This document summarizes the goals of the Open Tree of Life project, which aims to assemble a complete draft tree of life by synthesizing existing phylogenetic trees. The project will publish this draft tree online with tools to allow community annotation, addition of new data, and download of the whole tree or subtrees. The project is in its early stages and seeks community input and participation to help curate data and further develop the online platform.

1. A community-assembled, continually updated
evolutionary history of all life
Karen A. Cranston
National Evolutionary Synthesis Center
Duke University

2. opentreeoflife.org
Karen Cranston (NESCent) Laura Katz (Smith)
Gordon Burleigh (Florida) Rick Ree (FMNH)
Keith Crandall (GWU) Stephen Smith (Michigan)
Karl Gude (MSU) Doug Soltis (Florida)
David Hibbett (Clark) Tiffani Williams (TAMU)
Mark Holder (Kansas)
AVAToL: Assembling, Visualizing and Analysis of
the Tree of Life

3. Phylogeny'papers,'1978;2008'
12000"
10000"
Number'of'papers'published'
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""
graph from David Hillis

4. Where can I browse,
search and download a
complete tree of life?
You can’t. (Yet)

6. DATA AVAILABILITY
Community norm to archive
sequence data
~4% of all published
phylogenetic trees

7. Year one goals
1. Synthesize a complete draft tree of life from existing
phylogenetic trees
2. Publish this draft tree with:
a. ability to add annotations and upload new data sets
b. highlighted areas of conflict and links to source data
c. utilities to download whole tree and subtrees

8. + taxonomies of living and extinct species
+ digital phylogenetic data:
Assembling the Tree of Life (and other) projects
recent high-profile phylogenies
ribosomal RNA trees for Bacteria and Archaea
TreeBASE and Dryad trees
Graph database holding thousands of input
trees with millions of nodes

9. Dipsicales graph
taxonomy data (578 taxa) +
Soltis et al APG III phylogeny (30 taxa)

10. Dipsicales graph Synthesized tree (favouring
phylogenetic branches); contains
all 578 taxa

11. Graph database holding
thousands of input trees with • filter / weight input trees
millions of nodes
• build synthetic trees
• compare to alternate trees
• input new data sets

12. AUTOMATIC UPDATING
update trees
with new
sequence data
detect and synthesize newly
published trees

13. SMART GENERATION OF FIGURES FOR
PUBLICATION
• Semantic annotation layers
• Collaborative editing
EVOLUTION
• Integrated submission of
data and annotations to
archives
Weigmann et al. PNAS, 2011
ig. 1. Combined molecular phylogenetic tree for Diptera. Partitioned ML analysis of combined taxon sets of tier 1 and tier 2 FLYTREE data samples (−lnL =

14. ?
• Increasing
availability of digital data associated with
phylogeny publications
• Makingsynthetic tree open to community annotation
and data submission
• Simple access to search and download the tree of life

15. ?
• Open Science
• project wiki: opentree.wikispaces.com
• mailing list (opentreeoflife@googlegroups.com)
• development board (trello.org/opentree)

17. • provide complete phylogenetic
framework
• link to biodiversity and systematics
content

18. • provide complete phylogenetic
framework
• link to biodiversity and systematics
content
• API for downloading subtrees to analysis tools

19. • provide complete phylogenetic
framework
• link to biodiversity and systematics
content
• API for downloading subtrees to analysis tools
• source / storage of underlying data

20. opentreeoflife.org
• We’ve only just started (June 1)
• Looking for input, feedback and participation:
• join the mailing list
• add publications to the Mendeley group
• vote / comment on plans on the Trello boards
• participate in virtual data curation sprint in August