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Carleton Biology talk : March 2014
The document discusses the tree of life and efforts to construct a complete digital tree of life. It notes that an ideal tree of life would be complete, continuously updated, and digitally available. Several challenges are outlined, including how to handle incongruences between trees and how to synthesize data across the entire tree. Efforts are underway to synthesize published phylogenetic data and make tree of life resources and data openly available online. Remaining challenges include improving taxonomic coverage, incorporating time information, and enabling community feedback and annotation. The goal is to move beyond a single tree and provide tools to enable custom synthesis and integration with other resources and data.
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Carleton Biology talk : March 2014
- 1. @kcranstn! http://slideshare.net/kcranstn Enabling science with thetree of life Karen Cranston! National Evolutionary Synthesis Center (NESCent)
- 2. The tree oflife provides a means for organizing and explaining biodiversity data Weigmann et al. PNAS, 2011
- 3. What do wewant from a Tree of Life? ❖ complete = contains all of biodiversity! ❖ dynamic = continuously updated with new data! ❖ available digitally = browse, query, download Image: http://evolution.berkeley.edu
- 4. ❖ Create acomplete tree of life by synthesizing published phylogenetic data! ❖ Provide tools for managing, synthesizing & sharing phylogenetic data http://opentreeoflife.org
- 5. Synthetic science ❖ Novelmethods & analysis tools! ❖ Big data from existing data Biodiversity Synthesis Center / Encyclopedia of Life National Evolutionary Synthesis Center
- 6. Challenges ❖ Incongruence: Howdo we detect and use conflict between trees?! ❖ Availability: What data do we have to construct a tree of life?! ❖ Synthesis: How do we combine data across the tree of life?
- 7. What can welearn from conflict between trees?
- 8.
- 9. Bayesian phylogenetic inference Input:sequence data + evolutionary model Output = list of sampled phylogenies
- 10. 0 0.02 0.04 0.06 0.08 0.1 0.12 0.14 0.16 0.18 1 3 57 9 11 13 15 17 19 21 23 25 27 29 31 33 35 37 39 41 43 45 47 49 Sampled trees Probability Number of times sampled ∝ probability Is there a stable backbone among the trees?! What taxa have unstable placement?
- 11. Summarize with agreementsubtrees 0.20 0.15 0.25Pr=0.40 1 23 4 5 1 2 3 4 51 23 4 5 1 2 3 4 5 Pr=1.00 0.20 0.15 0.25Pr=0.40 1 3 4 5 1 3 4 5 1 3 4 51 3 4 5
- 12. 0.20 0.15 0.25Pr=0.40 1 234 5 1 2 4 3 51 23 4 5 1 2 3 4 5 Pr=0.85 0.20 0.15 0.25Pr=0.40 1 3 4 5 1 4 3 5 1 3 4 51 3 4 5 Cranston, K.A. and B.H. Rannala. Summarizing a posterior distribution of phylogenies using agreement subtrees. Systematic Biology 2007: 56(4), pp. 578-590.
- 13.
- 14. Phylogenomics of rice(Oryza) 820,000 BAC-end sequences for 9 diploid Oryza species 1720 gene fragments! 2.4 million nucleotides Cranston, K.A., B. Hurwitz, M.J. Sanderson, D. Ware, R.A. Wing, L. Stein. Phylogenomic analysis from deep BAC-end sequence libraries of rice. Systematic Botany, 35:3, 2010 What are the biological causes of gene tree incongruence in rice?! Do we need full genomes to answer these questions?
- 15. Phylogenomics of rice(Oryza) Cranston, K.A., B. Hurwitz, M.J. Sanderson, D. Ware, R.A. Wing, L. Stein. Phylogenomic analysis from deep BAC-end sequence libraries of rice. Systematic Botany, 35:3, 2010 Concatenated analysis
- 16. Gene trees inOryza ❖ Gene tree methods: recover every possible topology! ❖ Species tree methods: many clades not statistically significant Cranston, K.A., B. Hurwitz, D. Ware, L. Stein, R.A. Wing. Species trees from highly incongruent gene trees in rice. Systematic Biology. 2009: doi: 10.1093/syst- bio.syp054 Supermatrix topology ❖ Suggest incomplete lineage sorting and hybridization / introgression in evolutionary history of rice
- 17. What data dowe have for creating a complete tree of life?
- 18. Gene tree signalin GenBank How many trees can we build using all of the data in GenBank and how are those trees distributed across the tree of life?
