iplant tree of life
DESCRIPTION
iPlant Tree of LifeGiven at PAG XIX (2011)Overview of the ToL projectTRANSCRIPT
iPlant Tree of Life
Naim MatasciPlant and Animal Genome XIX Conference
Jan 15-19, 2011
Nothing in biology makes sense except in the light of evolution.
T. G. Dobzahnsky
Phylogenetic Insights
Tree of Life
A metaphor for the phylogeny of all species or a large group of
species
Scalability
Ackerly, 2009; J. Felsenstein, ca. 1980; Ranger Cluster at TACC
iPToL Challenges
Large phylogenetic inferenceBuilding a tree of life for up to 500,000 green plants
Tree VisualizationScalable visualization for small to large trees
Data Assembly and IntegrationAcquisition, organization and processing the data
Taxonomic IntelligenceSorting out different names for the same species
Tree ReconciliationResolving discordant gene and species trees
Trait EvolutionUsing tree to understand how traits evolved
Big TreesTo optimize existing methods to construct phylogenetic trees in the order of 500K taxa.
Tree Building
Number of atoms in the universe
Factorial (trees)
E10
E2
Big Trees
NINJA (Travis Wheeler)Neighbor-Joining implementation that can analyze > 200K species Software rewritten from Java to C with an MPI Six day run time reduced 32-fold to 4.5 hours for 220K species data setTwo/three day run time reduced 1,800-folds to 2 minutes for distance matrix calculation on 220K set
RAxML (Alexandros Stamatakis)Large Scale Maximum Likelihood implementation Added check-pointing Re-implementing pthreads implementation to an MPI
In the works
• Source code releases• Further improvements• Building the Tree of Life
Tree VisualizationTo develop an application for viewing, analyzing and exploring large phylogenetic trees.
Tree Visualization
• > 500K Taxa• Fast• Platform independent• Semantic zooming• Metadata driven display of information
iPlant Tree Viewer Prototype
My-Plant.orgTo easily share information and research, collaborate, and stay on top of the latest news in the field.
• The usual suspects in social networking features
– Image gallery– File sharing– Group/private messaging– Forums– Group posts– “Colleagues”– User profiles– Searchable content
Social Networking for the Plant Sciences
My Clades
My Clades
In the works
• Integration with other social networks/services– Twitter, Facebook
• Expanding the number of active clades
November 13, 2010
Sign up today!
• Go to http://my-plant.org• Click on Registration• Try it out!
• Check out poster (Software session)
1KPCollaboration (1KP) – To support the data analysis of the Thousand Plant Transcriptome Project
1KP
unexplored territory
N(g
enes
)
dozens of species completed genomes
N(species)
dozens of genes PCR in 104 species
Broad phylogenetic coverage
algae non-flowering flowering (angiosperm)
on role of polyploidy in
Darwin’s “abominable
mystery”
phylogenomics of 1000 species across plant taxa
Tuesday Afternoon, 18 January 2011 - 3:50 pm to 6:00 pm
Gene Expression Analysis Workshop - Pacific Salon 3
Organizers: David Galbraith, University of Arizona and Greg May, NCGR, Santa Fe
@ 4:00 pm - Gane Ka-Shu Wong , University of Alberta
"1KP: an International Consortium Sequencing the Transcriptomes of 1000 Phylogenetically Diverse Plants from Angiosperms to Green Algae"
Taxonomic Name ResolutionCollaboration (BIEN) - To unify and resolve synonymous, erroneous, or other conflicting taxonomic names.
Taxonomic Intelligence
Arabidopsis thaliana
Arabis thaliana
Taxonomic Intelligence
Arabidopsis thaliana
Arabis thaliana
Mouse-ear cress
Thale cress
Taxonomic Intelligence
Arabidopsis thaliana
Arabis thaliana
Mouse-ear cress
Thale cress
1A12_ARATH
Q06402
Taxonomic Intelligence
cress
Taxonomic Intelligence
cress
Image courtesy of Brad Boyle.
Taxonomic Name Resolution Service
Taxonomic Name Resolution Service
Taxonomic Name Resolution Service (Demo)
In the works
• Higher and lower taxonomic orders• Synonymy• API
Tree ReconciliationTo reconcile the evolutionary history of genes and species.
Origins of incongruence
• Lineage sorting and hybridization• Gene duplications• Horizontal gene transfer
Tree Reconciliation allows us to infer the occurrence of these evolutionary events
Species Tree
Gene Tree
Gene family data courtesy John Bowers
Tree Reconciliation
Tree Reconciliation (Demo)
In the works
• Additional search capabilities• New visualization style• Interactive mode
Trait EvolutionTo develop an infrastructure for downstream analysis of large trees.
Trait Evolution
• Toolkit to study the evolution of traits of interest on very large phylogenies– Diversification– Biogeographic patterns– Adaptation– Co-evolution – …
Current analyses
• Phylogenetically Independent Contrasts(Felsenstein 1985)
• Continuous Ancestral Character Estimation (Schulter et al. 1997, Paradis 2004)
• Discrete Ancestral Character Estimation (Pagel 1994, Paradis 2004)
Pylogenetically Independent Contrasts
Video
In the works
• Various tree stretching models• Evolutionary models fitting• Contrasts for discrete traits (Pagel 1994)
• Tighter integration with the Discovery Environment
• More tools and methods from the community