RPG iEvoBio 2010 Keynote

Biodiversity Discovery and Documentation in the Information and Attention Age
Presented by: Rob Guralnick
Authors: Rob Guralnick and Andrew Hill
Contributors: Meredith Lane, Dan Janies, Walter Jetz, and lots of other folks.
Funding support: Global Biodiversity Information Facility, National Biological
Information Infrastructure, Defense Advanced Research Projects Agency,
National Science Foundation.
#ievobio

WHAT IS BIODIVERSITY DISCOVERY AND DOCUMENTATION?
IMPEDIMENTS
ACTION
Linnean shortfall (too few taxonomists,
antiquated and laborious process)
Wallacean shortfall (very coarse
resolution, scattered data, no integration)
Darwinian shortfall (trees scattered in
literature, no “mother of all trees”)
Multiple repositories that do not
communicate well storing genetic,
phenotypic data. Phenotypic
knowledge-bases lag behind.
Discovering and documenting
new units of biodiversity
distributions of lineages
relationship among lineages
lineage traits from genomes
to phenotype.

app
Pace of Species Description and Documentation for 2008
Approx. 1.922 million named species (all taxa)
~4-30 million undiscovered
From the State of Observed Species report, http://species.asu.edu/files/SOS2010.pdf

Pace of Species Description and Documentation for 2008
Assuming a relatively conservative number
(eg. 10 million undescribed species), it will take another
360 years to discover and document them at our current
pace. Why is discovery and documentation so slow?
Taxonomists proceed in the same manner today as they did one hundred years ago.
Few products are generated along the way. This also means the process is vulnerable (to loss of computers to the loss of taxonomists themselves).
Discovery and documentation are coupled.

State and Scale of Knowledge in Environmental Sciences
Slide from Walter Jetz (thanks Walter)

90 meter
resolution
SRTM
elevation
data for a
Portion of
Colorado
A view of the
world at different
resolutions
100 times
as coarse
1000 times
as coarse

Distribution Knowledge Is Scattered
Points are from GBIF
data portal
Expert opinion range
map from IUCN Red
List
IUCN also lists some
habitat preferences
(cropland, meadows,
mountain valleys)
Microtusmontanus

Documenting our
biodiversity matters
because it is under
increasing threat.

“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.”
- E. O. Wilson

HOW DO WE DO THIS?
DEVELOP KNOWLEDGEBASES OF SPECIES
DISTRIBUTIONS AND SPECIES RELATIONSHIPS.
PROVIDE MEANS TO INTEGRATE ACROSS
THESE KNOWLEDGE-BASES
PROVIDE TOOLS TO RAPIDLY AND EASILY
EXLORE THESE DATA ACROSS SPACE AND TIME
MAKE THIS A COMMUNITY EFFORT –
LEVERAGE COMMUNITY SOURCING

Phylo-, Biodiversity and
Ecological Informatics
Analytical Methods
means to summarize data & select hypotheses
Growing
Toolbox
Application Services
automated workflow for biodiversity science
X
Tools
Encoding analytical methods
X
Initial Research Questions
Raw global data
lineage, occurrence,
environmental
New Research Questions
X
Concepts
and ideas
Processed global data
Species, distributions, new envir. layers
Growing data
and information
repositories

Growing data
Repositories, formats
Growing Toolbox
Concepts and ideas
Paup, Phyml/Raxml, MrBayes,
Beast, Mesquite, etc.
Tree of Life
Population Genetics
GenBank, TreeBase
(Nexus/Newick/PhyloXML,
etc)
TCS/NCA, MsBayes. BayesSCC,
Structure, etc.
Inference-based
Satellites (Modis/GOES/Landat, etc)
Satellite image repositiories,
Worldclim, PRISM , PMIP
(erdapp, netCDF, GIS
formats)
Earth Surface
Satellites; historical, current in-situ,
GCMs, etc.
Climate
Infrared Imaging Spectrometer ,
etc
Ecosystem fluxes
Instrument-based raw
Statistical/inferential
TaxonX, automated
Species name extraction
ITIS, Catalog of Life,
Zoobank, Zookeys, etc.
Species named
Lucid, Ontologies, RDF
Species traits
Species distributions
Morphbank, TraitNet, etc.
GIS, habitat suitability models,
SDMs/ENMs, Survey Gap,etc.
GBIF, VertNet, OBIS
(species occurrence),
Map of Life, IUCN
Observations and model-based

The Interconnected Nature of Biodiversity Ideas, Outputs, Repositories
From Peterson et al. In Press Systematics and Biodiversity

DECOUPLING SPECIES DISCOVERY AND DOCUMENTATION
(OR GET IT OUT THERE FOR OTHERS TO USE AND REPURPOSE)
(OR CLAIM NEW BIODIVERSITY, PROVISIONALLY, BEFORE FORMAL PUBLICATION)
repositories
Community
sourcing
Publish step 1
Generate new data
from specimens
Genbank
Scratch-
pads
Morphbank
Life-desks
Comparartive
analyses
Treebase
Link new unit of
biodiversity
onto tree of life
(claim discovery)
Publish step 2
Formal publication
(documentation)

