OpenTree at NESCent Academy 2012
Upcoming SlideShare
Loading in...5
×
 

OpenTree at NESCent Academy 2012

on

  • 304 views

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

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

Statistics

Views

Total Views
304
Views on SlideShare
304
Embed Views
0

Actions

Likes
0
Downloads
2
Comments
0

0 Embeds 0

No embeds

Accessibility

Categories

Upload Details

Uploaded via as Adobe PDF

Usage Rights

CC Attribution License

Report content

Flagged as inappropriate Flag as inappropriate
Flag as inappropriate

Select your reason for flagging this presentation as inappropriate.

Cancel
  • Full Name Full Name Comment goes here.
    Are you sure you want to
    Your message goes here
    Processing…
Post Comment
Edit your comment

    OpenTree at NESCent Academy 2012 OpenTree at NESCent Academy 2012 Presentation Transcript

    • A community-assembled, continually updated evolutionary history of all life Karen A. Cranston National Evolutionary Synthesis Center Duke University
    • 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""
    • Where can I browse,search and download the tree of life? You can’t. (Yet)
    • 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""
    • DATA AVAILABILITY High archival rate of sequence data ~4% of all published phylogenetic trees
    • 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–
    • 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 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
    • Tree of life• 1.8 million named species• Millions more unnamed / undiscovered
    • COMPARATIVE BIOLOGY Conventional Evolutionarystatistics assume: trees provide: Modified from Garland and Carter, 1994
    • 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 data sharing through software products4. Develop novel methods for phylogenetic synthesis
    • + 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
    • 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)
    • 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
    • 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)
    • Lonicera ciliosa Heptacodium miconioides Diervilla rivularis Valeriana celtica Viburnum densiflorum Lonicera ciliosa Heptacodium miconioides Valeriana celtica Viburnum densiflorumDiervilla rivularis
    • NESCent hackathon to architect and implement a phylogenetic pruning service for megatrees http://www.evoio.org/wiki/Phylotastic
    • 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 =
    • YEAR 2 & 3: AUTOMATIC UPDATING update trees with new sequence data detect and incorporate newly published trees
    • Community assembly of thetree of life (Open Tree of Life)Next generation Phenomics(PI O’Leary)Arbor: Comparative AnalysisWorkflows (PI Harmon)
    • 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
    • BIGGEST CHALLENGES?• Lack of digitally-available trees• Visualization• Engaging community to annotate and update• Producing usable and visually appealing software
    • “OPEN” TREE OF LIFE? http://opentreeoflife.org