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Andy J Value Of A Coordinate Montpellier Nov 2009


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Presentation at TDWG 2009 in montpellier on the value of geographic coordinates for exploring agricultural biodiversity patterns, and influencing conservation policy.

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Andy J Value Of A Coordinate Montpellier Nov 2009

  1. 1. Value of a coordinate: geographic analysis of agricultural biodiversity<br />Andy Jarvis, Julian Ramirez, Nora Castañeda, Samy Gaiji, Luigi Guarino, Hector Tobón, and Daniel Amariles<br />
  2. 2. Contents<br />Why crop wild relatives?<br />How a coordinate can help us complete the collections<br />Cleaning coordinate data<br />Needs from standards<br />
  3. 3. Wild relatives of crops<br />Includeboth progenitor species and closelyrelatedspecies of cultivatedcrops<br />Faba beans – 0 wild relatives<br />Potato – 172 wild relativespecies<br />Increasinglyuseful in breeding, especiallyforbioticresistance<br />
  4. 4. Wild relative species<br />A. batizocoi - 12 germplasm accessions<br />A. cardenasii - 17 germplasm accessions <br />A. diogoi - 5 germplasm accessions<br />Florunner, with no root-knot nematode resistance<br />COAN, with population density of root-knot nematodes &gt;90% less than in Florunner<br />
  5. 5. Gap Analysis: Strategiestofilltheholes in ourseedcollections<br />
  6. 6. The Gap Analysisroadmap<br />Taxonomy review<br />Data gathering<br />Georeferentiaton<br />Environmental<br />data gathering<br />Gap Analysis<br />process<br />Final<br />recommendations<br />
  7. 7. The Gap Analysis process<br />Proxy for:<br /><ul><li> Diversity
  8. 8. Possibly biotic traits</li></ul>Proxy for:<br /><ul><li> Range of traits</li></ul>Proxy for:<br /><ul><li> Abiotic traits</li></li></ul><li><br />
  9. 9. Total number of herbariumspecimens and germplasmaccessionsavailableforeachmajorcrop wild relativegenepoolthroughthe GBIF portal<br />
  10. 10. Environmental coverage<br />
  11. 11. HERBARIUM<br />GERMPLASM<br />
  12. 12. NO<br />GERMPLASM<br />DEFICIENT<br />GERMPLASM<br />
  13. 13. POTENTIAL<br />RICHNESS<br />RARE<br />ENVIRONMENTS<br />
  14. 14. Which species, and where<br />
  15. 15. Wild Vigna collecting priorities<br />Spatial analysis on current conserved materials<br />*Gaps* in current collections<br />Definition and prioritisation of collecting areas<br />8 100x100km cells to complete collections of 23 wild Vigna priority species<br />
  16. 16. Richness in collecting zones at genepool level<br />
  17. 17. Predictedchange in speciesrichnessto 2050.<br />
  18. 18.
  19. 19. Exploration and ex-situ conservation of Capsicum flexuosum<br /><ul><li>Uncommon species of wild chili, found in Paraguay and Argentina, historically used by local indigenous communities
  20. 20. 18 known registers of the plant prior to this work
  21. 21. 2 germplasm accessions conserved in the USDA
  22. 22. GIS used to target field collections
  23. 23. 6 new collections of C. flexuosum
  24. 24. 160 seeds conserved ex situ</li></ul>OBJECTIVE: Locate and collect germplasm of this species in Paraguay<br />
  25. 25. Behind all this<br />Data Quality<br />
  26. 26. The GBIF database: status of the data<br />The database holds 177,887,193 occurrences<br />Plantae occurrences are 44,706,505 (25,13%) <br />33,340,000 (74.5%) have coordinates<br />How many of them are correct, and reliable?<br />How many new georreferences could we get?<br />CURRENT STATUS OF<br />THE Plantae RECORDS<br />
  27. 27. The GBIF database: status of the data<br />How to make the terrestrial data reliable enough?<br />Verify coordinates at different levels<br />Are the records where they say they are?<br />Are the records inside land areas (for terrestrial plant species only)<br />Are all the records within the environmental niche of the taxon?<br />Correct wrong references<br />Add coordinates to those that do not have<br />Cross-check with curators and feedback to the database<br />
  28. 28. Using a random sample of 950.000 occurrences with coordinates<br />
  29. 29. Are the records where they say they are?: country-level verification<br />Records with null country: 58.051  6,11% of total <br />Records with incorrect country: 6.918  0,72% of total<br />Total excluded by country 64.969  6,83% of total<br />Records mostly located<br />in country boundaries<br />Inaccuracies in<br />coordinates<br />
  30. 30. <ul><li>Are the terrestrial plant species in land?: Coastal verification</li></ul>Records in the ocean: 9.866  1,03% of total <br />Records near land (range 5km): 34.347  3,61% of total<br />Records outside of mask: 369  0,04% of total<br />Total excluded by mask 44.582  4.69% of total<br />Errors, and more errors<br />
  31. 31. Not so bad at all… stats<br />44’706.505 plant records<br />33’340.008 (74,57%) with coordinates<br />From those<br />88.5% are geographically correct at two levels<br />6.8% have null or incorrect country (incl. sea plant species)<br />4.7% are near the coasts but not in-land<br />Summary of errors or misrepresented data<br />
  32. 32. RESULTING DATABASE<br />TOTAL EVALUATED RECORDS: 950.000<br />Good records: 840.449  88.47% of total <br />
  33. 33. Next steps<br />It now takes 27 minutes to verify 950,000 records, 177million would be 83 hours (3 ½ days)<br />Identify terrestrial plant species and separate them from sea species<br />Use a georreferencing algorithm to:<br />Correct wrong references<br />Incorporate new location data to those with NULLlat,lon<br />Interpret 2nd & 3rd-level administrative boundaries and use them too<br />Implement environmental cross-checking (outliers)<br />
  34. 34. Geo-referencing: BioGeomancer<br /><br />
  35. 35. Conclusions<br />A coordinate can tell us a lot, and answer a number of interesting research questions, solve a lot of problems<br />Agricultural world sadly behind the mainstream biodiversity world<br />Data not online, not available<br />Databases not connected<br />Quality of coordinate data is critical:<br />We need the concept of precision included<br />We need fields such as location descriptions, and administrative 2nd and 3rd level descriptions for georeferencing<br />We need effective two way communications for verifying, correcting and assigning coordinates from nodes to indexes and vice-versa Economy of scale<br />
  36. 36.<br />