TAKE HOME MESSAGE 1:
We need to use the web as a collaborative work environment for biodiversity knowledge generation
We need to claim knowledge of the existence of new species before all of the formal steps to document it are complete
We need to publish new data about species soon after generation and prior to publication

What about monitoring an evolving Earth System?
Tracking the spread of disease lineages with known important mutations through time & space
Questions:
How are drug resistant strains of H5N1 circulating around the globe?
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
Viral structure

Methods:
Collect public genome data for H5N1 avian
influenza (676 full genomes).
Use tools for more efficient alignment and
phylogeneticanalysis of data
Test whether mutations on M2 gene (L26I, V27A/I, A30S, S31N) that provide resistance to adamantanes (a class of drugs used to treat influenza A) are under positive selection, purifying selection or are neutral (across the full sampled population of H5N1 inf. A)
Make GoogleEarthTMvizualizations available
.

Global View of Spread of H5N1 (blue branches are lineages with mutation for higher transmissibility among mammals)

Resistant mutant found at position 31 of the M2 protein – colored red below
Altitude of node X = a+ [(n− 1) ×b]

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)

Table 2Amantadine use in chicken farms in Northern China in 1 year (from October 2004 to September 2005)
From He, 2007, Antiviral Research

So What Did We Find Out?
Drug resistance to adamantanes is under positive selection
for at least some mutations (S31N and V27A/I).
Drug resistant lineages can spread quickly across the globe
Emergence of drug resistance has been through mutation not
recombination and hitch-hiking (results not shown)
Effectively treating a potential H5N1 pandemic is based on
continued monitoring of evolution and spread of resistance to
adamantanesand oseltimivir(Tamiflu)

TAKE HOME MESSAGES 2:
It is possible to not just develop observing systems of species but of
evolving lineages.
These monitoring or observing systems can provide a unique view into
evolution, selection and adaptation.
Such systems are essential for more accurate forecasting.
Developing such a system means creating automated workflows.

WHAT ABOUT ALLOWING OTHERS TO MAKE THEIR OWN GEOPHYLOGENY?
http:// geophylo.appspot.com/
Hill and Guralnick, in press, Ecography
Google App Engine application

GeoPhylo Engine - Written in Python, open source,
and deployed on Google App Engine.
Advantages of cloud-based deployment:
Scalable (near infinite computation resources)
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

Geophylogenies provide rich visualizations of multidimensional data that can be examined at multiple spatial (and temporal) scales
Such visualizations may appeal beyond our community of evolutionary biologists to the broader scientific and policy community
Automated approaches and workbench-oriented tools allow for updating, community-driven content to be generated
Our ultimate goal should be an ever-growing “mother of all trees” from which we can attach new “twigs” as we discover them.

Can We Really Track Distributions of Lineages Through Space and Time?

Map of Life Will:
Provide expert opinion range maps for almost all terrestrial vertebrates (and means to accumulate more maps for other taxa)
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)

Overlaying expert opinion maps and model outputs

Common data model
for range maps
Web-services based
for sharing maps
Focus on
improvement
through
modeling and
community
involvement both
Map of Life Connections

Integrating phylogenetic and distributional data in GoogleEarthTM

Work
Workflows
combining
phlyogenetic
approaches,
conservation
status and
species
occurrence

Map of Life fills a critical gap in our global biodiversity knowledge by integrating different sources of species distribution into high resolution range maps for community use.
The ultimate goal is to integrate such species distribution knowledge with knowledge about relationships among species and conservation knowledge
Such integration, at global scale, and across large taxonomic groups, is the next step forward

Relational
Modeling
Patterns
Predictions

Community Sourcing and the Attention Age
At the heart of the message here today is also a challenge:
The vision here suggests that data publishing and “sharing” is as important as academic “kudos”
Can we act for collective good of our community and by so doing see gains for all?
Lets change our model of credit!

http://phylogenomics.blogspot.com	88
http://phylogenomics.blogspot.ca	6
http://phylogenomics.blogspot.de	4
http://phylogenomics.blogspot.com.br	4
http://phylogenomics.blogspot.fr	4
http://phylogenomics.blogspot.co.uk	3
http://phylogenomics.blogspot.ch	3
http://phylogenomics.blogspot.ie	2
http://phylogenomics.blogspot.nl	2
http://phylogenomics.blogspot.com.au	2
http://phylogenomics.blogspot.com.es	2
http://kaboodle.nescent.org	1
http://phylogenomics.blogspot.cz	1
http://phylogenomics.blogspot.pt	1
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RPG iEvoBio 2010 Keynote

by Rob Guralnick on Jun 30, 2010

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