Value of a coordinate: geographic analysis of agricultural biodiversity<br />Andy Jarvis, Julian Ramirez, Nora Castañeda, ...
Contents<br />Why crop wild relatives?<br />How a coordinate can help us complete the collections<br />Cleaning coordinate...
Wild relatives of crops<br />Includeboth progenitor species and closelyrelatedspecies of cultivatedcrops<br />Faba beans –...
Wild relative species<br />A. batizocoi - 12 germplasm accessions<br />A. cardenasii - 17 germplasm accessions <br />A. di...
Gap Analysis: Strategiestofilltheholes in ourseedcollections<br />
The Gap Analysisroadmap<br />Taxonomy review<br />Data gathering<br />Georeferentiaton<br />Environmental<br />data gather...
The Gap Analysis process<br />Proxy for:<br /><ul><li> Diversity
 Possibly biotic traits</li></ul>Proxy for:<br /><ul><li> Range of traits</li></ul>Proxy for:<br /><ul><li> Abiotic traits...
Total number of herbariumspecimens and germplasmaccessionsavailableforeachmajorcrop wild relativegenepoolthroughthe GBIF p...
Environmental coverage<br />
HERBARIUM<br />GERMPLASM<br />
NO<br />GERMPLASM<br />DEFICIENT<br />GERMPLASM<br />
POTENTIAL<br />RICHNESS<br />RARE<br />ENVIRONMENTS<br />
Which species, and where<br />
Wild Vigna collecting priorities<br />Spatial analysis on current conserved materials<br />*Gaps* in current collections<b...
Richness in collecting zones at genepool level<br />
Predictedchange in speciesrichnessto 2050.<br />
Exploration and ex-situ conservation of Capsicum flexuosum<br /><ul><li>Uncommon species of wild chili, found in Paraguay ...
18 known registers of the plant prior to this work
2 germplasm accessions conserved in the USDA
GIS used to target field collections
  6 new collections of C. flexuosum
  160 seeds conserved ex situ</li></ul>OBJECTIVE: Locate and collect germplasm of this species in Paraguay<br />
Behind all this<br />Data Quality<br />
The GBIF database: status of the data<br />The database holds 177,887,193 occurrences<br />Plantae occurrences are 44,706,...
The GBIF database: status of the data<br />How to make the terrestrial data reliable enough?<br />Verify coordinates at di...
Using a random sample of 950.000 occurrences with coordinates<br />
Are the records where they say they are?: country-level verification<br />Records with null country: 	58.051 	 	6,11% of ...
<ul><li>Are the terrestrial plant species in land?: Coastal verification</li></ul>Records in the ocean: 	9.866  	 	1,03% ...
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...
Upcoming SlideShare
Loading in …5
×

Andy J Value Of A Coordinate Montpellier Nov 2009

695 views
655 views

Published on

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

Published in: Technology
0 Comments
4 Likes
Statistics
Notes
  • Be the first to comment

No Downloads
Views
Total views
695
On SlideShare
0
From Embeds
0
Number of Embeds
0
Actions
Shares
0
Downloads
14
Comments
0
Likes
4
Embeds 0
No embeds

No notes for slide

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>http://gisweb.ciat.cgiar.org/gapanalysis/<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 />http://bg.berkeley.edu/<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. a.jarvis@cgiar.org<br />

×