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Castaneda2013 capfitogen bases_de_datos

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  • 1. Descarga de datos de bases de datos públicas. Caso: GBIF y GENESYS Nora Patricia Castañeda-ÁlvarezFoto: Neil Palmer, CIAT
  • 2. Usos• Modelación de especies• Descripción de ambientes• Mapas descriptivos (exploración de información)• Análisis de conservación en áreas protegidas• Estimaciones del impacto de cambio climático
  • 3. Registros de herbario Parientes silvestres de Avena
  • 4. Registros de germoplasma Parientes silvestres de Avena
  • 5. Solanum peruvianumFoto: TGRC Tomato Genetic Resources Center http://tgrc.ucdavis.edu
  • 6. Kernel-density plot of the first two dimensions of an assessment based on variablesderived from temperature and precipitation, for the section Lycopersicoides, genusSolanum
  • 7. Solanum chilense
  • 8. Puntosgeorreferenciados Algoritmo de modelación (Maxent)Capas ambientales Tomato (Solanum lycopersicum L.) wild relatives potential richness map. This maps depicts the number of taxa that are potentially found per unit of area. Darker colours represent greater richness of the tomato genepool. (Map by N. P. Castañeda Álvarez/May 2012)
  • 9. Fuentes de datos Datos ambientales
  • 10. Climate •Interpolated climate surfaces for the globe up to 1km resolution: WorldClim (www.worldclim.org) •Downscaled layers from future climate models (GCMs): Climate Change Agriculture and Food Security (CCAFS) (www.ccafs-climate.org) •Reconstructed paleoclimates: US National Oceanic and Atmospheric Administration (NOAA) (www.ncdc.noaa.gov/paleo/paleo.html) Topography •Elevation, watershed and related variables for the globe at 1km resolution: US Geological Survey (USGS) (http://eros.usgs.gov) •High-quality elevation data for large portions of the tropics and other areas of the developing world: SRTM 90m Elevation Data (http://srtm.csi.cgiar.org) Remote sensing (satellite) •Various land-cover datasets: Global Land Cover Facility (GLCF) (http://glcf.umiacs.umd.edu/data) •Various atmospheric and land products from the MODIS instrument: National Aeronautics and Space Administration (NASA) (http://modis.gsfc.nasa.gov/data) Soils •Harmonized World Soil Database (www.iiasa.ac.at/Research/LUC/External-World-soil-database/HTML) Other spatial data •Relevant links and data at DIVA-GIS website (country level, global level, global climate, species occurrence); near global 90-meter resolution elevation data, high-resolution satellite images (LandSat) (www.diva-gis.org/Data) •Spatial database of the worlds administrative areas (or administrative boundaries): Global Administrative Areas (GADM) (www.gadm.org) •Database with eight million place names with geographical coordinates: GeoNames (www.geonames.org) •Automatic georeferencing tools: BioGeomancer (www.biogeomancer.org)Van Zonneveld, M., Thomas, E., Galluzzi, E., Scheldeman, X. Mapping the ecogeographic distribution of biodiversity and GIStools for plant germplasm collectors. Collecting plant genetic diversity: Technical guidelines. 2011
  • 11. Algoritmos de modelación Modelling algorithm Type of input required Software sourceMaxent (Phillips et al. 2006) Presence and absence data www.cs.princeton.edu/~schapire/maxent (pseudo-absences allowed)Bioclim Presence data http://diva-gis.org, http://openmodeller.sourceforge.netDOMAIN (Carpenter et al. 1993) Presence data http://diva-gis.orgArtificial Neural Networks (ANN) Presence data http://openmodeller.sourceforge.netEcological-Niche Factor Analysis – ENFA- Presence data www2.unil.ch/biomapper ,(Hirzel et al. 2002) http://openmodeller.sourceforge.netGenetic Algorithm for Rule Set Production Presence and absence data www.nhm.ku.edu/desktopgarp,–GARP- (Stockwell & Noble 1992) http://openmodeller.sourceforge.netHABITAT (Walker & Cocks 1991) Presence dataGeneralized Linear Model (GLM) Presence and absence data R: package “dismo”, function “glm” R: package “BIOMOD”Generalized Additive Model (GAM) Presence and absence data R: package “mgcv” R: package “BIOMOD”Mahalanobis Distance (MD) Presence data www.jennessent.com/arcview/mahalanobis_grids.h tmClassification Tree Analysis (CTA) R: package “BIOMOD”Surface Range Envelope (SRE) R: package “BIOMOD”Generalized Boosting Model (GBM) Presence and absence data R: package “BIOMOD”Breiman and Cutler’s random forest for R: package “BIOMOD”classification and regression (RF)Flexible Discriminant Analysis (FDA) R: package “BIOMOD”Multiple Adaptive Regression Splines Presence and absence data R: package “BIOMOD”(MARS)
  • 12. Fuentes de datos Datos biológicos
  • 13. Nombre PáginaJSTOR Plant Science http://plants.jstor.org/GENESYS http://www.genesys-pgr.org/European Plant Genetic Resources Search Catalogue (EURISCO) http://eurisco.ecpgr.org/nc/home_page.htmlSystem-wide Information Network for Genetic Resources (SINGER) http://singer.cgiar.orgGenetic Resources Information Network of the United States www.ars-grin.gov/npgs/searchgrin.htmlDepartment of Agriculture (GRIN)ENSCONET http://enscobase.maich.gr/Botanic Garden Conservation International (BGCI) database http://www.bgci.org/plant_search.phpNational program: Russia http://www.agroatlas.ru/National program: Brazil http://www.cria.org.br/National program: Japan http://www.gene.affrc.go.jp/databases_en.phpNational program: Mexico http://www.biodiversidad.gob.mx/genes/proyectoMaices.htmlHarold and Adele Lieberman Germplasm Bank (cereals) http://www.tau.ac.il/lifesci/units/ICCI/genebank1.htmlManchester Museum http://emu.man.ac.uk/mmcustom/BotQuery.phpMillennium Seed Bank, Kew http://www.kew.org/science-conservation/save-seed- prosper/millennium-seed-bank/index.htmNational History Museum, UK http://www.nhm.ac.uk/research- curation/collections/departmental-collections/botany- collections/search/index.phpRoyal Botanic Gardens Kew http://apps.kew.org/herbcat/navigator.doRoyal Botanical Garden of Edinburgh http://www.rbge.org.uk/databasesSolanaceaeSource http://www.nhm.ac.uk/research- curation/research/projects/solanaceaesourceUnited States Virtual Herbarium http://usvirtualherbarium.org/
  • 14. Por qué GBIF y GENESYS?
  • 15. GBIF
  • 16. GBIF
  • 17. Genesys EuriscoSinger Grin Genesys
  • 18. Estudio de caso:Phaseolus coccineus
  • 19. Ingreso a: data.gbif.org Campo para ingresar nombre de la especie de interes
  • 20. Primeros resultados
  • 21. Selección de campos para descargar
  • 22. www.genesys-pgr.org Opciones de búsqueda
  • 23. OJO: filtrar resultados! DATA SUMMARIES > By Genus / Species
  • 24. Descarga de información
  • 25. Descarga de información OJO CON LA SELECCION DE CAMPOS!

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