1. Open Tree of
Life, v 1.0
Karen Cranston!
National Evolutionary Synthesis Center!
@kcranstn @opentreeoflife!
http://slideshare.net/kcranstn
Community-enabled
phylogenetic synthesis

2. Gordon Burleigh!
Keith Crandall!
Karl Gude!
David Hibbett!
Mark Holder!
Laura Katz!
Rick Ree!
Stephen Smith!
Doug Soltis!
Tiffani Williams!
+ many postdocs,
grad students and
undergrads
@NESCent: Karen Cranston, Jonathan Rees, Jim Allman
http://avatol.org

3. If we had the tree of life…
❖ complete = contains all
biodiversity!
❖ dynamic = updates when
new results published!
❖ digitally available =
browse, query, download

4. ❖ Synthesize published phylogenetic trees!
❖ Enable comment & feedback on synthetic tree!
❖ Allow updating through upload of new data

5. ❖ Expectation: Tree of life that represents our collective
phylogenetic knowledge!
❖ Reality: Tree of life that illustrates digital availability
of open phylogenetic and biodiversity data

6. Inputs:
Published phylogenies
Taxonomic hierarchies
• filter / weight input trees
• synthesize into binary tree
• process feedback
• input new data sets
complete tree of life

7. NCBI taxonomy (578 taxa)
Soltis et al APG III phylogeny (30 taxa)
Dipsicales graph

8. Dipsicales graph
Synthesized tree;
phylogenetic
structure with all
578 taxa

9. More details about synthesis
❖ Smith, Brown, and Hinchliff. "Analyzing and
Synthesizing Phylogenies Using Tree Alignment Graphs."
PLoS computational biology 9.9 (2013): e1003223.!
❖ phyloseminar.org/recorded!
❖ Cranston: Technical and social challenges to
synthesizing the tree of life!
❖ Smith: Exploring graphs for mapping and synthesizing
phylogenies

10. 2.22 million tips !
!
7 taxonomies,
including NCBI,
GBIF, SILVA!
!
~3000 phylogenetic
studies; 335 in
synthetic tree
tip = lineage with >= 500 descendants!
grey = lineage with > 1 tip from a phylogeny
Open Tree of Life, v 1.0

11. node provenance
http://tree.opentreeoflife.org

12. edge provenance
http://tree.opentreeoflife.org

15. >10000 per year
~ 4% deposited in
TreeBASE / Dryad
publishedphylogenies
estimates from Stoltzfus et al 2012, Drew et al 2013
phylogenetic
knowledge
digitally available
phylogenetic knowledge
increase to 16% by
contacting authors
directly

16. TREE Fig._S1 = [&R] (2,1,((3,7),(4,(6,(33,(15,((20,(47,((51,
(49,50)),(46,(48,(52,16)))))),(((44,45),((18,(12,(13,(43,42)))),
((41,((39,38),(40,17))),((35,9),(34,(36,37)))))),(32,(((21,19),
((30,14),(22,((11,31),((27,25),(23,((28,(24,8)),(10,(26,
(5,29)))))))))),((((72,(63,57)),((65,64),((66,67),(68,(69,(70,
(71,54))))))),(((82,59),(60,(61,(62,55)))),((80,(81,56)),((53,
(77,78)),((75,73),(76,(58,74))))))),((88,((86,87),((85,84),
(83,89)))),(79,((91,(93,(95,(92,(96,(94,90)))))),((100,(99,98)),
(97,(((168,((172,185),((159,101),(109,157)))),(((181,(179,180)),
((102,(183,187)),(175,(176,(178,177))))),(212,((195,(210,211)),
(199,((201,(196,202)),((194,197),((203,(192,205)),(204,(193,((209,
(208,206)),(198,(200,207))))))))))))),(113,(((154,((169,170),
(103,191))),((131,126),(128,((134,135),(129,(125,((132,130),
(104,133)))))))),((((190,166),((162,171),((116,120),(115,114)))),
((122,(188,(186,108))),((118,(119,105)),(117,(158,(184,189)))))),
((123,124),(((148,((165,161),(174,182))),((106,121),(163,
(167,127)))),((173,(156,(155,160))),(164,(((136,137),(139,
(138,107))),((153,145),(112,(((146,143),(144,(140,141))),
((142,152),(147,((110,111),(149,
(150,151)))))))))))))))))))))))))))))))));
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
EVOLUTION
re-root!
clean up taxon labels!
add annotations

22. How do I get OpenTree data?
❖ browse: http://tree.opentreeoflife.org!
❖ synthetic tree: http://files.opentreeoflife.org/trees!
❖ taxonomy: http://files.opentreeoflife.org/ott !
❖ input trees: http://github.com/OpenTreeOfLife/
phylesystem !
❖ API access: https://github.com/OpenTreeOfLife/opentree/
wiki/Open-Tree-of-Life-APIs

23. @opentreeoflife @iEvoBio
❖ Using a git-based datastore for community contributed
phylogenies : Emily Jane McTavish!
❖ Using peyotl and Open Tree of Life APIs : Mark Holder!
❖ Taxonomic data exchange as expression and synthesis of
phylogenetic claims : Jonathan Rees
http://ievobio.org

24. For further information:!
bit.ly/1ioPPMc
Tree-for-all!
A hackathon to develop / access
Open Tree of Life data and services
Tree of Life
OPEN
September 15 to 19!
University of Michigan, Ann Arbor
Applications open now! Due July 8!