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Biodiversity Discovery and Documentation in the Information and Attention Age,[object Object],Presented by: Rob Guralnick,[object Object],Authors:  Rob Guralnick and Andrew Hill,[object Object],Contributors: Meredith Lane, Dan Janies, Walter Jetz, and lots of other folks.,[object Object],Funding support:  Global Biodiversity Information Facility, National Biological,[object Object],Information Infrastructure, Defense Advanced Research Projects Agency, ,[object Object],National Science Foundation.,[object Object],#ievobio,[object Object]
WHAT IS BIODIVERSITY DISCOVERY AND DOCUMENTATION?,[object Object],IMPEDIMENTS,[object Object],ACTION,[object Object],Linnean shortfall (too few taxonomists,,[object Object],antiquated and laborious process),[object Object],Wallacean shortfall (very coarse ,[object Object],resolution, scattered data, no integration),[object Object],Darwinian shortfall (trees scattered in ,[object Object],literature,  no “mother of all trees”),[object Object],Multiple repositories that do not ,[object Object],communicate well storing genetic, ,[object Object],phenotypic data.  Phenotypic ,[object Object],knowledge-bases lag behind.,[object Object],Discovering and documenting,[object Object], new units of biodiversity,[object Object],Discovering and documenting,[object Object],distributions of lineages,[object Object],Discovering and documenting,[object Object],relationship among lineages,[object Object],Discovering and documenting,[object Object],lineage traits from genomes,[object Object],to phenotype.,[object Object]
app,[object Object],Pace of Species Description and Documentation for 2008,[object Object],Approx. 1.922 million named species (all taxa),[object Object],~4-30 million undiscovered,[object Object],From the State of Observed Species report, http://species.asu.edu/files/SOS2010.pdf,[object Object]
Pace of Species Description and Documentation for 2008,[object Object],Assuming a relatively conservative number ,[object Object],(eg. 10 million undescribed species), it will take another,[object Object],360 years to discover and document them at our current ,[object Object],pace.  Why is discovery and documentation so slow?,[object Object],Taxonomists proceed in the same manner today as they did one hundred years ago.,[object Object],Few products are generated along the way.  This also means the process is vulnerable (to loss of computers to the loss of taxonomists themselves).,[object Object],Discovery and documentation are coupled.  ,[object Object]
State and Scale of Knowledge in Environmental Sciences,[object Object],Slide from Walter Jetz (thanks Walter) ,[object Object]
90 meter,[object Object],resolution ,[object Object],SRTM ,[object Object],elevation,[object Object],data for a ,[object Object],Portion of ,[object Object],Colorado,[object Object],A view of the,[object Object],world at different,[object Object],resolutions,[object Object],100 times,[object Object],as coarse,[object Object],1000 times,[object Object],as coarse,[object Object]
Distribution Knowledge Is Scattered,[object Object],[object Object],   data portal,[object Object],[object Object],   map from IUCN Red ,[object Object],   List,[object Object],[object Object],   habitat preferences ,[object Object],   (cropland, meadows,   ,[object Object],   mountain valleys),[object Object],Microtusmontanus,[object Object]
Documenting our ,[object Object],biodiversity matters,[object Object],because it is under,[object Object],increasing threat.  ,[object Object]
“Overall, we are locked into a race.  We must hurry to acquire the knowledge on which a wise policy of conservation and development can be based for centuries to come.”,[object Object],- E. O. Wilson,[object Object]
HOW DO WE DO THIS?  ,[object Object],DEVELOP KNOWLEDGEBASES OF SPECIES ,[object Object],DISTRIBUTIONS AND SPECIES RELATIONSHIPS.  ,[object Object],PROVIDE MEANS TO INTEGRATE ACROSS,[object Object], THESE KNOWLEDGE-BASES,[object Object],PROVIDE TOOLS TO RAPIDLY AND EASILY ,[object Object],EXLORE THESE DATA ACROSS SPACE AND TIME,[object Object],MAKE THIS A COMMUNITY EFFORT – ,[object Object],LEVERAGE COMMUNITY SOURCING ,[object Object]
Phylo-, Biodiversity and ,[object Object],Ecological Informatics,[object Object],Analytical Methods,[object Object],means to summarize data & select hypotheses,[object Object],Growing ,[object Object],Toolbox,[object Object],Application Services,[object Object],automated workflow for biodiversity science,[object Object],X,[object Object],Tools,[object Object],Encoding analytical methods,[object Object],X,[object Object],Initial Research Questions,[object Object],Raw  global data,[object Object],lineage, occurrence,,[object Object],environmental,[object Object],New Research Questions,[object Object],X,[object Object],Concepts ,[object Object],and ideas,[object Object],Processed global data ,[object Object],Species, distributions, new envir. layers,[object Object],Growing data,[object Object],and information,[object Object],repositories,[object Object]
Growing data ,[object Object],Repositories,  formats,[object Object],Growing  Toolbox,[object Object],Concepts and ideas,[object Object],Paup, Phyml/Raxml, MrBayes, ,[object Object],Beast, Mesquite, etc.,[object Object],Tree of Life,[object Object],Population Genetics,[object Object],GenBank, TreeBase,[object Object],(Nexus/Newick/PhyloXML,,[object Object],etc) ,[object Object],TCS/NCA, MsBayes. BayesSCC,,[object Object],Structure, etc.,[object Object],Inference-based,[object Object],Satellites (Modis/GOES/Landat, etc),[object Object],Satellite image repositiories, ,[object Object],Worldclim, PRISM , PMIP,[object Object],(erdapp,  netCDF, GIS ,[object Object],formats),[object Object],Earth Surface,[object Object],Satellites; historical, current in-situ, ,[object Object],GCMs,  etc.,[object Object],Climate,[object Object],Infrared Imaging Spectrometer , ,[object Object],etc,[object Object],Ecosystem fluxes,[object Object],Instrument-based  raw,[object Object],Statistical/inferential,[object Object],TaxonX, automated,[object Object],Species name extraction,[object Object],ITIS, Catalog of Life, ,[object Object],Zoobank, Zookeys, etc.,[object Object],Species named,[object Object],Lucid, Ontologies, RDF,[object Object],Species traits,[object Object],Species distributions,[object Object],Morphbank, TraitNet, etc.,[object Object],GIS, habitat suitability models, ,[object Object],SDMs/ENMs, Survey Gap,etc.,[object Object],GBIF, VertNet, OBIS ,[object Object],(species occurrence), ,[object Object],Map of Life, IUCN,[object Object],Observations and model-based,[object Object]
