Andy J Value Of A Coordinate Montpellier Nov 2009

Value of a coordinate: geographic analysis of agricultural biodiversity
Andy Jarvis, Julian Ramirez, Nora Castañeda, Samy Gaiji, Luigi Guarino, Hector Tobón, and Daniel Amariles

Contents
Why crop wild relatives?
How a coordinate can help us complete the collections
Cleaning coordinate data
Needs from standards

Wild relatives of crops
Includeboth progenitor species and closelyrelatedspecies of cultivatedcrops
Faba beans – 0 wild relatives
Potato – 172 wild relativespecies
Increasinglyuseful in breeding, especiallyforbioticresistance

Wild relative species
A. batizocoi - 12 germplasm accessions
A. cardenasii - 17 germplasm accessions
A. diogoi - 5 germplasm accessions
Florunner, with no root-knot nematode resistance
COAN, with population density of root-knot nematodes >90% less than in Florunner

Gap Analysis: Strategiestofilltheholes in ourseedcollections

The Gap Analysisroadmap
Taxonomy review
Data gathering
Georeferentiaton
Environmental
data gathering
Gap Analysis
process
Final
recommendations

The Gap Analysis process
Proxy for:
Diversity
Possibly biotic traits
Proxy for:
Range of traits
Proxy for:
Abiotic traits

http://gisweb.ciat.cgiar.org/gapanalysis/

Total number of herbariumspecimens and germplasmaccessionsavailableforeachmajorcrop wild relativegenepoolthroughthe GBIF portal

Environmental coverage

HERBARIUM
GERMPLASM

NO
GERMPLASM
DEFICIENT
GERMPLASM

POTENTIAL
RICHNESS
RARE
ENVIRONMENTS

Which species, and where

Wild Vigna collecting priorities
Spatial analysis on current conserved materials
*Gaps* in current collections
Definition and prioritisation of collecting areas
8 100x100km cells to complete collections of 23 wild Vigna priority species

Richness in collecting zones at genepool level

Predictedchange in speciesrichnessto 2050.

Exploration and ex-situ conservation of Capsicum flexuosum
Uncommon species of wild chili, found in Paraguay and Argentina, historically used by local indigenous communities
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
OBJECTIVE: Locate and collect germplasm of this species in Paraguay

Behind all this
Data Quality

The GBIF database: status of the data
The database holds 177,887,193 occurrences
Plantae occurrences are 44,706,505 (25,13%)
33,340,000 (74.5%) have coordinates
How many of them are correct, and reliable?
How many new georreferences could we get?
CURRENT STATUS OF
THE Plantae RECORDS

The GBIF database: status of the data
How to make the terrestrial data reliable enough?
Verify coordinates at different levels
Are the records where they say they are?
Are the records inside land areas (for terrestrial plant species only)
Are all the records within the environmental niche of the taxon?
Correct wrong references
Add coordinates to those that do not have
Cross-check with curators and feedback to the database

Using a random sample of 950.000 occurrences with coordinates

Are the records where they say they are?: country-level verification
Records with null country: 58.051  6,11% of total
Records with incorrect country: 6.918  0,72% of total
Total excluded by country 64.969  6,83% of total
Records mostly located
in country boundaries
Inaccuracies in
coordinates

Are the terrestrial plant species in land?: Coastal verification
Records in the ocean: 9.866  1,03% of total
Records near land (range 5km): 34.347  3,61% of total
Records outside of mask: 369  0,04% of total
Total excluded by mask 44.582  4.69% of total
Errors, and more errors

Not so bad at all… stats
44’706.505 plant records
33’340.008 (74,57%) with coordinates
From those
88.5% are geographically correct at two levels
6.8% have null or incorrect country (incl. sea plant species)
4.7% are near the coasts but not in-land
Summary of errors or misrepresented data

RESULTING DATABASE
TOTAL EVALUATED RECORDS: 950.000
Good records: 840.449  88.47% of total

Next steps
It now takes 27 minutes to verify 950,000 records, 177million would be 83 hours (3 ½ days)
Identify terrestrial plant species and separate them from sea species
Use a georreferencing algorithm to:
Correct wrong references
Incorporate new location data to those with NULLlat,lon
Interpret 2nd & 3rd-level administrative boundaries and use them too
Implement environmental cross-checking (outliers)

Geo-referencing: BioGeomancer
http://bg.berkeley.edu/

Conclusions
A coordinate can tell us a lot, and answer a number of interesting research questions, solve a lot of problems
Agricultural world sadly behind the mainstream biodiversity world
Data not online, not available
Databases not connected
Quality of coordinate data is critical:
We need the concept of precision included
We need fields such as location descriptions, and administrative 2nd and 3rd level descriptions for georeferencing
We need effective two way communications for verifying, correcting and assigning coordinates from nodes to indexes and vice-versa Economy of scale

a.jarvis@cgiar.org

Andy J Value Of A Coordinate Montpellier Nov 2009

by CIAT on Nov 09, 2009

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Andy J Value Of A Coordinate Montpellier Nov 2009 — Presentation Transcript