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Plants, Herbivores, and Parasitoids A Model System for the study of Tri-Trophic Associations. NSF ADBC Digitization TCN Randall Schuh American Museum of Natural History. TCN Partners. This project is predicated on broad institutional cooperation. ENTOMOLOGY

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plants herbivores and parasitoids a model system for the study of tri trophic associations

Plants, Herbivores, and ParasitoidsA Model System for the study of Tri-Trophic Associations

NSF ADBC Digitization TCN

Randall Schuh

American Museum of Natural History

tcn partners
TCN Partners

This project is predicated on broad institutional cooperation.

ENTOMOLOGY

  • Randall Schuh, American Museum of Natural History
  • Christine Johnson, American Museum of Natural History
  • Christiane Weirauch, University of California, Riverside
  • John Heraty, University of California, Riverside
  • Charles Bartlett, University of Delaware
  • Benjamin Normark, University of Massachusetts, Amherst
  • Neal Evenhuis, BP Bishop Museum, Honolulu
  • David Kavanaugh ,California Academy of Sciences
  • Stephen D. Gaimari ,California Dept. Food and Agriculture
  • Chen Young, Carnegie Museum, Pittsburg
  • Boris C. Kondratieff, Colorado State University
  • James K. Liebherr, Cornell University
  • Dmitry Dmitriev, Illinois Natural History Survey
  • Richard Brown, Mississippi State University
  • Andy Deans, North Carolina State University
  • David Maddison, Oregon State University
  • John Oswald, Texas A&M University
  • Kipling Will, University of California, Berkeley
  • Caroline Chaboo , University of Kansas
  • Michael Sharkey , University of Kentucky

Data Contributors

  • Canadian National Collection, Ottawa
  • University of California, Davis
  • Kansas State University

BOTANY

  • Robert Naczi, New York Botanical Garden
  • Robert Magill, Missouri Botanical Garden
  • Richard Rabeler, University of Michigan
  • Melissa Tulig, New York Botanical Garden
  • Margaret Koopman, Eastern Michigan University
  • Loy Phillippe, Illinois Natural History Survey
  • Deborah Lewis, Iowa State University
  • Michael Vincent, Miami University
  • Timothy Hogan, University of Colorado
  • Mary Ann Feist, University of Illinois
  • Craig Freeman, University of Kansas
  • Christopher Cambell, University of Maine
  • Anita Cholewa, University of Minnesota
  • Beryl Simpson, University of Texas
  • Kenneth Cameron, University of Wisconsin

Data Contributors

  • Consortium of Pacific Northwest Herbaria
  • Consortium of California Herbaria
  • Southwest Biodiversity Consortium
a tri trophic example
A Tri-Trophic Example

Crop Plants

(Solanaceae)

Aphids

(Hemiptera)

Parasitoids

Plants

Insect Herbivores

Parasitic wasps

(Hymenoptera)

Produce fruits and tubers a significant economic value.

Pierce stems and leaves to feed on the plants – specialize on one species or numerous species, reduce plant vigor or transmit disease, cause reduction in yield or make fruits or tubers inedible.

Lay eggs directly inside the aphids and consume them from the inside out.

a tri trophic approach
A Tri-Trophic Approach

About 85% of Hemiptera are herbivorous with high host specificity for many plant families (e.g., Asteraceae, Fabaceae, Fagaceae, and Poaceae)

Hempitera are serious agricultural pests (armored scales, mealy bugs, potato leafhoppers, Lygus bugs)

Vectors of viral and bacterial diseases (Green peach aphid is a vector of over 100 plant viruses)

Parasitic Hymenoptera are very beneficial as biological control agents

The relationship among these groups is of significant ecological and economic importance

data contributors
Data Contributors

Botanical

Access data from 3 existing consortia covering the western United States

Entomological

Incorporate data for Aphidoidea through cooperation with Robert Foottit, Agriculture Canada, primarily as slide images

Incorporate data for Coccoidea from collections with data already captured (e.g., UC Davis)

