Nora Patricia Castañeda-Álvarez

Descarga de datos de bases de datos públicas. Caso: GBIF y GENESYS

Foto: Neil Palmer, CIAT

Usos

• Modelación de especies• Descripción de ambientes• Mapas descriptivos (exploración de

información)• Análisis de conservación en áreas protegidas• Estimaciones del impacto de cambio climático

Registros de herbario

Parientes silvestres de Avena

Registros de germoplasma

Parientes silvestres de Avena

Solanum peruvianum

Foto: TGRC Tomato Genetic Resources Center http://tgrc.ucdavis.edu

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

Solanum chilense

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)

Fuentes de datos

Datos ambientales

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

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

Fuentes de datos

Datos biológicos

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

Por qué GBIF y GENESYS?

GBIF

GBIF

Genesys

Genesys

Singer

Eurisco

Grin

2.348.549

Estudio de caso:

Phaseolus coccineus

Ingreso a: data.gbif.org

Campo para ingresar nombre de la especie de interes

Primeros resultados

Selección de campos para descargar

www.genesys-pgr.org

Opciones de búsqueda

OJO: filtrar resultados!DATA SUMMARIES > By Genus / Species

Descarga de información

Descarga de información

OJO CON LA SELECCION DE

CAMPOS!