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John La Salle - Opening Plenary

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The “Barcode Blitz”: accelerating the targeted capture of barcode data

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John La Salle - Opening Plenary

  1. 1. The “Barcode Blitz”: accelerating the targeted capture of barcode data John La Salle, Beth Mantle CSIRO Ecosystem Sciences, Canberra, Australia Jeff Webb, Rodolphe Rougerie, Paul Hebert Biodiversity Institute of Ontario, Guelph Canada
  2. 2. The “Barcode Blitz” - ANIC Lepidoptera <ul><ul><li>A coordinated assault for targeted and priority capture of barcode data on ANIC Lepidoptera </li></ul></ul><ul><ul><li>Has shown it is possible to gather large amounts of data quickly </li></ul></ul><ul><ul><li>Built a substantive library for a megadiverse group at continental scale in a short time frame </li></ul></ul><ul><ul><li>Fits into / supports </li></ul></ul><ul><ul><ul><li>Large scale digitisation efforts </li></ul></ul></ul><ul><ul><ul><li>Research outcomes </li></ul></ul></ul><ul><ul><ul><li>Operational outcomes </li></ul></ul></ul><ul><ul><ul><li>Rapid species discovery </li></ul></ul></ul>
  3. 3. The “Barcode Blitz” <ul><ul><li>Two visits from BIO / Guelph team to ANIC </li></ul></ul><ul><ul><li>5 people x 5 weeks each </li></ul></ul><ul><ul><li>Jaclyn McCormick Paul Hebert </li></ul></ul><ul><ul><li>Jayme Sones Rodolphe Rougerie </li></ul></ul><ul><ul><li>Stephanie deWaard Jeff Webb </li></ul></ul><ul><ul><li>Cirsty Carr Jeremy deWaard </li></ul></ul><ul><ul><li>Renee Labbee Patrick Strutzenberger </li></ul></ul><ul><ul><li>Valerie Levesque-Beaudin Mari Kekkonen </li></ul></ul>
  4. 4. The “Barcode Blitz” <ul><ul><li>In 10 weeks </li></ul></ul><ul><ul><li>28,000 specimens processed </li></ul></ul><ul><ul><li>8,000 species </li></ul></ul><ul><ul><li>Databased, geocoded, imaged on site </li></ul></ul><ul><ul><li>Leg taken </li></ul></ul><ul><ul><li>Sequenced in Canada </li></ul></ul>
  5. 5. Assembly line processing
  6. 6. Assembly line processing
  7. 7. Selecting specimens <ul><ul><li>Multiple specimens per OTU </li></ul></ul>
  8. 8. Selecting specimens <ul><ul><li>From collection to array box </li></ul></ul>
  9. 9. Specimens into array boxes <ul><ul><li>Each space numbered </li></ul></ul><ul><ul><li>Aligns with number of wells in lysis plate </li></ul></ul>
  10. 10. <ul><ul><li>Position of every specimen taken from collection marked </li></ul></ul>
  11. 11. Specimens databased and geocoded
  12. 12. Specimens into processing boxes <ul><ul><li>Specimens labelled as they are processed </li></ul></ul><ul><ul><ul><li>BOLD label </li></ul></ul></ul><ul><ul><ul><li>ANIC label </li></ul></ul></ul>
  13. 13. Every specimen photographed
  14. 14. Leg removed for barcoding
  15. 15. <ul><ul><li>Each lysis plate gets unique label that ties it back to array box </li></ul></ul>
  16. 16. Specimens back to collection <ul><ul><li>Specimens returned to exactly where they were taken </li></ul></ul>
  17. 17. The “Barcode Blitz” <ul><ul><li>In 10 weeks </li></ul></ul><ul><ul><li>28,000 specimens processed </li></ul></ul><ul><ul><li>8,000 species </li></ul></ul><ul><ul><li>Databased, geocoded, imaged on site </li></ul></ul><ul><ul><li>Uploaded to BOLD within 24 hours </li></ul></ul><ul><ul><li>Leg taken </li></ul></ul><ul><ul><li>Sequenced in Canada </li></ul></ul>
  18. 18. The “Barcode Blitz” - what did we achieve Despite an average age of 30 years, COI sequences were recovered from more than 95% of the specimens
  19. 19. The “Barcode Blitz” - what did we achieve Provided the first continent-wide data set for a megadiverse insect group in Australia within a short period of time (about 90% of named Lepidoptera) Provides a model for inclusion in other initiatives aimed at the high-throughput accumulation of priority data sets. Establishes the great value of existing natural history collections as a basis for fast tracking the development of comprehensive DNA barcode libraries.
