Phyloseminar about the Open Tree of Life project, given Feb 2014 by Karen Cranston http://phyloseminar.org

1. TECHNICAL AND SOCIAL CHALLENGES
IN SYNTHESIZING THE TREE OF LIFE
Karen Cranston
National Evolutionary Synthesis Center
@kcranstn
http://slideshare.net/kcranstn

2. IF WE “HAD” A TREE OF LIFE?
complete = contains all of
biodiversity
dynamic = continuously updated
with new data
available digitally = browsing,
querying, downloading

3. Produce a digitally-available phylogeny that
contains all of biodiversity
Provide tools for managing, analyzing and sharing
phylogenetic data
http://avatol.org

4. CHALLENGE: COMPLETENESS

5. Even if there were phylogenies for all
species in GenBank, would only have a
small fraction of biodiversity

6. NCBI taxonomy data (578 taxa)
Soltis et al APG III phylogeny (30 taxa)
from Stephen Smith

7. Dipsicales graph
Synthesized tree; contains
structure of phylogeny but all
578 taxa
from Stephen Smith

8. Inputs:
Published phylogenies
Taxonomies
•
•
•
•
filter / weight input trees
synthesize into single data
structure
process feedback
input new data sets
complete tree of life

9. CHALLENGE: ACCESS TO
PUBLISHED PHYLOGENIES

10. “Phylogeny provides a mechanism through which to
interpret the patterns and processes of evolution and to
predict the responses of life to rapid environmental change.
Phylogenies and phylogenetic methods are now being used
to enhance agriculture, identify and combat diseases,
conserve biodiversity, and predict responses to global
climate change and to biological invasions.” *
(tl;dr: We need trees to do cool and important science)
* OpenTree grant proposal

11. Expertise in
phylogenetic
inference
Expertise in
methods
that use
phylogenies

12. EVOLUTION
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)))))))))))))))))))))))))))))))));
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 improved 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.
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.
Wiegmann et al.
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
import phytools!
flyTree<-read.tree(“flies.tre”)!
contMap(flyTree,flyData)
PNAS Early Edition | 3 of 6
Weigmann et al. PNAS, 2011

13. Archiving sequence data is a
community norm
~ 4% of all published
phylogenetic trees
Stoltzfus et al 2012
Archiving phylogenetic data is quite rare

14. OPENTREE PHYLOGENY INPUTS
Surveyed >7000 phylogenetic studies in plants, fungi and animals,
unicellular organisms
Result: data for >2700 studies, >4800 trees

15. CHALLENGE: SELECTING
BACKBONE TAXONOMY

16. Complete?
Up to date with taxonomic literature?
Phylogenetically-informed?
Systematics
research
very slow…..
Online taxonomic
resources

17. OPEN TREE TAXONOMY
+
+
+
+
patch files for manual edits
(requires source info!)

18. •
•
3,133,028 nodes and 2,559,835 ‘species’
https://github.com/OpenTreeOfLife/reference-taxonomy

19. CHALLENGE: PHYLOGENY
CURATION

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)))),
((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)))))))))))))))))))))))))))))))));
How was this tree inferred?
What are the tip labels?
Is it rooted correctly?
What clade was the focus of the study?

21. CURATOR TOOLS

22. Data curation
NeXSON
(NeXML as JSON)
Tree synthesis

24. Input names
Mapped to
taxonomy

26. Tree synthesis
API layer
Common data store of NexSON files (NeXML as JSON)

27. •
•
•
•
•
Open source software tools for managing open
data
Publicly-accessible data store
Full provenance data (who changed what & when?)
Allows access & download through standard
protocols (git)
Where possible, using Creative Commons 0 waiver

28. CHALLENGE: SYNTHESIZING
PHYLOGENY AND TAXONOMY

29. Graph databases are key
Image:

30. Open Tree of Life

31. Thanks to Joseph Brown, Stephen Smith, Jonathan Rees, Jim Allman
for getting the latest version up last night!

32. Thanks to Joseph Brown, Stephen Smith, Jonathan Rees, Jim Allman
for getting the latest version up last night!

33. Synthesis details next week from Stephen
Smith, University of Michigan
Thursday, February 13, 1 pm EST
phyloseminar.org

34. WHAT CAN WE DO WITH THESE
DATA AND TOOLS?

35. Comparing phylogeny and taxonomy
Rick Ree & Lyndon Coghill

36. Conflict within sets of trees
Open Tree of Life
Stephen Smith

37. Highlight under-studied parts of the tree
Label internal nodes on phylogenies
Test various methods for synthesis
Quantify and visualize phylogenetic conflict
Extract phylogeny given list of taxa
Infer branch lengths on synthetic trees
Organize biodiversity data phylogenetically
… and many more, enabled by phylogenetic synthesis and digitally
available phylogenetic data

38. COMING IN 2014
Hackathon, jointly with
Clade-based curation and analysis workshops

39. QUESTIONS? PARTICIPATE?
opentreeoflife@googlegroups.com
opentreeoflife-software@googlegroups.com
irc: #opentreeoflife on freenode
http://github.com/OpenTreeOfLife

40. 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