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Open Tree of
Life, v 1.0
Karen Cranston!
National Evolutionary Synthesis Center!
@kcranstn @opentreeoflife!
http://slidesha...
Gordon Burleigh!
Keith Crandall!
Karl Gude!
David Hibbett!
Mark Holder!
Laura Katz!
Rick Ree!
Stephen Smith!
Doug Soltis!
...
If we had the tree of life…
❖ complete = contains all
biodiversity!
❖ dynamic = updates when
new results published!
❖ digi...
❖ Synthesize published phylogenetic trees!
❖ Enable comment & feedback on synthetic tree!
❖ Allow updating through upload ...
❖ Expectation: Tree of life that represents our collective
phylogenetic knowledge!
❖ Reality: Tree of life that illustrate...
Inputs:
Published phylogenies
Taxonomic hierarchies
• filter / weight input trees	

• synthesize into binary tree
• process...
NCBI taxonomy (578 taxa)
Soltis et al APG III phylogeny (30 taxa)
Dipsicales graph
Dipsicales graph
Synthesized tree;
phylogenetic
structure with all
578 taxa
More details about synthesis
❖ Smith, Brown, and Hinchliff. "Analyzing and
Synthesizing Phylogenies Using Tree Alignment G...
2.22 million tips !
!
7 taxonomies,
including NCBI,
GBIF, SILVA!
!
~3000 phylogenetic
studies; 335 in
synthetic tree
tip =...
node provenance
http://tree.opentreeoflife.org
edge provenance
http://tree.opentreeoflife.org
>10000 per year
~ 4% deposited in
TreeBASE / Dryad
publishedphylogenies
estimates from Stoltzfus et al 2012, Drew et al 20...
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))...
How do I get OpenTree data?
❖ browse: http://tree.opentreeoflife.org!
❖ synthetic tree: http://files.opentreeoflife.org/trees...
@opentreeoflife @iEvoBio
❖ Using a git-based datastore for community contributed
phylogenies : Emily Jane McTavish!
❖ Usin...
For further information:!
bit.ly/1ioPPMc
Tree-for-all!
A hackathon to develop / access
Open Tree of Life data and services...
Open Tree of Life at Evolution 2014
Open Tree of Life at Evolution 2014
Open Tree of Life at Evolution 2014
Open Tree of Life at Evolution 2014
Open Tree of Life at Evolution 2014
Open Tree of Life at Evolution 2014
Open Tree of Life at Evolution 2014
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Open Tree of Life at Evolution 2014

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Open Tree of Life at Evolution 2014

  1. 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. 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. 3. If we had the tree of life… ❖ complete = contains all biodiversity! ❖ dynamic = updates when new results published! ❖ digitally available = browse, query, download
  4. 4. ❖ Synthesize published phylogenetic trees! ❖ Enable comment & feedback on synthetic tree! ❖ Allow updating through upload of new data
  5. 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. 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. 7. NCBI taxonomy (578 taxa) Soltis et al APG III phylogeny (30 taxa) Dipsicales graph
  8. 8. Dipsicales graph Synthesized tree; phylogenetic structure with all 578 taxa
  9. 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. 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. 11. node provenance http://tree.opentreeoflife.org
  12. 12. edge provenance http://tree.opentreeoflife.org
  13. 13. >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
  14. 14. 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
  15. 15. 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
  16. 16. @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
  17. 17. 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!

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