iPlant Tree of Life
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iPlant Tree of Life Given at PAG XIX (2011) Overview of the ToL project
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iPlant Tree of Life
- 1. iPlant Tree of Life Naim Matasci Plant and Animal Genome XIX Conference Jan 15-19, 2011
- 2. Nothing in biology makes sense except in the light of evolution. T. G. Dobzahnsky
- 4. Tree of Life A metaphor for the phylogeny of all species or a large group of species
- 5. Scalability Ackerly, 2009; J. Felsenstein, ca. 1980; Ranger Cluster at TACC
- 9. Factorial (trees) E10 E2 Number of atoms in the universe
- 14. iPlant Tree Viewer Prototype
- 18. My Clades
- 19. My Clades
- 23. 1KP unexplored territory N(genes) dozens of species completed genomes N(species) dozens of genes PCR in 10 4 species
- 24. Broad phylogenetic coverage algae non-flowering flowering (angiosperm) on role of polyploidy in Darwin ’s “abominable mystery” phylogenomics of 1000 species across plant taxa
- 25. 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 "
- 27. Taxonomic Intelligence Arabidopsis thaliana Arabis thaliana
- 28. Taxonomic Intelligence Arabidopsis thaliana Arabis thaliana Mouse-ear cress Thale cress
- 29. Taxonomic Intelligence Arabidopsis thaliana Arabis thaliana Mouse-ear cress Thale cress 1A12_ARATH Q06402
- 32. Taxonomic Name Resolution Service Image courtesy of Brad Boyle.
- 33. Taxonomic Name Resolution Service
- 34. Taxonomic Name Resolution Service (Demo)
- 38. Species Tree
- 39. Gene Tree
- 40. Tree Reconciliation Gene family data courtesy John Bowers
- 41. Tree Reconciliation (Demo)
- 46. Pylogenetically Independent Contrasts Video
Editor's Notes
- Left tree: Maple tree phylogeny from D. Ackerly Left picture: Joe Felsenstein, ca. 1980 Right picture: Ranger cluster at TACC
- Exponential growth is fast. The number of trees grows even faster (factorially). With exponential growth, you multiply by a constant factor (i.e., 10 x 10 x 10). With trees, this factor keeps increasing 3 x 5 x 7 x 9 x 11…. At just around 50 taxa, there are more possible topologies than there are atoms in the universe. We want a tree of 500K taxa: how many possible trees are there with that many?
- Distance matrix calculation compared to FASTREE
- Ninja extended abstract submitted
- BIEN: biological information and ecology network
- Slide for illustrative purposes only.
- BIEN: Biological information and ecology network NCEA: Nation center for ecological analysis and sythesis
- Tree Reconciliation allows us to infer the occurrence of these evolutionary events
- N-J bootstraps Branch lengths ML with HKY model TreeBeST: The resultant tree is bootstrapped for 100 times, reconciled with the species tree and rooted by minimizing with the number of duplications and losses
- Provide the scientific community with a toolkit that will allow them to study the evolution of traits of interest Adaptation in response to past climate change Co-evolution of pollinators and flowers or hosts and parasites
- Contrast: Test for correlation of continuous traits, taking into account phylogeny DACE: Estimating the status of a discrete trait (e.g. presence/absence of fruit, color) in the ancestors of a group of taxa CACE: Estimating the value of a continuous trait (e.g. yield, hight) in the ancestors of a group of taxa
- Tighter integration: e.g. launching analyses from visualizer