A community-assembled, continually updated evolutionary                  history of all life                   Karen A. Cr...
Phylogenypapers,1978;2008                              12000"                              10000"Numberofpaperspublished  ...
Where can I browse,search and download the       tree of life?     You can’t. (Yet)
Phylogenypapers,1978;2008                              12000"                              10000"Numberofpaperspublished  ...
DATA AVAILABILITY   High archival rate of sequence data                      ~4% of all published                       ph...
Most trees published                                                                                                      ...
Pictures of independent phylogenies
• Ideas Lab = 5-day workshop• Self-assembly into groups• Pitched pre-proposals and end of lab• NSF invited full proposals
Karen Cranston, lead PI (Duke)                              Gordon Burleigh (Florida)                              Keith C...
Tree of life• 1.8    million named species• Millions       more unnamed / undiscovered
COMPARATIVE BIOLOGY  Conventional                      Evolutionarystatistics assume:                 trees provide:      ...
PHYLOGENETIC PLACEMENTMetagenomic reads         +Reference phylogeny                      Kembel et al 2011
1. Build the first complete draft tree of life2. Engage the community in refinement and   annotation3. Promote a culture of ...
+ taxonomies of living and extinct species+ any digital phylogenetic data we can get:   NSF Assembling the Tree of Life pr...
Graph database holding thousands of input      trees with millions of nodesFilter / weight input data (number of taxa, siz...
Graph database holding a ‘cloud’of thousands of input trees with       millions of nodes           • filter input trees    ...
Ability to annotate                                                                                        and improve    ...
Lonicera ciliosa   Heptacodium miconioides   Diervilla rivularis   Valeriana celtica   Viburnum densiflorum        Lonicer...
NESCent hackathon to architect and implement a  phylogenetic pruning service for megatrees      http://www.evoio.org/wiki/...
YEAR 2 & 3: SMART GENERATION OF                                         FIGURES FOR PUBLICATION                           ...
YEAR 2 & 3: AUTOMATIC UPDATING         update trees           with new        sequence data                        detect ...
Community assembly of thetree of life (Open Tree of Life)Next generation Phenomics(PI O’Leary)Arbor: Comparative AnalysisW...
POTENTIAL                            IMPACTS• Phylogenies   for any set of species easily available• Benchmark     for cur...
BIGGEST                             CHALLENGES?• Lack   of digitally-available trees• Visualization• Engaging   community ...
“OPEN” TREE OF LIFE?     http://opentreeoflife.org
OpenTree at NESCent Academy 2012
OpenTree at NESCent Academy 2012
OpenTree at NESCent Academy 2012
OpenTree at NESCent Academy 2012
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OpenTree at NESCent Academy 2012

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Open Tree of Life talk given at the 2012 NESCent Academy NGS course

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OpenTree at NESCent Academy 2012

