This document summarizes the goals and progress of the Open Tree of Life project, which aims to synthesize a complete draft tree of life using existing phylogenetic data. The project has collected phylogenetic data from over 7000 studies and stored it using graph databases. An open public interface allows users to browse, download and query the tree. The project is on track to release an initial draft tree in year 1 and refine it based on user feedback in year 2, while expanding collaborations and incentives for data contributors.

1. Karen Cranston
National Evolutionary Synthesis Center
@kcranstn
http://www.slideshare.net/kcranstn
opentreeoflife.org

2. What does it mean to “have” the tree of life?
complete & dynamic
browse, download, query
use for research questions
implies digital access

3. 0"
2000"
4000"
6000"
8000"
10000"
12000"
1978"1979"1980"1981"1982"1983"1984"1985"1986"1987"1988"1989"1990"1991"1992"1993"1994"1995"1996"1997"1998"1999"2000"2001"2002"2003"2004"2005"2006"2007"2008"
Number'of'papers'published'
Year'
Phylogeny'papers,'1978;2008'
Source:"ISI"Web"of"Science""
Rapid"increase"in"applica?ons"of"
phylogeny,"beginning"in"early"1990s"
graph from David Hillis

4. Goals
1. Synthesize a complete draft tree of life from existing phylogenies
2. Release in year 1 with:
a. engaging public interface
b. ability to upload new data, explore conflict, see provenance
c. open data: tree, subtrees and source data

5. Graph databases of
taxonomy + source trees
•filter / weight input trees
•combine into synthetic trees
•feedback
•input new data sets

6. ~ 4% of all published
phylogenetic trees
Stoltzfus et al 2012
Inputs: Phylogenetic data
Archiving sequence data is a community norm

7. assembly
alignment
inference
expertise
time
$$$
thermore, a paraphyletic relationship of phorids and syrphids
would support the hypothesis that their shared special mode of
extraembryonic development (dorsal amnion closure) (26)
evolved in the stem lineage of Cyclorrhapha and preceded the
origin of the schizophoran amnioserosa.
To test this hypothesis, we used a relatively recent phylogenomic
marker: small, noncoding, regulatory micro-RNAs (miRNAs).
miRNAs exhibit a striking phylogenetic pattern of conservation
across the metazoan tree of life, suggesting the accumulation and
maintenance of miRNA families throughout organismal evolution
Fig. 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–
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
of origins of each trait was estimated with reference to the phylogeny, the distribution of each trait among genera within a family, and the known biology of
the organisms.
Wiegmann et al. PNAS Early Edition | 3 of 6
Why do we need to database phylogenetic trees?

8. Heroic data collection efforts
Surveyed >7000 phylogenetic studies in plants, fungi and
animals, unicellular organisms
Result: repository of data for >2300 studies, >4800 trees
Remaining data not available digitally
Manuscript accepted to PLoS Biology

9. Inputs: Taxonomy
Large fraction of species not represented in phylogenies
taxonomy provides backbone & coverage at tips
Need name resolution services for data cleaning

10. Process
Source trees
(Phylografter) Data storage &
synthesis
(treemachine)
OpenTree:
visualization,
search, downloadTaxonomies
(taxamachine)

11. Source tree management
phylografter.opentreeoflife.org

12. Source tree & taxonomy synthesis
Novel graph database for phylogenies (treemachine) and
taxonomy (taxomachine)
Allows for efficient storage and retrieval

13. OpenTree
dev.opentreeoflife/opentree

14. Public tree of life
publictreeoflife.com/tree

15. open data: requiring CC0 license on source trees
open source software: https://github.com/OpenTreeOfLife
wiki: http://opentree.wikispaces.com/ (52 members)
public mailing list (67 members)
“Open” Tree of Life

16. Community engagement
~50 visitors per day to blog.opentreeoflife.org
@opentreeoflife on Twitter (~900 followers)
Tree of Life symposium: Evolution 2013
Hackathon in year 2 (joint with Arbor)

17. Collaborations
providing images and text for public tree
developing methods for subtree extraction
summer student providing links to ToLWeb
pages
treeviz project from U Indiana MOOC,
upcoming summer intern
year 2-3 plans for data archiving / harvest

18. Assessment: PI survey
general satisfaction with progress on data collection,
synthesis and software development
more focus on incentives for users
more integration across labs

19. Assessment: Advisory board
Members:
David Hillis (UT Austin)
Jan Reichelt (Mendeley)
Andy Sinauer (Sinauer Associates)
Planning meeting for start of year 2

20. On track for year 1 release
1. Synthesize a complete draft tree of life from existing phylogenies
2. Release in year 1 with:
a. engaging public interface
b. ability to upload new data, explore conflict, see provenance
c. open data: tree, subtrees and source data

21. Goals for year 2
Refine draft tree based on user feedback
Empirical use cases drive development
Incentives for users / data contributors
Collaboration with external projects (AVAToL, ToLWeb,
Phylotastic, Dryad)

22. opentreeoflife.org