CBOL, DNA Barcoding and Long-Term Ecological Studies

1. CBOL, DNA Barcoding and Long-Term Ecological Studies David E. Schindel, Executive Secretary National Museum of Natural History Smithsonian Institution SchindelD@si.edu; http://www.barcoding.si.edu 202/633-0812; fax 202/633-2938

2. “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.”

3. A sample should be more than a sample

4. 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

5. 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

6. Harvard Forest Long-Term Ecological Research Site

7. Smithsonian Environmental Research Center, Edgewater, MD

8. 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]

9. 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

10. 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

11. GOs: How and Where? • Add to existing networks? (LTER, NEON)? Or • Should GOs be more mobile, work faster, conduct shallower repeatable sampling?

12. 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

13. 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?

14. Biocode Inventory Progress June 2011

15. Arctic Canada Barcode ATBI

16. Michelle Van der Bank, Univ. of Johannesburg Accepting Toyotas for South African Barcoding Blitzes

17. 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

19. 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

20. 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

21. BARCODE Records in INSDC Specimen Metadata Voucher Specimen Species Name GeoreferenceHabitatCharacter setsImagesBehaviorOther genes Indices - Catalogue of Life - GBIF/ECAT Nomenclators - Zoo Record - IPNI - NameBank Publication links - New species Barcode Sequence Trace files Primers Literaturecitation Record in BOLD Databases - Provisional sp.

24. 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

25. 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

26. Rod Page’s ‘Dark Taxa’ R. Page, iPhyloblogspot, 12 April 2011

27. Darwin Core TripletStructured Link to Vouchers Collection Code : Catalog ID Institutional Acronym : : : NHM LEP 123456 : : personal DHJanzen SRNP12345

28. CBOL/GBIF/NCBI Registry of Biorepositories www.biorepositories.org

29. 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

30. 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

31. 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