Incorporate data from previously databased Hemiptera collections (Kansas State University)

project management
Project management
  • Steering Committee of 10 PIs
    • Randall Schuh (AMNH), Committee Chair
    • First TCN meeting Oct. 29-30th in NY
  • Full-time Project Manager at AMNH (Katja Seltman)
    • Daily project management, training of entomology partners, centralized georeferencing, and technical capacity
  • Full-time Project Coordinator at NYBG (Kim Watson)
    • Training of botany partners, barcoding of NYBG specimens, and databasing of herbarium specimens for all partner institutions
  • Digitization assistants
    • Hourly staff at all partner institutions to image or database specimens
infrastructure
Infrastructure

Utilize existing database infrastructure at AMNH (PBI funded) and NYBG (EMu)

Utilize existing imaging infrastructure at AMNH (Visionary Digital) and NYBG (custom light box)

Utilize existing Storage Area Networks and web servers at NYBG & AMNH (mirror AMNH-PBI database at UCR)

Utilize Discover Life web portal for data integration, as modeled by AMNH’s NSF PBI Plant Bug project; send data copies to iDigBio, GBIF & other networks

Cooperate on development of solutions and tools by iDigBio & others

plants workflow
Specimens are barcoded, given a “filed as” name, and imaged at partner institutions

Image files are sent to NYBG

Each image file gets a database record with the institution, barcode number, “filed as” determination, and preliminary OCR of the label

Use Tropicos database from Missouri Botanical Garden as botanical nomenclature authority file

NYBG Project Coordinator completes the partial records

Send DarwinCore specimen data to DiscoverLife and back to each partner institution

Plants Workflow
how do we complete georeference 1 200 000 partial records
How do we complete & georeference 1,200,000+ partial records?

Send image files through SALIX/HERBIS

Merge existing partner datasets and expect duplicates

Scatter, Gather, Reconcile; FilteredPush

Crowd sourcing & citizen scientists

Georeferencing tools: GEOLocate, BioGeomancer & others

All ideas welcome!

bottlenecks
Bottlenecks
  • Curation
    • Outdated names and identifications: specimens of the same species filed under more than one name
  • Combined data
    • Duplicates and differing names – how to know which is correct, how to report discrepancies back to home institutions
  • File transfer
    • What’s the best way to move 1,000,000 images to NY?
  • Long-term archival image storage for all institutions?
    • Potentially 36+ TB of raw files
insect workflow
Insect Workflow
  • Organize specimens by species, then…
  • Organize specimens by collection event
  • Attach barcodes to each specimen
  • Perform data entry for all specimens
  • Take close up images of representative specimens of every species

AMNH Matrix-code labels

databasing
Databasing

Use existing online PBI database for most data entry

streamlined interface for rapid data entry
Streamlined Interface for Rapid Data Entry

Taxon names

Locality data

Collection Events

Specimen Data

Host names

specimen imaging
Specimen Imaging
  • Image representative specimens for each species
  • Use existing imaging stations at partner institutions
  • About 30% of Hemiptera are already imaged
  • Expect to produce about 20,000 new images
combine datasets in discover life
Combine datasets in Discover Life
  • PBI database is already set up as a data provider to Discover Life
  • Generates species pages that include specimen data, maps, and images
  • Creates a linkage between host/herbivore/parasitoid data
  • Updates PBI data every 24 hours to deliver up-to-date information
overall challenges
Overall Challenges

Adequately train personnel to capture de novo data for more than 2 million specimens

Implement authority files for all groups in all databases

Insure accuracy of specimen identifications

Integrate data across databases

Integrate data across trophic groups for effective access by broadest user community

Maintain data over the long haul

what can be done with these 4 000 000 combined data records
What can be done with these 4,000,000+ combined data records?

Systematics: assembly of specimen data

Biogeography: large data pool for studies of endemism

Ecology: host-herbivore-parasitoid relationships and origins

Conservation biology: management decision making

Agricultural sciences: invasive/pest species data and management, identifications at ports

Climate change studies: ecological niche modeling; phenological changes; distributional changes

meeting of ttd tcn subcontracts
Meeting of TTD-TCN subcontracts:

The PIs would like to convene as many of the

subcontracting institutions as possible during the

banquet this evening. This will provide an

opportunity to discuss potential problems, compare

notes, and answer questions you may have.

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