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Big Data for Virginia Plant Taxonomy

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Presentation for the February 11, 2016 meeting of the Virginia Native Plant Society Potowmack Chapter, by Dr. Andrea Weeks.

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Big Data for Virginia Plant Taxonomy

  1. 1. Andrea Weeks, Ph.D. Associate Professor, Plant Systematics Director, Ted R. Bradley Herbarium George Mason University Virginia Native Plant Society Potowmack Chapter, February 11, 2016
  2. 2. Outline • Big data defined for botany • Biodiversity informatics: why bother? • Virginia herbarium digitization • How you can become involved
  3. 3. Vast amounts of consumer data from internet changing business management
  4. 4. Vast amounts of genomic data improving disease treatment
  5. 5. http://www2.nrm.se/fbo/hist/munchen.html.en Herbarium specimens from 1699-1702
  6. 6. http://www2.huh.harvard.edu/libraries/Gray_Bicent/graybio.htm Herbarium specimens from 19th century Happy birthday, Darwin!
  7. 7. Herbarium specimens from 21st century
  8. 8. Herbarium specimens: morphology & phenology location, ecological notes, date, collector
  9. 9. Centuries of data about plant species Isolated online databases Off-line databases Spreadsheets Printed publications Field notebooks Natural history specimens Age Accessibility volume
  10. 10. Biodiversity Informatics • uses modern technologies to • convert vast amount of data on biodiversity into • knowledge, wisdom, and environmental outcomes Arthur Chapman: https://www.youtube.com/watch?v=w5_y6o9G
  11. 11. "A world in which biodiversity information is freely and universally available for science, society and a sustainable future." 2007
  12. 12. • Species discovery • Retrospective distribution mapping: Climate change • Predictive distribution modeling: Climate change http://nyti.ms/1M0KQiw
  13. 13. http://www.theatlantic.com/science/archive/2016/02/the-unexplored-marvels-locked-away-in-our-natural-history-museums/459306/ Natural History Museums are Teeming with Undiscovered Species. (February 8, 2016)
  14. 14. Bebber DP, Carine MA, Wood JRI, et al. 2010. Herbaria are a major frontier for species discovery. PNAS 107: 22169 – 22171. doi:10.1073/pnas.1011841108. Herbaria are a major frontier for species discovery. Between 1970 - 2010 • 84% new species based on >5 y old specimens, with nearly one-quarter of new species descriptions involving specimens >50 y old. • Of the estimated 70,000 species still to be described, more than 35,000 already have been collected and are stored in herbaria, unnoticed.
  15. 15. Altitudinal shifts of the native and introduced flora of California in the context of 20th century warming‐ 681,609 herbarium records between 1895 - 2009 4426 native & exotic species 15% native shifted up in elevation 27% exotic shifted up in elevation Global Ecology and Biogeography 20 JAN 2016 DOI: 10.1111/geb.12423 http://onlinelibrary.wiley.com/doi/10.1111/geb.12423/full#geb12423-fig-0001
  16. 16. https://www.idigbio.org/content/research-spotlight-using-museum-specimens-refine-models-species-distribution Using museum specimens to refine models of species distribution in Florida • Herbarium records of 1,548 Florida plant species tied to yearly climate information. • Refined contemporary potential distribution maps • Future plant diversity under two CO2 scenarios
  17. 17. Hot spots of plant endemism in the southeast (Estill & Cruzan 2001)Hot spots of plant endemism in the southeast (Estill & Cruzan 2001) A biodiverse region with intense human population pressures A rich tradition of botanical collection yet many herbaria under-resourced. Estill, J. C., & Cruzan, M. B.. (2001). Phytogeography of Rare Plant Species Endemic to the Southeastern United States. Castanea, 66(1/2), 3–23.
