CBOL, DNA Barcoding and Long-Term Ecological

Studies

David E. Schindel, Executive SecretaryNational Museum of Natural History

Smithsonian InstitutionSchindelD@si.edu;

http://www.barcoding.si.edu202/633-0812; 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

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?

Marine Verts

Marine Invertebrates

Algae

Terrestrial Inverts

Plants

Fungi

10 100 1000 10000 100000

unique species

DNA barcoded

Specimens

Biocode Inventory Progress

June 2011

Arctic Canada Barcode ATBI

Michelle Van der Bank, Univ. of JohannesburgAccepting 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 NeededNot 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 Sequence

Voucher Specimen

Species Name

Specimen Metadata

Literature citation

BARCODE Records in INSDC

Indices - Catalogue of Life - GBIF/ECAT

Nomenclators - Zoo Record - IPNI - NameBank

Publication links - New species

GeoreferenceHabitat

Character setsImages

BehaviorOther genes

Trace files Primers

Databases - Provisional sp.

Record in BOLD

Traditional Taxonomy

GSC Minimum Standards

(MI*)

Traditional GenBank

Voucher specimen ID XXX XXXSpecies ID XXX X X

Identified by XXXDNA sequence XXX XXXGene region XXXGeographic origin (country, ocean) XXX XLatitude/Longitude XXX XXX

Collection date, collector name XXX XXX

Trace files XXX XXPrimer information X 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 TripletStructured Link to Vouchers

Institutional Acronym

Collection Code

Catalog ID

: :

NHM LEP 123456: :

personal 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