The Interconnected Nature of Biodiversity Ideas, Outputs, Repositories ,[object Object],From Peterson et al. In Press Systematics and Biodiversity,[object Object]
RPG iEvoBio 2010 Keynote
DECOUPLING SPECIES DISCOVERY AND DOCUMENTATION,[object Object],(OR GET IT OUT THERE FOR OTHERS TO USE AND REPURPOSE),[object Object],(OR CLAIM NEW BIODIVERSITY, PROVISIONALLY, BEFORE FORMAL PUBLICATION),[object Object],repositories,[object Object],Community ,[object Object],sourcing,[object Object],Publish step 1,[object Object],Generate new data ,[object Object],from specimens,[object Object],Genbank,[object Object],Scratch-,[object Object],pads,[object Object],Morphbank,[object Object],Life-desks,[object Object],Comparartive,[object Object],analyses,[object Object],Treebase,[object Object],Link new unit of ,[object Object],biodiversity ,[object Object],onto tree of life,[object Object],(claim discovery),[object Object],Publish step 2,[object Object],Formal publication ,[object Object],(documentation),[object Object]
TAKE HOME MESSAGE 1:,[object Object],We need to use the web as a collaborative work environment for biodiversity knowledge generation,[object Object],We need to claim knowledge of the existence of new species before all of the formal steps to document it are complete,[object Object],We need to publish new data about species soon after generation and prior to publication,[object Object]
What about monitoring an evolving Earth System?,[object Object],Tracking the spread of disease lineages with known important mutations through time & space,[object Object],Questions:,[object Object],[object Object]
How did drug resistance arise in the H5N1 population?
Are mutations that give rise to drug resistance in H5N1 under positive selection?
Can we provide ways for researchers and the general public to near real-time track this spread?Hosts and strains of avian influenza A,[object Object],Viral structure,[object Object]
Methods:,[object Object],[object Object],  	influenza (676 full genomes).,[object Object],[object Object],phylogeneticanalysis of data ,[object Object],[object Object]
Make GoogleEarthTMvizualizations available.,[object Object]
Global View of Spread of H5N1 (blue branches are lineages with mutation for higher transmissibility among mammals) ,[object Object]
Resistant mutant found at position 31 of the M2 protein – colored red below,[object Object],Altitude of node X = a+ [(n− 1) ×b],[object Object]
RPG iEvoBio 2010 Keynote
Dn/ds measurements across the M2 protein (high Dn/ds ratios (>1) suggest that more non-synonymous substitutions are occurring than expected and therefore are likely being maintained in population),[object Object]
Table 2Amantadine use in chicken farms in Northern China in 1 year (from October 2004 to September 2005),[object Object],From He, 2007, Antiviral Research,[object Object]
So What Did We Find Out?,[object Object],[object Object],  for at least some mutations (S31N and V27A/I).,[object Object],[object Object]
 Emergence of drug resistance has been through mutation not   recombination and hitch-hiking (results not shown),[object Object],[object Object],  continued monitoring of evolution and spread of  resistance to ,[object Object],adamantanesand oseltimivir(Tamiflu) ,[object Object]
TAKE HOME MESSAGES 2:,[object Object],[object Object],    evolving lineages.,[object Object],[object Object],   evolution, selection and adaptation.,[object Object],[object Object]
   Developing such a system means creating automated workflows. ,[object Object]
WHAT ABOUT ALLOWING OTHERS TO MAKE THEIR OWN GEOPHYLOGENY?,[object Object],http:// geophylo.appspot.com/,[object Object],Hill and Guralnick, in press, Ecography,[object Object],Google App Engine application,[object Object]
GeoPhylo Engine -   Written in Python, open source, ,[object Object],and deployed on Google App Engine.  ,[object Object],Advantages of cloud-based deployment:,[object Object],[object Object]
All versioning kept intact so developers can easily link to latest and greatest
Storage of persistent KMLs for users who want to share and modify their KMLs.
Easily deployable as a web service ,[object Object]
Can We Really Track Distributions of Lineages Through Space and Time?,[object Object]
Map of Life Will:,[object Object],[object Object]
Provide means for the community to annotate those maps
Assemble point occurences, habitat preference data and environmental data (e.g. climate, landcover, soil, etc)
Provide a modeling approach to generate much finer scale distribution models (on the order of a kilometer resolution),[object Object]
RPG iEvoBio 2010 Keynote

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RPG iEvoBio 2010 Keynote

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  • 18. How did drug resistance arise in the H5N1 population?
  • 19. Are mutations that give rise to drug resistance in H5N1 under positive selection?
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  • 34. All versioning kept intact so developers can easily link to latest and greatest
  • 35. Storage of persistent KMLs for users who want to share and modify their KMLs.
  • 36.
  • 37.
  • 38.
  • 39. Provide means for the community to annotate those maps
  • 40. Assemble point occurences, habitat preference data and environmental data (e.g. climate, landcover, soil, etc)
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