- 19. All-vs-all BLAST ateach NCBI taxonomy node Sanderson, M.J., D.T. Boss, D. Chen, K.A. Cranston, and A. Wehe. The PhyLoTA Browser: Processing GenBank for molecular phylogenetics research. Systematic Biology 2008: 57(3). Arachis hypogaea Arachis hypogaea subsp. fastigiata Arachis hypogaea subsp. hypogaea Arachis glabrata subtree clusters Arachis
- 20. All possible clusters,alignments and trees aactgtcgcatgttgacg... aattgtcg-atgttgacg... aac-gtcgcatgtcgacg... aac-gtcgcatgtcgacg... aac-gtcgcatgtcgacg... aactgtcgcatgtcgacg... aactgtcgcatgtcgacg... aactgtcgcatgtcgacg... ❖ ~90000 clusters, alignments, trees available for download! ❖ data availability matrix at each NCBI node
- 22. ❖ complete =contains all of biodiversity! ❖ dynamic = continuously updated with new data! ❖ available digitally = browse, query, download http://opentreeoflife.org
- 23. Gordon Burleigh Keith Crandall KarlGude David Hibbett Mark Holder Laura Katz Rick Ree Stephen Smith Doug Soltis Tiffani Williams Computer science! Systematics! Evolutionary theory! Computational biology! Bioinformatics! Journalism
- 25. Even if therewere phylogenies for all sequence clusters in GenBank, would only represent a small fraction of biodiversity
- 26. Two types ofinputs Phylogeny! highly resolved! computationally derived! limited coverage Taxonomy! poorly resolved! manually curated! much more complete
- 27. ~7000 trees from~2600 studies Phylografter: Rick Ree, Field Museum of Natural History
- 28. Fig. 1. Combinedmolecular phylogenetic tree for Diptera. Partitioned ML analysis of combined taxon sets of tier 1 and tier 2 FLYTREE data samples (−lnL = 344155.6169) calculated in RAxML. Circles indicate bootstrap support >80% (black/bp = 95–100%, gray/bp = 88–94%, white/bp = 80–88%). Nodes with im- proved bootstrap values resulting from postanalysis pruning of unstable taxa are marked by stars (black/bp = 95–100%, gray/bp = 88–94%, white/bp = 80– 88%). Colored squares on terminal branches indicate the presence, in at least one species of a family, of ecological traits as shown to lower left. The number EVOLUTION ~ 4% of all published phylogenetic trees Stoltzfus et al 2012 Trees generally published as pictures in PDFs
- 29. OpenTree Reference Taxonomy + + + patchfiles for manual edits + 3,133,028 nodes and 2,559,835 ‘species’ Jonathan Rees, NESCent
- 30. How do wecombine data to build and use a tree of life?
- 31. Novel datastore forsynthesis Treemachine: Stephen Smith, Cody Hinchliff, Joseph Brown, U Michigan
- 33.
- 34. Manual synthesis basedon all data Automated synthesis based on limited data
- 35. Inputs: Published phylogenies Taxonomies • filter/ weight input trees • re-synthesize • process feedback • input new trees synthetic tree of life
- 36. Improving the synthetictree ❖ Branch lengths & divergence times! ❖ Better synthesis using tree metadata! ❖ Community engagement! ❖ data deposition & curation! ❖ feedback & annotation
- 37. Moving beyond asingle tree ❖ Detecting conflict and coverage! ❖ Visualization! ! ❖ Enabling custom synthesis! ❖ Building out to other tools & resources
- 38. Leaf Tree of Life OPEN Whatcan we do with a tree of life?
- 39. aactgtcgcatgttgacg... aattgtcg-atgttgacg... aac-gtcgcatgtcgacg... aac-gtcgcatgtcgacg... aac-gtcgcatgtcgacg... aactgtcgcatgtcgacg... aactgtcgcatgtcgacg... aactgtcgcatgtcgacg... + = Image: Zephyrisat the English language Wikipedia 10 million years 24 million years
- 41. Acer macrophyllum! Betula lutea! Aesculusglabra! Tilia americana! Ulmus rubra Leaf patterns image from Walls RL: American Journal of Botany 2011, 98(2):244-253. Acer macrophyllum Betula alleghaniensis Aesculus glabra Tilia americana Ulmus rubra
- 42. Stoltzfus, A., Lapp,H., Matasci, N., … Cranston, K.A., ... & Jordan, G. (2013). Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient. BMC bioinformatics, 14(1), 158.
- 44. Collaborative data collection! Validationof datasets! Search & download across datasets
- 45.
- 46. Leaf Tree of Life OPEN Whatcan we do with a tree of life?
- 47. University of Alberta:! ! Bruce Rannala! ! University of Arizona: ! ! Michael Sanderson! ! NESCent:! ! Jonathan Rees! ! Jim Allman