0
Building a DNA
Barcode library
of Alaska's
nonmarine
arthropods
Derek Sikes & Casey Bickford
University of Alaska Museum
F...
© Henri Goulet
Map of all georeferenced spider records in Arctos 2012-11-14
Mission
To create a resource that makes publicly available as
much information as possible concerning the nonmarine arthro...
Mission
Which species occur in Alaska?
~8,000 nonmarine arthropod species
USFWS Kenai National Wildlife Refuge
- hope to u...
Cumulative AK Species Added to Database
all records

8191

UAM specimen based records
2596
Methods
Plan:
Contribute to iBoL, DNA Barcodes of
2-3 specimens per authoritatively identified species
< 10yrs old

~2000 ...
Methods
Compared two labs
Canadian Centre for DNA Barcoding (CCDB)
$12/specimen
Smithsonian Institute (SI)
$9/specimen
Two...
Methods
Compared two labs
Both agreed that the lab not chosen would
forfeit payment for the test plate
If Smithsonian was ...
Methods
Compared two labs
CCDB had higher success rate (95% vs 80%)
SI lab had a contamination issue

CCDB more efficient
...
Smithsonian test plate
CCDB test plate
95 Specimens removed from collection
Simple, single photo of each specimen, ~ 2 min each
not stacked (~30 min e)
Middle leg or portion thereof removed from each
Arctos records linked to BoLD records / GenBank records
BIN Discordance...
Smithsonian Curation Standards
and Profiling System
Numerical coding system

Identifies curation status of storage units
-...
Smithsonian Curation Standards
and Profiling System
LEVEL 1: materials conservation
LEVEL 2-4: specimen accessibility
LEVE...
Final Thoughts
- Not entirely altruistic...
- photos of 2-3 examples of all specimens identified
to species (even if DNA b...
Final Thoughts
- If funding for databasing and photography is
available (often standard in BRC grants)
- then DNA barcodin...
Acknowledgments
-Graduate Curatorial Assistants
Jill Stockbridge
Joey Slowik
Brandi Fleshman

-Current lab techs:
Sayde Ri...
Questions?
Sikes ecn2013 dn_ab
Sikes ecn2013 dn_ab
Sikes ecn2013 dn_ab
Sikes ecn2013 dn_ab
Sikes ecn2013 dn_ab
Sikes ecn2013 dn_ab
Sikes ecn2013 dn_ab
Sikes ecn2013 dn_ab
Sikes ecn2013 dn_ab
Sikes ecn2013 dn_ab
Sikes ecn2013 dn_ab
Sikes ecn2013 dn_ab
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Transcript of "Sikes ecn2013 dn_ab"

  1. 1. Building a DNA Barcode library of Alaska's nonmarine arthropods Derek Sikes & Casey Bickford University of Alaska Museum Fairbanks, AK Entomological Collections Network Austin, TX 2013-11-09
  2. 2. © Henri Goulet
  3. 3. Map of all georeferenced spider records in Arctos 2012-11-14
  4. 4. Mission To create a resource that makes publicly available as much information as possible concerning the nonmarine arthropods of Alaska. Using specimens + literature + „grey‟ literature Which species occur in Alaska? Where do these species occur? What do they do? / Are they changing?
  5. 5. Mission Which species occur in Alaska? ~8,000 nonmarine arthropod species USFWS Kenai National Wildlife Refuge - hope to use DNA Barcode methods for monitoring - must first build a DNA Barcode library for Alaska‟s arthropod species
  6. 6. Cumulative AK Species Added to Database all records 8191 UAM specimen based records 2596
  7. 7. Methods Plan: Contribute to iBoL, DNA Barcodes of 2-3 specimens per authoritatively identified species < 10yrs old ~2000 species, ~6,250 specimens ~30% of the state fauna – all nonmarine arthropod taxa
  8. 8. Methods Compared two labs Canadian Centre for DNA Barcoding (CCDB) $12/specimen Smithsonian Institute (SI) $9/specimen Two 95 well plates with tissues from same 95 specimens
  9. 9. Methods Compared two labs Both agreed that the lab not chosen would forfeit payment for the test plate If Smithsonian was chosen they would provide sequences/chromatograms and we would upload (= more work for us).
  10. 10. Methods Compared two labs CCDB had higher success rate (95% vs 80%) SI lab had a contamination issue CCDB more efficient 95 * $12 = $1,140 / plate
  11. 11. Smithsonian test plate
  12. 12. CCDB test plate
  13. 13. 95 Specimens removed from collection
  14. 14. Simple, single photo of each specimen, ~ 2 min each not stacked (~30 min e)
  15. 15. Middle leg or portion thereof removed from each
  16. 16. Arctos records linked to BoLD records / GenBank records
  17. 17. BIN Discordance...
  18. 18. Smithsonian Curation Standards and Profiling System Numerical coding system Identifies curation status of storage units - insect drawers - alcohol jars / vials / racks - slide boxes McGinley, R.J. (1992) Where's the Management in Collections Management? Planning for Improved Care, Greater Use, and Growth of Collections. In: Palacios, F., C. Martínez & B. Thomas (Eds.) The International Symposium and First World Congress on the Preservation and Conservation of Natural History Collections, held in Madrid, 10-15 May 1992. Congress Book. Volume 3. Current Issues, Initiatives, and Future Directions for the Preservation and Conservation of Natural History Collections. pp. 309-338. 30
  19. 19. Smithsonian Curation Standards and Profiling System LEVEL 1: materials conservation LEVEL 2-4: specimen accessibility LEVEL 5-6: physical organization LEVEL 7-9: data capture LEVEL 10: scientific voucher material - DNA barcoded specimens, imaged = LEVEL 10 - GenBank vouchers 31
  20. 20. Final Thoughts - Not entirely altruistic... - photos of 2-3 examples of all specimens identified to species (even if DNA barcode failed) - specimen data digitized for all (in our case this was 99% done beforehand) - research / curatorial “fallout” : cryptic species, phylogeographic data, misidentifications - helps counter public‟s misperception of museums as “old-fashioned”
  21. 21. Final Thoughts - If funding for databasing and photography is available (often standard in BRC grants) - then DNA barcoding is not much extra work - but it is considerably extra cost ($1440 / 95 well plate) - can arrange with BOLD to have data served to GBIF
  22. 22. Acknowledgments -Graduate Curatorial Assistants Jill Stockbridge Joey Slowik Brandi Fleshman -Current lab techs: Sayde Ridling Trista Crass Sarah Meierotto - Volunteers: Steve Peek (Diptera) Mary Wyatt - National Science Foundation -USDA ARS / FHP -USFWS -NPS -ADFG -AK Div of Ag -USGS
  23. 23. Questions?
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