CBOL, DNA Barcoding and Long-Term Ecological Studies David E. Schindel, Executive Secretary National Museum of Natural History Smithsonian Institution / ; fax 202/

“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 Secure sites for long-term projects Heavily instrumented Heavily instrumented Environmental datastreams Environmental datastreams Rarely have biorepositories for voucher specimens Rarely have biorepositories for voucher specimens [Data standards for comparative research] [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 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 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 Georeference Habitat Character sets Images Behavior Other genes Trace filesPrimers Databases - Provisional sp. Record in BOLD

Traditional Taxonomy GSC Minimum Standards (MI*) Traditional GenBank Voucher specimen ID XXX Species ID XXXXX Identified by XXX DNA sequence XXX Gene region XXX Geographic origin (country, ocean) XXXX Latitude/Longitude XXX Collection date, collector name XXX Trace files XXXXX Primer information XXX

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 Collection Code Catalog ID : : NHMLEP : : personalDHJanzenSRNP12345 ::

CBOL/GBIF/NCBI Registry of Biorepositories

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 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