Thematic, Demand-driven Sampling: Economics of Three Strategies David E. Schindel, Executive Board Chairman Scientific Collections International (SciColl) National Museum of Natural History Smithsonian Institution

[email protected]

Investments in collected specimens What do we invest in each specimen? – Costs of: Permitting, collecting, transporting; Preparing, cataloging, curating; Providing suitable environmental conditions, security; Digitizing, mobilizing data; and Loan transactions, hosting visitors.

What returns do we get from investments? – Citations in publications

Is our mission to maximize ROI? Decisions on: – What to collect (Where? When? How many?) – How much destructive sampling? – What to keep? (Whole vouchers? Tissue?) – What to trade? (Specialized centers versus global coverage?) – What to deaccession?

Predicting likelihood of future demand

Three Collecting Strategies Insect Traps: • Many samples • Many samples/species • Low phylogenetic distance

Salle, Arthofer, Lieutier, Stauffer and Kerdelhue, 2007, Phylogeography of a host-specific insect: genetic structure of Ips typographus in Europe does not reflect past fragmentation of its host, Biological Journal of the Linnean Society 90: 239– 246.

Salle, Arthofer, Lieutier, Stauffer and Kerdelhue, 2007, Phylogeography of a host-specific insect: genetic structure of Ips typographus in Europe does not reflect past fragmentation of its host, Biological Journal of the Linnean Society 90: 239– 246.

Three Collecting Strategies Insect Traps: • Many samples • Many samples/species • Low phylogenetic distance Barcode of Wildlife Project: • Limited number of samples • Standard samples/species • Moderate phylogenetic distance

Barcode of Wildlife on Google+

BWP Goals Working with six Partner Countries: Demonstrate use of DNA barcode evidence in investigations, prosecutions; first convictions in Kenya Construct a reference BARCODE library to support Partner Country priorities – 200 Priority Endangered Species per country – 800 closely related/look-alike species

Partner Countries will formally adopt, implement and ‘mainstream’ DNA barcoding

Priority Species Viewer

http://www.barcodeofwildlife.org/priority_species.html

Required Elements for BARCODE Taxonomic identification to species Voucher specimen ID in Darwin Core Triplet format Name of barcode region Country/Ocean/Sea of origin Minimum sequence length and quality Forward and reverse 2 trace files in NCBI Forward/reverse primer sequences, names

Required BWP Data/Metadata Additional datafields in GenBank for BWP: – Name of identifier – Date of identification – Type status of voucher specimen – Basis of identification – Confidence level – Collected under chain of custody? (Y/N)

Basis of Identification The type of information used: – Overall similarity – Diagnostic characters – DNA BARCODE comparison

The form of the identified voucher specimen: – Living organism: Juvenile/Immature – Preserved specimen: Incomplete adult – Digital Image: Complete adult

The references against which the voucher specimen was compared

Levels of Confidence High confidence: There is an extremely high probability that the species-level identification is correct. This level of confidence can be entered only by professional taxonomists with experience in the group to which the voucher specimen has been assigned. Only well-preserved voucher specimens that display diagnostic features can be assigned to this level of confidence. Medium confidence: There is a high probability that the genus-level identification is correct but a lower likelihood that the species-level identification is correct. Experienced nonprofessionals can assign this level of confidence after making comparisons with taxonomic publications. Preliminary identification: The genus and species names are uncertain and a more expert identification is needed.

Scientific Collections International Infectious Diseases, Food Security

Published March 2015

Published January 2016

Stressors and Drivers of Food Security: Evidence from Scientific Collections 19-21 September 2016, Beltsville, MD

www.scicoll.org

Three Collecting Strategies Insect Traps: • Many samples • Many samples/species • Low phylogenetic distance Barcode of Wildlife Project: • Limited number of samples • Standard samples/species • Moderate phylogenetic distance Submersibles: • Few samples • Few samples/species • High phylogenetic distance

Phylogenetic Diversity (branch length)

Collecting Cost per Specimen

Cost of Sampling Genetic Variability Submersibles

Barcode of Wildlife Project

Insect Traps

Specimens per species/higher taxonomic unit

Leray and Knowlton, 2015, DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity, PNAS 112(7): 2076–2081

Vacant Dataspace

Crowded Dataspace

Per specimen sampling cost

Communities of Samplers

Submersibles

Barcode of Wildlife Project

Insect Traps

Per specimen likelihood of re-use