  1. 1. A community-assembled, continually updated evolutionary history of all life Karen A. Cranston National Evolutionary Synthesis Center Duke University
  2. 2. Phylogenypapers,1978;2008 12000" 10000"Numberofpaperspublished 8000" Rapid"increase"in"applica?ons"of" phylogeny,"beginning"in"early"1990s" 6000" 4000" 2000" 0" 1978" 979" 980"1981" 982" 983" 984"1985" 986"1987" 988" 989" 990"1991" 992" 993" 994"1995" 996"1997" 998" 999" 000"2001" 002" 003" 004"2005" 006"2007" 008" 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 Year Source:"ISI"Web"of"Science""
  3. 3. Where can I browse,search and download the tree of life? You can’t. (Yet)
  4. 4. Phylogenypapers,1978;2008 12000" 10000"Numberofpaperspublished 8000" Rapid"increase"in"applica?ons"of" phylogeny,"beginning"in"early"1990s" 6000" 4000" 2000" 0" 1978" 979" 980"1981" 982" 983" 984"1985" 986"1987" 988" 989" 990"1991" 992" 993" 994"1995" 996"1997" 998" 999" 000"2001" 002" 003" 004"2005" 006"2007" 008" 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 Year Source:"ISI"Web"of"Science""
  5. 5. DATA AVAILABILITY High archival rate of sequence data ~4% of all published phylogenetic trees
  6. 6. Most trees published as (beautiful) figures in PDF files EVOLUTION not reusable! Weigmann et al. PNAS, 2011Fig. 1. Combined molecular 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–
  7. 7. Pictures of independent phylogenies
  8. 8. • Ideas Lab = 5-day workshop• Self-assembly into groups• Pitched pre-proposals and end of lab• NSF invited full proposals
  9. 9. Karen Cranston, lead PI (Duke) Gordon Burleigh (Florida) Keith Crandall (BYU) Karl Gude (MSU) David Hibbett (Clark) Mark Holder (Kansas) Laura Katz (Smith)opentreeoflife.org Rick Ree (FMNH) Stephen Smith (Michigan) Doug Soltis (Florida) Tiffani Williams (TAMU) AVAToL: Assembling, Visualizing and Analysis of the Tree of Life
  10. 10. Tree of life• 1.8 million named species• Millions more unnamed / undiscovered
  11. 11. COMPARATIVE BIOLOGY Conventional Evolutionarystatistics assume: trees provide: Modified from Garland and Carter, 1994
  12. 12. PHYLOGENETIC PLACEMENTMetagenomic reads +Reference phylogeny Kembel et al 2011
  13. 13. 1. Build the first complete draft tree of life2. Engage the community in refinement and annotation3. Promote a culture of data sharing through software products4. Develop novel methods for phylogenetic synthesis
  14. 14. + taxonomies of living and extinct species+ any digital phylogenetic data we can get: NSF Assembling the Tree of Life projects recent high-profile phylogenies ribosomal RNA trees for Bacteria and Archaea TreeBASE and Dryad trees Graph database holding a ‘cloud’ of thousands of input trees with millions of nodes
  15. 15. Graph database holding thousands of input trees with millions of nodesFilter / weight input data (number of taxa, size of alignment, year of publication, etc) Synthesis (supertrees, grafting)
  16. 16. Graph database holding a ‘cloud’of thousands of input trees with millions of nodes • filter input trees • synthesize into summary trees • compare to previous trees • invite annotation • input new data sets
  17. 17. Ability to annotate and improve Clear links to source data and methods Compare your Flag results with synthetic Get citations tree Annotate Upload alternateTree image modified from Tree of Life Web Project page http://tolweb.org/Nymphalidae/12172 Pictures by Katja Schulz (queen butterfly; CCAttribution-NonCommercial) and Charles Lam (via Flicker;CCAttribution-ShareAlike)
  18. 18. Lonicera ciliosa Heptacodium miconioides Diervilla rivularis Valeriana celtica Viburnum densiflorum Lonicera ciliosa Heptacodium miconioides Valeriana celtica Viburnum densiflorumDiervilla rivularis
  19. 19. NESCent hackathon to architect and implement a phylogenetic pruning service for megatrees http://www.evoio.org/wiki/Phylotastic
  20. 20. YEAR 2 & 3: SMART GENERATION OF FIGURES FOR PUBLICATION • Semantic annotation layers • Collaborative editing EVOLUTION • Integrated submission of topology, branch lengths and annotations to archivesig. 1. Combined molecular phylogenetic tree for Diptera. Partitioned ML analysis of combined taxon sets of tier 1 and tier 2 FLYTREE data samples (−lnL =
  21. 21. YEAR 2 & 3: AUTOMATIC UPDATING update trees with new sequence data detect and incorporate newly published trees
  22. 22. Community assembly of thetree of life (Open Tree of Life)Next generation Phenomics(PI O’Leary)Arbor: Comparative AnalysisWorkflows (PI Harmon)
  23. 23. POTENTIAL IMPACTS• Phylogenies for any set of species easily available• Benchmark for current state of phylogenetic knowledge• Increasing rate of data archive• Placing “dark taxa” in global informatics framework
  24. 24. BIGGEST CHALLENGES?• Lack of digitally-available trees• Visualization• Engaging community to annotate and update• Producing usable and visually appealing software
  25. 25. “OPEN” TREE OF LIFE? http://opentreeoflife.org

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