  20. 20. Despite popular opinion …
  21. 21. The “Barcode Blitz” - Australian benefits <ul><ul><li>Digital records in ANIC, ALA, BOLD </li></ul></ul><ul><ul><ul><li>(28,000 databased, geocoded, imaged specimens) </li></ul></ul></ul>
  22. 22. The “Barcode Blitz” - results <ul><ul><li>What did we achieve </li></ul></ul>
  23. 23. The “Barcode Blitz” - results <ul><ul><li>What did we achieve </li></ul></ul>
  24. 24. The “Barcode Blitz” - Australian benefits <ul><ul><li>ANIC barcoding blitz activity is our clearest and most positive example of an accelerated and serious attempt to digitise a significant representative sample of a national collection. </li></ul></ul><ul><ul><li>Presenting the results in their fullness (including the capability of this process to highlight the range of undescribed diversity) would be a key element in a case to support a major national digitisation activity </li></ul></ul>
  25. 25. One example of international benefit <ul><ul><li>A message from South Africa </li></ul></ul><ul><ul><li>“ Note that the mitochondrion sequences we obtained from the groundnut leaf miner in South Africa matched 100% with the soybean moth Approaerema simplexella PS1 from Australia on the BOLD system, and that is the reason we are interested in the soybean moth in Australia.” </li></ul></ul>
  26. 26. The “Barcode Blitz” - Australian benefits <ul><ul><li>A searchable digital library for Australian Lepidoptera (including images and barcoding) </li></ul></ul><ul><ul><li>Foundation for a variety further studies </li></ul></ul><ul><ul><li>Facilitate identification </li></ul></ul><ul><ul><li>Able to connect life histories </li></ul></ul><ul><ul><li>Informs systematics, biodiversity, biosecurity </li></ul></ul><ul><ul><li>Foundation for Rapid Taxonomy efforts </li></ul></ul>
  27. 27. Rapid Taxonomy of Australian Xylorictidae <ul><ul><li>Generations of investment in morphology (through putative species sorted in the collection) </li></ul></ul><ul><ul><li>Estimated 250 new species – with most of them already sorted to morphospecies </li></ul></ul>
  28. 28. Rapid Taxonomy of Australian Xylorictidae <ul><ul><li>Group with no active specialist (last description in 1964) – no revisions on horizon. </li></ul></ul><ul><ul><li>Other major museums have made types of Australian xylorictids available for barcoding/study </li></ul></ul><ul><ul><li>Become a project for Patrick Strutzenberger (PhD student, Guelph) </li></ul></ul><ul><ul><li>DNA barcodes will be used to verify/validate morphospecies in collection </li></ul></ul><ul><ul><li>Produce standardized descriptions + images + barcodes (?plus genitalia) </li></ul></ul><ul><ul><li>Can progress taxonomic knowledge of this group rapidly </li></ul></ul><ul><ul><li>GOAL: 250 species described in 2 years, with 100 done by this time next year </li></ul></ul>
  29. 29. Accelerated Species Discovery <ul><ul><li>taxonomist </li></ul></ul><ul><ul><li>Accelerated phenomics </li></ul></ul><ul><ul><li>Accelerated DNA </li></ul></ul><ul><ul><li>Accelerated species discovery and description </li></ul></ul><ul><ul><li>Crowdsourcing citizen scientists </li></ul></ul>
  30. 30. Thank you Funding: Genome Canada CSIRO Transformational Biology <ul><li>Bio Team from Guelph: </li></ul><ul><ul><li>Jaclyn McCormick Rodolphe Rougerie </li></ul></ul><ul><ul><li>Jayme Sones Jeff Webb </li></ul></ul><ul><ul><li>Stephanie deWaard Jeremy deWaard </li></ul></ul><ul><ul><li>Cirsty Carr Patrick Strutzenberger </li></ul></ul><ul><ul><li>Renee Labbee Mari Kekkonen </li></ul></ul><ul><ul><li>Valerie Levesque-Beaudin </li></ul></ul>Contact Us Phone: 1300 363 400 or +61 3 9545 2176 Email: enquiries@csiro.au Web: www.csiro.au