  18. 18. State of Herbaria in the Southeast USA Data derived from Index Herbariorum (http://www.nybg.org/bsci/ih/ih.html) . • 233 collections vary in size from 3,000 to 750,000 specimens. • Curators are taxonomists, ecologists, paleobotanists, population biologists. • Some institutions with significant budgets, IT support and curatorial staff. • Some institutions are single person operations without budgets or IT support. • ESTIMATED 15 MILLION SPECIMENS FROM THE SOUTHEAST.
  19. 19. The Key to the Cabinets: Building and Sustaining a Research Database for a Global Biodiversity Hotspot A new NSF-Advancing Digitization in Biological Collections (ADBC) collaborative project in the southeast NSF ADBC #1410069 (plus collaborative awards (1410077 1410081 1410086 1410087 1410092 1410094 1410098 1410143 1410200 1410288 1410439 1410445)
  20. 20. The Project • Southeastern U.S. vascular plants • 93 collections will be digitized • 12 states • 28 hubs • 6 partners • 4.5M herbarium specimens will be served to GBIF.
  21. 21. Data Contributors in the SE US (yellow diamonds)
  22. 22. Shaw Goertzen 138,000 Johnson Mast Zomlefer Ruhfel Sasek Wallace W eakley Damrel W eeks Gillespie Evans McDowell Krosnick Kreuger Jabaily Morris Estes Horn Pollard Montgomery Jensen Long Grubbs Kilpatrick Nelson Krings M atthew s W indham W ieboldt Cowden Alerding Hayden Simpson M cM ullenZhangLickeyFuller Gonzales Gregg Triesel Harmon McKinley Mabry Ferrara Chatfield Ford- Werntz Link-Perez BurgessMorgan CarterHarvey ClarkMajor Saar Risk W hitson 389,000 212,000 748,000 286,000 981,000 30,000 0 196,000 135,000 301,000 138,000 M arisco W itsell Serviss W illyard Fawley Gentry Noyes 248,000
  23. 23. www.sernecportal.org is our central hub of digitization in the SE US
  24. 24. *AVCH: 4,200 11 Virginian herbaria are covered under NSF grant.
  25. 25. Workflow
  26. 26. Mason undergrad Ushna imaging GMUF, Summer 2015.
  27. 27. Each herbarium has its own standardized database interface
  28. 28. Workflow
  29. 29. http://www.notesfromnature.org/
  30. 30. https://www.wedigbio.org/ Citizen scientist in action!
  31. 31. http://www.notesfromnature.org/
  32. 32. Workflow
  33. 33. Data Management Workflow Specimen Image Capture “Herbarium Digitarium” Texas Advanced Computing Center Archival Storage Web Derivatives Citizen Scientists Metadata to Portal Batch Georeferenced Data to Portal Repatriation of Metadata to Local Institution Symbiota and Specify 4,700,000 SPECIMENS 100+ INSTITUTIONS 12 STATES
  34. 34. www.sernecportal.org
  35. 35. *AVCH: 4,200 VA progress to date: May 2015 – February 2016 2015 Virginia Native Plant Society Research Grant awarded 0 records accessible 94,207 online database entries 0 images available 40,689 online specimen images 11  15 Virginian herbaria using our infrastructure Training documents created At least 22 curators, staff & students trained
  36. 36. A selection of herbaria already on sernecportal.org
  37. 37. Online database fostering new conversations, e.g. nativity of Magnolia tripetala in Fairfax Co.
  38. 38. *AVCH: 4,200 Challenges & Opportunities for 2016 Notes From Nature platform, although fully functional, may not be serving Virginian specimens for transcription until 2017. We have a great alternative: SERNEC transcription portal. We need beta testers for SERNEC transcription portal.
  39. 39. click Step 1: login by following private hyperlink (see handout)
  40. 40. click Step 2: Select one of GMUF’s specimens to transcribe
  41. 41. click CTRL + click to enlarge Step 3: Set up your transciption window
  42. 42. Step 4: Transcribe 8 database fields & Save Edits
  43. 43. Looking forward…. Thank you

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