepositories
– 11 unconfirmed
– 7 unlisted
Virtual Repository for the
Tree of Life (VRTL)
Exploratory workshop at Smithsonian
National Museum Natural History, Oct 2011
23 participants, 11 institutions, 9 countries
Representing major cryo-collections
Advanced facilities like AMNH
Integrated network: Germany DNA Bank
Vision for virtual global resource for sample
and data access
Potential Impact
Improved practices and policies within
instiutions;
Code of conduct leads to international
access agreements
Integrated distribtion maps enables gap
analysis, more cost-effective collecting
Virtual repository’s scale and data sharing
requires