castaneda2013 capfitogen bases_de_datos
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TRANSCRIPT
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Nora Patricia Castañeda-Álvarez
Descarga de datos de bases de datos públicas. Caso: GBIF y GENESYS
Foto: Neil Palmer, CIAT
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Usos
• Modelación de especies• Descripción de ambientes• Mapas descriptivos (exploración de
información)• Análisis de conservación en áreas protegidas• Estimaciones del impacto de cambio climático
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Registros de herbario
Parientes silvestres de Avena
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Registros de germoplasma
Parientes silvestres de Avena
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Solanum peruvianum
Foto: TGRC Tomato Genetic Resources Center http://tgrc.ucdavis.edu
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Kernel-density plot of the first two dimensions of an assessment based on variables derived from temperature and precipitation, for the section Lycopersicoides, genus Solanum
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Solanum chilense
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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)
Puntos georreferenciados
Capas ambientales
Algoritmo de modelación (Maxent)
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Fuentes de datos
Datos ambientales
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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 world's 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 GIS tools for plant germplasm collectors. Collecting plant genetic diversity: Technical guidelines. 2011
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Modelling algorithm Type of input required Software sourceMaxent (Phillips et al. 2006) Presence and absence data
(pseudo-absences allowed)www.cs.princeton.edu/~schapire/maxent
Bioclim Presence data http://diva-gis.org, http://openmodeller.sourceforge.net
DOMAIN (Carpenter et al. 1993) Presence data http://diva-gis.orgArtificial Neural Networks (ANN) Presence data http://openmodeller.sourceforge.net Ecological-Niche Factor Analysis – ENFA- (Hirzel et al. 2002)
Presence data www2.unil.ch/biomapper , http://openmodeller.sourceforge.net
Genetic Algorithm for Rule Set Production –GARP- (Stockwell & Noble 1992)
Presence and absence data www.nhm.ku.edu/desktopgarp, http://openmodeller.sourceforge.net
HABITAT (Walker & Cocks 1991) Presence data Generalized 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.htm
Classification 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 classification and regression (RF)
R: package “BIOMOD”
Flexible Discriminant Analysis (FDA) R: package “BIOMOD”Multiple Adaptive Regression Splines (MARS)
Presence and absence data R: package “BIOMOD”
Algoritmos de modelación
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Fuentes de datos
Datos biológicos
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Nombre Página
JSTOR 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.html
System-wide Information Network for Genetic Resources (SINGER) http://singer.cgiar.org
Genetic Resources Information Network of the United States Department of Agriculture (GRIN)
www.ars-grin.gov/npgs/searchgrin.html
ENSCONET http://enscobase.maich.gr/
Botanic Garden Conservation International (BGCI) database http://www.bgci.org/plant_search.php
National 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.php
National program: Mexico http://www.biodiversidad.gob.mx/genes/proyectoMaices.html
Harold and Adele Lieberman Germplasm Bank (cereals) http://www.tau.ac.il/lifesci/units/ICCI/genebank1.html
Manchester Museum http://emu.man.ac.uk/mmcustom/BotQuery.php
Millennium Seed Bank, Kew http://www.kew.org/science-conservation/save-seed-prosper/millennium-seed-bank/index.htm
National History Museum, UK http://www.nhm.ac.uk/research-curation/collections/departmental-collections/botany-collections/search/index.php
Royal Botanic Gardens Kew http://apps.kew.org/herbcat/navigator.do
Royal Botanical Garden of Edinburgh http://www.rbge.org.uk/databases
SolanaceaeSource http://www.nhm.ac.uk/research-curation/research/projects/solanaceaesource
United States Virtual Herbarium http://usvirtualherbarium.org/
Virtual Australian Herbarium http://plantnet.rbgsyd.nsw.gov.au/HISCOM/Virtualherb/virtualherbarium.html#Virtual
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Por qué GBIF y GENESYS?
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GBIF
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GBIF
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Genesys
Genesys
Singer
Eurisco
Grin
2.348.549
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Estudio de caso:
Phaseolus coccineus
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Ingreso a: data.gbif.org
Campo para ingresar nombre de la especie de interes
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Primeros resultados
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Selección de campos para descargar
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www.genesys-pgr.org
Opciones de búsqueda
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OJO: filtrar resultados!DATA SUMMARIES > By Genus / Species
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Descarga de información
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Descarga de información
OJO CON LA SELECCION DE
CAMPOS!